Information

Which protein complex is composed of the greatest number of different kinds of proteins, and how many types are involved?

Which protein complex is composed of the greatest number of different kinds of proteins, and how many types are involved?


We are searching data for your request:

Forums and discussions:
Manuals and reference books:
Data from registers:
Wait the end of the search in all databases.
Upon completion, a link will appear to access the found materials.

Why are some protein complexes composed of many different types of proteins? How many different types are they composed of? In particular, which protein complex has the greater number of different types of proteins in it?

For example, I've read that the ribosome consists of 70-80 different types of proteins.

How many different types of proteins are in the spliceosome for example?

I'm using the phrasing "types of proteins" to distinguish aggregates/complexes composed of many different copies of the same protein (i.e. some viral capsids) from those composed of many different kinds (i.e. ribosome, exosome complex, spliceosome).


In this paper detailed analysis has been made on spliceosome (U2-type) composition. It should be noted that this complex has dynamic composition. In the paper authors state that up to 170 proteins may associate to a metozoan spliceosome during its course of action. Individual assemblies contain approx 110 proteins (human). Similar complex of the yeast contains approx 60 proteins (precatalytic B complex), while C complexes have 50 proteins, altogether 90 different were identified in yeast. See the linked paper for details.


CHE 120 - Introduction to Organic Chemistry - Textbook

/>
Unless otherwise noted, this work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

The Basics of General, Organic, and Biological Chemistry

By David W. Ball, John W. Hill, and Rhonda J. Scott

Attribution-NonCommercial-ShareAlike
CC BY-NC-SA


Protein Types and Their Functions

Contractile Proteins

These proteins are responsible for the movement of muscles in the body. They are involved in the transport of nutrients in cells, the genetic make up, cell division, as well as muscular coordination.

Example:- The proteins myosin and actin, together produce muscle contractions and relaxations.

Defensive Proteins

The antibodies produced by the body to fight diseases or prevent injury are called defensive proteins. Presence of an antigen or a foreign particle like bacteria, viruses, pollen or non-matching blood types, triggers the production of antibodies. It opposes the antigen and weakens it, so that it can be eradicated or destroyed by the white blood cells. Antibodies are also called immunoglobulins.

Example:- Fibrinogen and thrombin are antibodies that facilitate blood clotting, and prevent the loss of blood following an injury. They also aid in the healing process, so that an individual recovers faster.

Enzymatic Proteins

Enzymes are the catalysts of biochemical reactions that occur in the body. They accelerate and alleviate these reactions, which otherwise may take years to complete. Thus, they increase the metabolic rate, and regulate various life processes like digestion, blood clotting, etc. About 2,000 enzymes have been identified, which catalyze specific reactions in the body, and help sustain life.

Example:- The enzymes amylase and pepsin aid digestion by breaking down complex molecules like starch and proteins respectively, into simpler ones, so they can be absorbed by the small intestine.

Hormonal Proteins

Hormones are secretions that act as messengers to initiate or influence a function and coordinate certain metabolic processes in the body. These hormonal proteins help in regulating these actions.

Would you like to write for us? Well, we're looking for good writers who want to spread the word. Get in touch with us and we'll talk.

Example:- In females, oxytocin is the hormone that stimulates contractions during childbirth. Insulin regulates glucose in the blood.

Storage Proteins

These proteins store amino acids and metal ions needed in the body. They also act as food reserves that provide energy as and when required by the body.

Example:- The protein ferritin stores iron and controls the amount of iron present in the human body. Casein, found in milk, is another type of storage protein that provides certain amino acids, carbohydrates, calcium, and phosphorous.

Structural Proteins

These proteins help maintain structure and provide support to the human body. They give strength and protection to the human anatomy.

Example:- The protein collagen is the major component of tendons, cartilages, and bones. Hair and fingernails consist an insoluble protein called keratin.

Transport Proteins

These proteins help transport various molecules which include nutrients, gases, and all the essential chemicals that help maintain balance in the human body.

Example:- Hemoglobin that carries oxygen to the lungs and various cells in the human body, and lipoproteins which help transport lipids or fats, are examples of transport proteins.


Discussion

The enormous numbers of available variants and protein structures offer an unprecedented resource for investigating the direct impact of variants on protein structure, which is fundamentally important to the design of targeted cancer drugs. Here we developed HotSpot3D to provide new capabilities not found in existing tools. First, HotSpot3D handles any mutation and variation data, has no limitation on the number of clusters per protein, and considers all available structures, thus maximizing the potential for discovery of new clusters and interactions in studies not limited to cancer. Second, it uses discovery of many different entities under a single algorithm—significant clusters within a single protein, at the interface of protein–protein complexes, and near drugs. To our knowledge, it is the first tool to effectively handle mutation–drug clusters. Third, it provides comprehensive downstream analyses in prioritizing clusters that are significantly enriched in mutations from multiple patient samples and supports the discovery of rare and medium-recurrent functional mutations.

We used HotSpot3D to analyze TCGA pan-cancer data, discovering a large set of mutations and identifying their relationships with known drivers. This is a rich resource for future functional explorations (Supplementary Table 22). Our HotSpot3D drug analysis also indicated that only 14 unique mutations in the significant mutation–drug clusters have been reported in the four standard databases we searched, implying discovery of over 800 new drug-interacting candidate mutations. The larger implications of this work are threefold: (i) the use of non-cancer drugs to treat cancers, (ii) the application of cancer-type-specific drugs to treat patients with other types of cancer, and (iii) the use of targeted drugs to treat patients with non-canonical cancer-associated variants that cluster with known druggable variants.

Although we have experimentally validated a small subset of predictions using high-throughput phosphorylation data and in vitro cell-based assays, additional experimental testing of all putative new drivers and drug-interacting mutations discovered in our study is required to confirm their biological functions. We envision that structure-based analyses using HotSpot3D will lead to discoveries of many types of relationships among variants undetectable by conventional approaches, for example, in human variations identified from population-based studies, as well as germline variations and de novo mutations that have roles in many common diseases.


Which protein complex is composed of the greatest number of different kinds of proteins, and how many types are involved? - Biology

Proteins are complex, organic compounds composed of many amino acids linked together through peptide bonds and cross-linked between chains by sulfhydryl bonds, hydrogen bonds and van der Waals forces. There is a greater diversity of chemical composition in proteins than in any other group of biologically active compounds. The proteins in the various animal and plant cells confer on these tissues their biological specificity.

Proteins can be classified as:

(a) Simple proteins. On hydrolysis they yield only the amino acids and occasional small carbohydrate compounds. Examples are: albumins, globulins, glutelins, albuminoids, histones and protamines.

(b) Conjugated proteins. These are simple proteins combined with some non-protein material in the body. Examples are: nucleoproteins, glycoproteins, phosphoproteins, haemoglobins and lecithoproteins.

(c) Derived proteins. These are proteins derived from simple or conjugated proteins by physical or chemical means. Examples are: denatured proteins and peptides.

The potential configuration of protein molecules is so complex that many types of protein molecules can be constructed and are found in biological materials with different physical characteristics. Globular proteins are found in blood and tissue fluids in amorphous globular form with very thin or non-existent membranes. Collagenous proteins are found in connective tissue such as skin or cell membranes. Fibrous proteins are found in hair, muscle and connective tissue. Crystalline proteins are exemplified by the lens of the eye and similar tissues. Enzymes are proteins with specific chemical functions and mediate most of the physiological processes of life. Several small polypeptides act as hormones in tissue systems controlling different chemical or physiological processes. Muscle protein is made of several forms of polypeptides that allow muscular contraction and relaxation for physical movement.

Proteins can also be characterized by their chemical reactions. Most proteins are soluble in water, in alcohol, in dilute base or in various concentrations of salt solutions. Proteins have the characteristic coiled structure which is determined by the sequence of amino acids in the primary polypeptide chain and the stereo configuration of the radical groups attached to the alpha carbon of each amino acid. Proteins are heat labile exhibiting various degrees of lability depending upon type of protein, solution and temperature profile. Proteins can be reversible or irreversible, denatured by heating, by salt concentration, by freezing, by ultrasonic stress or by aging. Proteins undergo characteristic bonding with other proteins in the so-called plastein reaction and will combine with free aldyhyde and hydroxy groups of carbohydrates to form Maillard type compounds.

The nitrogen content of most proteins found in animal, nut and grain tissue is about 16 percent therefore, protein content is commonly expressed as nitrogen content × 6.25.

Ingested proteins are first split into smaller fragments by pepsin in the stomach or by trypsin or chymotrypsin from the pancreas. These peptides are then further reduced by the action of carboxypeptidase which hydrolyzes off one amino acid at a time beginning at the free carboxyl end of the molecule or by aminopeptidase which splits off one amino acid at a time beginning at the free amino end of the polypeptide chain. The free amino acids released into the digestive system are then absorbed through the walls of the gastro intestinal tract into the blood stream where they are then resynthesized into new tissue proteins or are catabolyzed for energy or for fragments for further tissue metabolism.

Gross protein requirements have been determined for a few species of fish (see Table 1). Simulated whole egg protein component of test diets contains an excess of indispensable amino acids. These diets were kept approximately isocaloric by adjusting total protein plus digestible carbohydrate components to a fixed amount as the protein diet treatments were varied over the ranges tested. Tests in feeding fry, fingerling, and yearling fish have shown that gross protein requirements are highest in initial feeding fry and that they decrease as fish size increases. To grow at the maximum rate, fry must have a diet in which nearly half of the digestible ingredients consist of balanced protein at 6-8 weeks this requirement is decreased to about 40 percent of the diet for salmon and trout and to about 35 percent of the diet for yearling salmonids raised at standard environmental temperature (SET). See Figures 1 and 2. Gross protein requirements for young Catfish appear to be less than those for salmonids. Initially feeding fry require that about 50 percent of the digestible components of the ration be protein, and the requirement decreases with size. Some feeding trials with salmon have indicated direct relationships between changes in the protein requirements of young fish and changes in water temperature. Chinook salmon in 7 C water require about 40 percent whole egg protein for maximum growth the same fish in 15 C water require about 50 percent protein. Salmon, trout and catfish can use more protein than required for maximum growth because of efficiency in eliminating nitrogenous wastes in the form of soluble ammonia compounds through the gill tissue directly into the water environment. This system for eliminating nitrogen is more efficient than that available to fowl and mammals. Fowl and mammals consume energy to synthesize urea, uric acid, or other nitrogen compounds which are excreted through the kidney tissue and expelled in urine. Digestible carbohydrate and fat will spare excess protein in the diet as long as the protein requirement for maximum growth is met (Figures 1 and 2).

Table 1 - Estimated Dietary Protein Requirement of Certain Fish 1/

Crude protein level in diet for optimal growth (g/kg)

Rainbow trout ( Salmo gairdneri )

Chinook salmon ( Oncorhynchus tshawytscha )

Plaice ( Pleuronectes platessa )

Gilthead bream ( Chrysophrys aurata )

Grass carp ( Ctenopharyngodon idella )

Red sea bream ( Chrysophrys major )

Yellowtail ( Seriola quinqueradiata )

Fig. 1. Protein requirement of chinook salmon at 47°F. Top curve: initial individual average weight of fish, 1.5g. Bottom curve: initial individual average weight of fish, 5.6g.

Fig. 2. Protein requirement of chinook salmon at 58°F. Top curve: initial individual average weight of fish, 2.6g. Bottom curve: initial individual average weight of fish, 5.8g.

(Both figures adapted from: DeLong, D.C., J.E. Halver and E.T. Mertz, 1958, J.Nutr ., 65:589-99)

Basically the fish must be given a diet containing graded levels of high quality protein and energy and adequate balances of essential fatty acids, vitamins and minerals over a prolonged period. From the resulting dose/response curve the protein requirement is usually obtained by an Almquist plot. These differences in apparent protein requirement are thought to be due to differences in culture techniques and diet composition.

The relatively high dietary protein levels required for maximal growth of certain fish such as grass carp, Ctenopharyngodon idella, and Brycon spp. are surprising as these fish are omnivorous. Brycon spp. are grown on unwanted fruit and other plant material of low protein content and under these conditions there is presumably a substantial contribution to their protein intake from a natural food chain.

Protein requirement of eurythaline fish such as the rainbow trout, Salmo gairdneri, and the coho salmon, Oncorhynchus kisutch, reared in water of salinity 20 ppt is about the same as the requirement in freshwater. No data are available for the protein requirement of these species in full strength sea water.(35 ppt).

The amino acids are the building blocks of proteins about 23 amino acids have been isolated from natural proteins. Ten of these are indispensable for fish. The animal is incapable of synthesizing indispensable amino acids and must therefore obtain these from the diet.

Salmon, trout and channel catfish fed diets devoid of arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan or valine failed to grow (Fig. 3). These same fish fed diets devoid of other L-amino acids grew as well as fish receiving all 18 amino acids tested (Fig. 4). The nitrogen component in the test diets was made up of 18 L-amino acids in the pattern found in whole egg protein. All fish on test recovered rapidly when the missing amino acid was replaced in the diet. The slope of the growth curve of the recovery group was identical with that of fish receiving the complete amino acid test diet.

Dispensable amino acids tested were alanine, aspartic acid, cystine, glutamic acid, glycine, proline, serine, and tyrosine. These amino acids were found to be not essential for the growth of salmon, trout and channel catfish.

Quantitative studies on the requirements of the 10 indispensable amino acids used a casein-gelatin mixture supplemented with crystalline L-amino acids. The test diet had an amino acid pattern of 40 percent whole egg protein for the nitrogen component. Experiments conducted with carp and eel showed a similar lack of growth when an indispensable amino acid was absent from the diet.

Fig. 3. Growth of arginine deficient fish. The deficient group was divided after six weeks on the deficient diet and the missing amino acid was replaced in one of the two sub-lots.

Fig. 4. Growth of cystine deficient fish.

(Both figures adapted from: DeLong, D.C., J.E. Halver and E.T. Mertz, 1958, J.Nutr., 65:589-99)

If the essential amino acid requirements of fish are known, it should be possible to meet these needs in culture systems in a number of ways from different food proteins or combinations of food proteins.

Phenylalanine is spared by tyrosine. It is not known to be chemically modified nor rendered unavailable by the harsh conditions to which feedstuff proteins are normally subjected during processing. Measurement of phenylalanine in proteins is uncomplicated so that the provision and evaluation of phenylalanine in proteins in practical diets presents little difficulty.

Lysine is a basic amino acid. In addition to the a -amino acid group normally bound in peptide linkage, it also contains a second, a -amino group. This a -amino group must be free and reactive, otherwise the lysine, although chemically measurable, will not be biologically available. During the processing of feedstuff proteins the a -amino group of lysine may react with non-protein molecules present in the feedstuff to form additional compounds that render the lysine biologically unavailable.

Methionine is spared by cystine. However, measurement of the methionine content of feed proteins is not easy as the amino acid is subject to oxidation during processing. After processing, methionine may be present as such or as the sulphoxide or as the sulphone. The sulphoxide may be formed from methionine during acid hydrolysis of the feed protein prior to measurement of its any-no acid composition. Acid hydrolysis of proteins before analysis disturbs the original equilibrium between the two compounds so that the composition of the hydrolysate no longer reflects that of the protein. In determining the methionine content of pure proteins, oxidation of the amino acid to methionine sulphone is normally quantitative. In the case of feed proteins, however, this will not reveal how much methionine or methionine sulphoxide was present in the protein prior to performate oxidation and hydrolysis.

Methionine sulphoxide may have some biological value for fish which may have some capability of reconverting it to methionine and thus partially make up for some of the methionine oxidized during processing.

Methods have recently been reported for measurement of methionine in proteins using an iodoplatinate reagent before and after reduction with titanium trichloride, to give values for both methionine and the sulphoxide in the original protein. A method for measuring methionine specifically by cyanogen bromide cleavage has also been described. Both methods remain to be independently assessed. Microbiological assay of methionine in feed proteins is a valuable tool although there is the danger that oxides of methionine may differ in their activity for micro-organisms and misrepresent values.

Quantitative requirements by salmonids for the ten indispensable amino acids were determined by feeding linear increments of one amino acid at a time in a test diet containing an amino acid profile identical with whole egg protein except for the amino acid tested. Replicate groups of fish were fed the diet treatments until gross differences appeared in the growth of test lots. An Almquist plot of growth response indicated the level of amino acids required for maximum growth under those specific test conditions. Diets were designed to contain protein at or slightly below the optimum protein requirement for that species and test condition to assure maximum utilization of the limiting amino acid. A comparison of the requirements for the ten indispensable amino acids between species is shown in Table 2.

A recent innovation has been the use in test diets of proteins relatively deficient in a given essential amino acid. Thus combinations of fishmeal and zein have been used in test diets to define the requirement of rainbow trout for arginine. Diets containing different relative amounts of casein and gelatin showed that an increase in the level of protein-bound arginine from 11 to 17 g/kg resulted in a significant increase in the growth of channel catfish.


ACKNOWLEDGMENTS

The authors acknowledge financial support by the National Natural Science Foundation of China (NSFC) Key Projects (grant Nos. 31630027 and 32030060), NSFC International Collaboration Key Project (grant No. 51861135103), NSFC-German Research Foundation (DFG) project (grant No. 31761133013), and China Postdoctoral Science Foundation funded project (grant No. 2020M680478). The authors also appreciate the support by “the Beijing-Tianjin-Hebei Basic Research Cooperation Project” (19JCZDJC64100), “Ten Thousand Elite Plan” (grant No. Y9E21Z11), and CAS international collaboration plan (grant No. E0632911ZX) as well as National Key Research & Development Program of China (grant No. 2018YFE0117800).


4.4 The Endomembrane System and Proteins

In this section, you will explore the following questions:

  • What is the relationship between the structure and function of the components of the endomembrane system, especially with regard to the synthesis of proteins?

Connection for AP ® Courses

In addition to the presence of nuclei, eukaryotic cells are distinguished by an endomembrane system that includes the plasma membrane, nuclear envelope, lysosomes, vesicles, endoplasmic reticulum, and Golgi apparatus. These subcellular components work together to modify, tag, package, and transport proteins and lipids. The rough endoplasmic reticulum (RER) with its attached ribosomes is the site of protein synthesis and modification. The smooth endoplasmic reticulum (SER) synthesizes carbohydrates, lipids including phospholipids and cholesterol, and steroid hormones engages in the detoxification of medications and poisons and stores calcium ions. Lysosomes digest macromolecules, recycle worn-out organelles, and destroy pathogens. Just like your body uses different organs that work together, cells use these organelles interact to perform specific functions. For example, proteins that are synthesized in the RER then travel to the Golgi apparatus for modification and packaging for either storage or transport. If these proteins are hydrolytic enzymes, they can be stored in lysosomes. Mitochondria produce the energy needed for these processes. This functional flow through several organelles, a process which is dependent on energy produced by yet another organelle, serves as a hallmark illustration of the cell’s complex, interconnected dependence on its organelles.

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 2 and Big Idea 4 of the AP ® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A Learning Objective merges required content with one or more of the seven Science Practices.

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis.
Enduring Understanding 2.B Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments.
Essential Knowledge 2.B.3 Eukaryotic cells maintain internal membranes that partition the cell into specialized regions.
Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices.
Learning Objective 2.13 The student is able to explain how internal membranes and organelles contribute to cell functions.
Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties.
Enduring Understanding 4.A Interactions within biological systems lead to complex properties.
Essential Knowledge 4.A.2 The structure and function of subcellular components, and their interactions, provide essential cellular processes.
Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices.
Learning Objective 4.5 The student is able to construct explanations based on scientific evidence as to how interactions of subcellular structures provide essential functions.

Teacher Support

Students will need help in visualizing the endomembrane system. For example, explain how the interior membrane surface of a vesicle will face the outside of the cell, once the vesicle fuses with the plasma membrane. Use rubber bands to simulate vesicles and mark the inside with a sharpie or a pen. Follow the ink marks as the “vesicle” rubber band fuses with the cell membrane (cut the rubber band to facilitate the fusion being modeled.)

Students may think that all ribosomes are attached to the rough endoplasmic reticulum. Stress that there are free ribosomes as well. They are found in the cytosol where they are involved in the synthesis of cytosolic proteins, which remain within the cytosol. Free and bound ribosomes are identical in structure . Individual ribosomes cycle between free and membrane-bound positions as needed.

Mitochondria and chloroplasts also contain ribosomes which resemble those of prokaryotes. This observation is one of the arguments in favor of the endosymbiotic theory.

“Smooth endoplasmic reticulum is not as important as the rough endoplasmic reticulum.” No, both endomembrane networks play important roles in the life of a cell.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 4.6]

The Endoplasmic Reticulum

The endomembrane system (endo = “within”) is a group of membranes and organelles (Figure 4.18) in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, which we’ve already mentioned, and the endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles. The endomembrane system does not include the membranes of either mitochondria or chloroplasts.

Visual Connection

  1. The vesicle travels from the endoplasmic reticulum to get embedded in plasma membrane.
  2. The vesicle travels from the Golgi to the plasma membrane to release the protein outside.
  3. The vesicle travels from the endoplasmic reticulum to the plasma membrane, and returns to the Golgi apparatus to get modified.
  4. The vesicle moves from the endoplasmic reticulum into the cytoplasmic area, remaining there.

The endoplasmic reticulum (ER) (Figure 4.18) is a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. However, these two functions are performed in separate areas of the ER: the rough ER and the smooth ER, respectively.

The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope.

Rough ER

The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope (Figure 4.19).

Ribosomes transfer their newly synthesized proteins into the lumen of the RER where they undergo structural modifications, such as folding or the acquisition of side chains. These modified proteins will be incorporated into cellular membranes—the membrane of the ER or those of other organelles—or secreted from the cell (such as protein hormones, enzymes). The RER also makes phospholipids for cellular membranes.

If the phospholipids or modified proteins are not destined to stay in the RER, they will reach their destinations via transport vesicles that bud from the RER’s membrane (Figure 4.18).

Since the RER is engaged in modifying proteins (such as enzymes, for example) that will be secreted from the cell, you would be correct in assuming that the RER is abundant in cells that secrete proteins. This is the case with cells of the liver, for example.

Smooth ER

The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface (Figure 4.18). Functions of the SER include synthesis of carbohydrates, lipids, and steroid hormones detoxification of medications and poisons and storage of calcium ions.

In muscle cells, a specialized SER called the sarcoplasmic reticulum is responsible for storage of the calcium ions that are needed to trigger the coordinated contractions of the muscle cells.

Link to Learning

You can watch an excellent animation of the endomembrane system here.

  1. The endomembrane system processes and ships proteins specified by the nucleus. In the nucleus, DNA is used to make RNA which exits the nucleus and enters the cytoplasm of the cell. The ribosomes on the rough ER use the RNA to create the different types of protein needed by the body.
  2. The endomembrane system processes and ships proteins specified by the nucleus. From the nucleus, DNA exits and enters the cytoplasm of the cell. The ribosomes on the rough ER use the DNA to create the different types of protein needed by the body.
  3. The endomembrane system processes and ships proteins specified by the nucleus. In the nucleus, DNA is used to make RNA which exits the nucleus and enters the cytoplasm of the cell. The smooth ER uses the RNA to create the different types of protein needed by the body.
  4. The endomembrane system processes and ships proteins specified by the nucleus. In the nucleus, DNA is used to make RNA which exits the nucleus and enters the cytoplasm of the cell. The ribosomes on the smooth ER use the RNA to create the different types of protein needed by the body.

Career Connection

Cardiologist

Heart disease is the leading cause of death in the United States. This is primarily due to our sedentary lifestyle and our high trans-fat diets.

Heart failure is just one of many disabling heart conditions. Heart failure does not mean that the heart has stopped working. Rather, it means that the heart can’t pump with sufficient force to transport oxygenated blood to all the vital organs. Left untreated, heart failure can lead to kidney failure and failure of other organs.

The wall of the heart is composed of cardiac muscle tissue. Heart failure occurs when the endoplasmic reticula of cardiac muscle cells do not function properly. As a result, an insufficient number of calcium ions are available to trigger a sufficient contractile force.

Cardiologists (cardi- = “heart” -ologist = “one who studies”) are doctors who specialize in treating heart diseases, including heart failure. Cardiologists can make a diagnosis of heart failure via physical examination, results from an electrocardiogram (ECG, a test that measures the electrical activity of the heart), a chest X-ray to see whether the heart is enlarged, and other tests. If heart failure is diagnosed, the cardiologist will typically prescribe appropriate medications and recommend a reduction in table salt intake and a supervised exercise program.

The Golgi Apparatus

We have already mentioned that vesicles can bud from the ER and transport their contents elsewhere, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles still need to be sorted, packaged, and tagged so that they wind up in the right place. Sorting, tagging, packaging, and distribution of lipids and proteins takes place in the Golgi apparatus (also called the Golgi body), a series of flattened membranes (Figure 4.20).

The receiving side of the Golgi apparatus is called the cis face. The opposite side is called the trans face. The transport vesicles that formed from the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted. The most frequent modification is the addition of short chains of sugar molecules. These newly modified proteins and lipids are then tagged with phosphate groups or other small molecules so that they can be routed to their proper destinations.

Finally, the modified and tagged proteins are packaged into secretory vesicles that bud from the trans face of the Golgi. While some of these vesicles deposit their contents into other parts of the cell where they will be used, other secretory vesicles fuse with the plasma membrane and release their contents outside the cell.

In another example of form following function, cells that engage in a great deal of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete antibodies) have an abundance of Golgi.

In plant cells, the Golgi apparatus has the additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which are used in other parts of the cell.

Career Connection

Geneticist

Many diseases arise from genetic mutations that prevent the synthesis of critical proteins. One such disease is Lowe disease (also called oculocerebrorenal syndrome, because it affects the eyes, brain, and kidneys). In Lowe disease, there is a deficiency in an enzyme localized to the Golgi apparatus. Children with Lowe disease are born with cataracts, typically develop kidney disease after the first year of life, and may have impaired mental abilities.

Lowe disease is a genetic disease caused by a mutation on the X chromosome. The X chromosome is one of the two human sex chromosomes, as these chromosomes determine a person's sex. Females possess two X chromosomes while males possess one X and one Y chromosome. In females, the genes on only one of the two X chromosomes are expressed. Females who carry the Lowe disease gene on one of their X chromosomes are carriers and do not show symptoms of the disease. However, males only have one X chromosome and the genes on this chromosome are always expressed. Therefore, males will always have Lowe disease if their X chromosome carries the Lowe disease gene. The location of the mutated gene, as well as the locations of many other mutations that cause genetic diseases, has now been identified. Through prenatal testing, a woman can find out if the fetus she is carrying may be afflicted with one of several genetic diseases.

Geneticists analyze the results of prenatal genetic tests and may counsel pregnant women on available options. They may also conduct genetic research that leads to new drugs or foods, or perform DNA analyses that are used in forensic investigations.

Lysosomes

In addition to their role as the digestive component and organelle-recycling facility of animal cells, lysosomes are considered to be parts of the endomembrane system. Lysosomes also use their hydrolytic enzymes to destroy pathogens (disease-causing organisms) that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis or endocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen (Figure 4.21).

Science Practice Connection for AP® Courses

Activity

Homemade Cell Project. Using inexpensive and common household items, create a model of a specific eukaryotic cell (e.g., neuron, white blood cell, plant root cell, or Paramecium) that demonstrates how at least three organelles work together to perform a specific function.

Think About It

A certain cell type functions primarily to synthesize proteins for export. What is the most likely route the newly made protein takes through the cell? Justify your prediction.

Teacher Support

The activity is an application of Learning Objective 2.13 and Science Practice 6.2 and Learning Objective 4.6 and Science Practice 1.4 because students are asked to create a model that describes various organelles in a specific cell type and then describe how organelles work together to perform a characteristic function of the cell.

The Think About It question is an application of Learning Objective 4.4 and Science Practice 6.4 because students are making a prediction about the interactions of subcellular organelles in performing a specific function.

The path is ribosomes→rough ER→vesicle→Golgi apparatus → vesicle and release. Use information in the text.

As an Amazon Associate we earn from qualifying purchases.

Want to cite, share, or modify this book? This book is Creative Commons Attribution License 4.0 and you must attribute OpenStax.

    If you are redistributing all or part of this book in a print format, then you must include on every physical page the following attribution:

  • Use the information below to generate a citation. We recommend using a citation tool such as this one.
    • Authors: Julianne Zedalis, John Eggebrecht
    • Publisher/website: OpenStax
    • Book title: Biology for AP® Courses
    • Publication date: Mar 8, 2018
    • Location: Houston, Texas
    • Book URL: https://openstax.org/books/biology-ap-courses/pages/1-introduction
    • Section URL: https://openstax.org/books/biology-ap-courses/pages/4-4-the-endomembrane-system-and-proteins

    © Jan 12, 2021 OpenStax. Textbook content produced by OpenStax is licensed under a Creative Commons Attribution License 4.0 license. The OpenStax name, OpenStax logo, OpenStax book covers, OpenStax CNX name, and OpenStax CNX logo are not subject to the Creative Commons license and may not be reproduced without the prior and express written consent of Rice University.


    What is Collagen?

    You might ask, “What is collagen?” Whatever type of collagen you’re talking about, collagen always refers to a prominent structural protein found in all animals. It makes up about a third of the proteins found in the human body.

    The word collagen comes from the Greek word kólla, which means glue. This refers to when collagen used to be used to produce glue.

    Once you turn 25 years old, your body starts to produce less and less collagen. It’s natural. But this causes wrinkled and saggy skin. More importantly, lowered collagen production means weaker cartilage in your knees, for instance.

    Science alert: If you want to get very technical, collagen molecules are a tight-packed, triple helix protein found in every known mammal. Type IV, however, lacks the amino acids to form the tight shape, so it turns into more of a sheet structure. Either way, collagen is found in almost all connective tissues found in animals, such as cartilage, skin, muscles — and the list goes on.

    Collagen synthesis happens constantly in your body. Collagen synthesis (when you produce collagen in your body, rather than take it in a supplement form) is kick-started by a unique concoction of amino acids: chiefly glycine and proline.

    Vitamin C is vital to this process. If you have a vitamin C deficiency, your collagen production will likely suffer. (3)

    As more and more collagen supplements burst onto the stage, it’s important to understand the different types of collagen, as well as the different sources and health benefits of each type. Since collagen powder supplements are derived from animals — namely mammals, birds, and fish — collagen is not vegan.

    Below, we’ll discuss the five most important types of collagen. Which promote bone health? Which enhance healthy, hydrated skin? Which types have side effects?


    Which protein complex is composed of the greatest number of different kinds of proteins, and how many types are involved? - Biology

    ​​​​​​​​​​​​​​​​​​​​​​​ 2.9 Photosynthesis - Photosynthesis uses the energy in sunlight to produce the chemical energy needed for life

    ∑ - Photosynthesis is the production of carbon compounds in cells using light energy.

    • Living organisms require complex carbon compounds to carry out life processes and build the structures in their cells
    • Photosynthesis involves the conversion of light energy into chemical energy (carbohydrates, lipids, protein and nucleic acids).
    • Chloroplasts absorb light energy from the sun and convert this energy into chemical energy (glucose) to be used by the organisms for energy.

    ∑ - Visible light has a range of wavelengths with violet the shortest wavelength and red the longest.

    • Light from the sun is composed of a range of wavelengths.
    • The visible spectrum is the portion of the electromagnetic spectrum that is visible to or can be detected by the human eye.
    • Electromagnetic radiation in this range of wavelengths (380 to 750 nm) is called visible light.
    • All these wavelengths together form white light, with violet/blue colours having shorter wavelengths (more energy) and red colours having longer wavelengths (less energy)

    ∑ - Chlorophyll absorbs red and blue light most effectively and reflects green light more than other colours.

    • Sunlight is a mixture of different wavelengths of visible light, which we see as colours.
    • The two main colours of light that are absorbed by chlorophyll are red and blue light.
    • The main colour that is reflected in the green light, which is why most leaves look green.

    ∑ - Oxygen is produced in photosynthesis from the photolysis of water.

    • Photolysis is one of the first and most important steps in the light-dependent reactions of photosynthesis
    • Two water (H2O) molecules are split by photons of light to produce 4 e- + 4H+ + O2

    ∑ - Energy is needed to produce carbohydrates and other carbon compounds from carbon dioxide.

    • Plants convert inorganic CO2 into organic carbohydrates through the process of photosynthesis
    • Carbon dioxide + Water --> CH2O (carbohydrates) + oxygen
    • Energy is required for this reaction to occur
    • Light energy from the sun is used and converted into chemical energy
    • The reactions are generally endothermic

    ∑ - Temperature, light intensity and carbon dioxide concentration are possible limiting factors on the rate of photosynthesis.

    • Light intensity, CO2 concentration, and temperature can all be limiting factors for the rate of photosynthesis
    • If any of these factors is below their optimal level, they can be limiting however, only one of these factors can be limiting at one time
    • This is usually the factor that is the furthest away from its optimal level
    • This is the only factor that can increase the rate of photosynthesis
    • As this factor gets closer to its optimal level, the limiting factor can change to one of the other factors

    Temperature

    • At low temperatures, the rate of photosynthesis is very low.
    • Because photosynthesis requires enzymes, as the temperature increases the amount of kinetic energy in the reactants increases, thereby increasing the rate of photosynthesis.
    • This rate increases until an optimum temperature is reached. In plants, this optimum temperature is usually between 25º and 35º C.
    • After the optimum temperature is reached, the rate of photosynthesis drops dramatically, because the temperature can cause the enzymes to denature (lose their shape and active site)

    The graph of photosynthesis rate vs. temperature is very similar to the enzyme/temperature graph.

    Light Intensity

    • Light is used to produce ATP and split water by photolysis to form H+ ions and oxygen.
    • As light intensity increases the rate of photosynthesis also increases.
    • At low light intensities, an increase in light causes a drastic increase in the rate of photosynthesis.
    • As light intensity increases the rate of photosynthesis begins to level off and becomes constant.
    • As light intensity increases further there is no change in the rate of photosynthesis as enzymes are working at their maximum rate.

    Carbon Dioxide Concentration

    • CO2 is an essential molecule in the formation of organic molecules.
    • At low CO2 concentrations, an increase in the amount of CO2 will increase the rate of photosynthesis. At very low levels, no photosynthesis will take place
    • As the CO2 concentration increases, the rate of photosynthesis begins to plateau.
    • At high levels of CO2 concentration, the rate of photosynthesis remains constant unless light intensity is increased to create more ATP or temperature is increased to provide more kinetic energy.

    *** Do the data-based questions on page 134***

    Applications and skills:

    ∑ - Changes to the Earth’s atmosphere, oceans and rock deposition due to photosynthesis.

    • Early bacterial life introduced oxygen to the atmosphere about 3.5 billion years ago.
    • As the first free oxygen was released through photosynthesis by cyanobacteria, it was initially soaked up by iron dissolved in the oceans and formed red coloured iron oxide, which settled to the ocean floor.
    • Over time, distinctive sedimentary rocks called banded iron formations were created by these iron oxide deposits. Once the iron in the oceans was used up, the iron oxide stopped being deposited and oxygen was able to start building up in the atmosphere about 2.4 billion years ago.
    • This was known as the “Great Oxidation Event”
    • The oxygen remained at about 2% until about 700 mya. Then there was then a significant rise in oxygen until it reached about 20%.
    • This lead to a huge increase in species as multicellular organisms evolved

    B - Skill: Drawing an absorption spectrum for chlorophyll and an action spectrum for photosynthesis.

    • The electromagnetic spectrum consists of the entire range of electromagnetic radiation.
    • The part of the spectrum that is involved in photosynthesis is called the visible light spectrum.
    • An action spectrum is the rate of photosynthesis plotted against wavelength of light. It shows which wavelength of light is most effectively used during photosynthesis.
    • The highest rates of photosynthesis occur at red and blue wavelengths.
    • The absorption spectrum shows the % of light absorbed by the photosynthetic pigments in chloroplasts at each different wavelength.
    • The graphs are very similar because photosynthesis occurs when light is absorbed by the chlorophyll pigments therefore the wavelengths that have the greatest rates of absorption will also have high rates of photosynthesis.
    • Green wavelength of light is reflected and therefore has a very low % absorption level on the absorption spectra (this is why most leaves are green).

    B Skill: Design of experiments to investigate the effect of limiting factors on photosynthesis. -

    B Skill: Separation of photosynthetic pigments by chromatography. (Practical 4)

    These would be two separate practicals. You could use the first investigation to carry out a full lab or a Mock IA in preparation for the internal assessment.

    2.7 DNA Replication, Transcription and Translation

    • Genetic information in DNA can be accurately copied and can be translated to make the proteins needed by the cell.

    Understandings:

    ∑ - The replication of DNA is semi-conservative and depends on complementary base pairing.

    • Complementary base-pairing ensures two identical DNA strands are formed after replication is complete.
    • In replication, the original strands are used as templates, allowing complementary bases to be added according to base-pairing rules.
    • DNA replication is semi-conservative, meaning the new DNA that is created consists of one old strand (template) and one new strand (synthesized strand).
    • The significance of complementary base pairing means that the two daughter cells have the exact same DNA genome as the parent cell.
    • Gene sequences (if no mutations occur) are therefore successfully passed on from generation to generation.
    • Adenine is always matched with thymine with two hydrogen bonds and guanine is always matched with cytosine with three hydrogen bonds.

    B - Skill: Analysis of Meselson and Stahl’s results to obtain support for the theory of semi-conservative replication of DNA.

    • Read through the article for Obtaining evidence for the theory of semi-conservative replication and complete the data-based question on the Analysis of Meselson and Stahl’s results on page 113- and 114

    ∑ - Helicase unwinds the double helix and separates the two strands by breaking hydrogen bonds.

    • The DNA strand is unwound and separated by an enzyme called helicase.
    • The separation is completed by breaking the hydrogen bonds between the base pairs
    • Energy from ATP is required for Helicase to move along the DNA and break the bonds

    ∑ - DNA polymerase links nucleotides together to form a new strand, using the pre-existing strand as a template.

    • Free nucleotides found in the nucleus are added to the strands of DNA by an enzyme called DNA polymerase.
    • DNA polymerase brings the nucleotide into position so a hydrogen bond can form between the base pairs
    • A covalent bond is formed between the phosphate on the free nucleotide and the sugar on the existing chain
    • Nucleotides are added to complementary bases on the DNA template strands according to base-pairing rules (adenine pairs with thymine and guanine pairs with cytosine).
    • Bases are added in one direction on one strand and are added in the opposite direction on the other strand.
    • Very few mistakes occur
    • The newly formed DNA strands rewind to form a double-helix spiral staircase shape once again.

    β - Applications and skills:

    β -Application: Use of Taq DNA polymerase to produce multiple copies of DNA rapidly by the polymerase chain reaction (PCR).

    • Click on Amplification to start the animation
    • Follow the animation and write down the steps involved in PCR
    • PCR (polymerase chain reaction) is a laboratory technique that takes a single or few copies of DNA and amplifies them to generate millions or more copies of a particular DNA sequence.
    • When you collect DNA from different sources such as sperm samples or small drops of blood, there are usually very little usable cells to collect DNA.
    • Therefore, PCR is used to create enough DNA to be analyzed for investigations such as forensics or custody cases.
    • Once large quantities of the DNA have been created, other methods such as gel electrophoresis are used to analyze the DNA.

    ∑ - Transcription is the synthesis of mRNA copied from the DNA base sequences by RNA polymerase.

    • Genes contained within a specific region of DNA code for a specific protein.
    • Protein synthesis occurs outside the nucleus on the ribosomes. Therefore a molecule needs to be synthesized that will relay the DNA code to allow the specific protein to be made correctly.
    • Transcription is the formation of an mRNA strand that is complementary to the DNA strand contained within the gene.
    • Transcription begins when the area of DNA that contains the gene is unwound by RNA polymerase
    • RNA nucleotides found in the nucleus are added to the template strand of the DNA by the enzyme RNA polymerase according to base-pairing rules.
    • RNA polymerase also creates covalent bonds between the nucleotides of the mRNA strand.
    • The mRNA strand contains the nitrogenous base uracil instead of thymine.
    • Once the gene has been transcribed, the mRNA strand falls off and exits the nucleus through the nuclear pore. It is then transported to the ribosomes for protein synthesis.
    • The DNA strand with the same base sequence as the mRNA is the called the sense (coding) strand and the other is called the antisense (template) strand

    Good animation

    Good Video on transcription and translation

    ∑- Translation is the synthesis of polypeptides on ribosomes.

    • The translation is the synthesis of polypeptides with a specific amino acid sequence that is determined by the base sequence on the mRNA molecule
    • That base sequence is determined by the specific gene
    • Translation takes place at the ribosomes in the cytoplasm or on the rough ER
    • The ribosomes consist of a large and a small subunit
    • Ribosomes are made of rRNA and protein

    ∑ - The amino acid sequence of polypeptides is determined by mRNA according to the genetic code.

    • Messenger RNA (mRNA) carries the information from the specific gene to the ribosomes in order to create the correct polypeptide
    • The mRNA that is created is specific for that polypeptide only

    ∑ - Codons of three bases on mRNA correspond to one amino acid in a polypeptide.

    • The mRNA strand created in transcription consists of triplet bases called codons.
    • Each triplet codon on the mRNA codes for a specific amino acid.
    • The protein synthesized is made up of a series of amino acids coded for by the mRNA strand which is a complimentary copy of the gene contained in the DNA.
    • All the different combinations of bases that make up the 64 triplet codons can code for one of the 20 amino acids.
    • However, 3 triplets, UAA, UAG, and UGA do not code for amino acids and are called stop codons.
    • The mRNA codon AUG, codes for the amino acid Methionine and is called the START codon because it signals the start of translation.
    • The genetic code is considered “degenerate” because more than one triplet codon can code for a specific amino acid.

    B Skill: Use a table of the genetic code to deduce which codon(s) corresponds to which amino acid.

    B Skill: Use a table of mRNA codons and their corresponding amino acids to deduce the sequence of amino acids coded by a short mRNA strand of known base sequence.

    B Skill: Deducing the DNA base sequence for the mRNA strand.

    Use the DNA strand below to transcribe a strand of mRNA and then identify the correct amino acids in the polypeptide strand.


    Template Strand GCC TAC TCG CCT TTT AAA GCT AGT ACT GGG CGC

    Coding Strand CGG ATG AGC GGA AAA TTT CGA TCA TGA CCC GCG

    mRNA Strand _____________________________________________________

    Amino Acids ________________________________________________________

    Also, complete the Decoding base sequences in your text.

    ∑ - Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA.

    • The process where amino acids are combined to form proteins (polypeptides).
    • mRNA has a sequence of codons (3 base pairs) that specifies the AA sequence of the polypeptide
    • tRNA has an anticodon that matches and binds to their complementary codon carrying the AA corresponding to that codon
    • rRNA binding site for the mRNA and tRNA and catalyzes the reaction to put together the polypeptide
    • After transcription occurs the transcribed mRNA moves out from the nucleus through the nuclear pore into the cytoplasm and binds to the ribosome unit either in the cytoplasm or attached to the rough ER
    • mRNA binds to the small subunit of the ribosome with its first two codons contained within the binding sites of the ribosome.
    • The first codon is called the start codon (AUG) which codes for methionine.
    • The corresponding tRNA attaches to the mRNA bringing the amino acid methionine to the ribosome to start the polypeptide chain.
    • While still attached, a second tRNA attaches to the mRNA at the second binding site on the ribosome, carrying the amino acid that corresponds to the mRNA codon.
    • The two amino acids are combined by a condensation reaction, forming a covalent dipeptide bond.
    • The bond between the first amino acid and the tRNA that carried it to the ribosome is broken by an enzyme.
    • The ribosome slides along the mRNA, moving down one codon releasing the tRNA back into the cytoplasm so it can go pick up another amino acid (in this case methionine).
    • Another tRNA moves into the empty site bringing the next amino acid that corresponds to the mRNA codon.
    • Again, the amino acid is attached to the polypeptide and the previous tRNA is released back into the cytoplasm as the ribosome moves along the mRNA.
    • This process continues until 1 of the 3 stop codons (UAA, UGA, and UAG) is reached. These tRNA's have no attached amino acid.
    • Finally, when the ribosome moves along the mRNA, the polypeptide will fall off and be released into the cytoplasm.

    β - Application: Production of human insulin in bacteria as an example of the universality of the genetic code allowing gene transfer between species.

    • A gene produces a certain polypeptide in an organism.
    • Since the genetic code is universal, when a gene is removed from one species and transferred to another, the sequence of amino acids in the polypeptide produced remains unchanged.
    • Animal insulin has been used for the treatment of diabetics for many years however, some people develop an allergic reaction to the animal insulin
    • Since 1982, human insulin created by the pancreas has been produced using gene transfer techniques with E. coli bacteria
    • Gene transfer is taking one gene from an organism and inserting it into another organism.
    • First, mRNA that codes for insulin produced in the pancreatic cells is extracted.
    • The enzyme reverse transcriptase is mixed with the mRNA. This enzyme produces a strand of coding DNA called cDNA.
    • Plasmids are small circles of DNA found in bacteria cells. These plasmids are cut with a restriction enzyme, leaving sticky ends to which the cDNA can attach.
    • DNA ligase is used to seal the nicks between the cDNA and the plasmid.
    • Linking sequences are added to the cDNA allowing them to be inserted into the plasmid.
    • The bacterial plasmid carrying the insulin gene is now inserted into the plasmid-free bacterial cell such as e.coli bacteria (with plasmid removed). This is known as the host cell.
    • These insulin-producing bacterial cells will now reproduce rapidly during fermentation, creating millions of insulin-producing bacteria cells.
    • Finally, the insulin produced is extracted from the cell and purified to be used by diabetics.

    Watch the video on the production of insulin and genetic engineering

    2.8 Cell respiration - Cell respiration supplies energy for the functions of life.​

    ∑ - Cell respiration is the controlled release of energy from organic compounds to produce ATP.

    • Organic compounds from the food we eat such as glucose contain stored energy within their covalent bonds.
    • All living organisms carry out cell respiration in order to convert stored energy into a form that can be used by the cell.
    • When organic molecules are broken down, the energy formed is eventually stored in a high energy molecule called ATP.
    • Cell respiration is the controlled release of energy from organic compounds in cells to produce ATP.

    ∑ - ATP from cell respiration is immediately available as a source of energy in the cell.

    • Energy for all types of cellular processes is immediately supplied by ATP
    • The main types of cellular activity include synthesizing large molecules (eg. DNA, RNA and protein), pumping ions across membranes by active transport, and moving things around the cell, such as vesicles and chromosomes. Muscle contractions also use ATP.

    Energy is released by spitting ATP -> ADP + Pi

    ∑ - Anaerobic cell respiration gives a small yield of ATP from glucose.

    • Glucose (6C) is broken down into 2 pyruvates (3C) in the cytoplasm by the process of glycolysis.
    • There is a net gain of 2 ATP molecules.
    • Glycolysis does not require oxygen.
    • Anaerobic respiration (without oxygen) occurs in the cytoplasm.
    • During glycolysis, glucose is converted into pyruvate with a net gain of 2 ATP.
    • After glucose is converted to pyruvate, if no oxygen is available, pyruvate is further converted into lactate or ethanol depending on the organism.
    • When no oxygen is available, humans convert pyruvate into lactate (lactic acid) with no further gain of ATP.
    • No CO2 is produced because like pyruvate, lactate is also a 3 carbon molecule.
    • In yeast and plants, pyruvate is converted into ethanol (2C) and carbon dioxide with no further yield of ATP.
    • Ethanol and CO2 are excreted as waste products.


    β - Applications and skills:

    β - Application: Use of anaerobic cell respiration in yeasts to produce ethanol and carbon dioxide in baking.

    Read through “Yeast and its uses” on page 124-125 and answer the data-based questions on page 125.

    β - Application: Lactate production in humans when anaerobic respiration is used to maximize the power of muscle contractions.

    Discusses anaerobic respiration in humans.

    ∑ - Aerobic cell respiration requires oxygen and gives a large yield of ATP from glucose.

    • Aerobic respiration also begins with glycolysis which produces 2 pyruvate molecules per glucose.
    • Aerobic respiration occurs in the mitochondria.
    • Aerobic respiration is much more efficient than anaerobic respiration as the glucose molecule is fully oxidized.
    • The products created in the redox reactions of the Kreb’s cycle, plus oxygen (terminal electron acceptor) will produce large quantities of ATP through oxidative phosphorylation (phosphate added to ADP to form ATP) in the ETC, with water being released.
    • Overall in aerobic respiration glucose + oxygen will produce carbon dioxide + water with a large yield of ATP
    • About 32-34 molecules of ATP are produced by aerobic respiration, while in anaerobic respiration, only 2 ATP molecules are produced

    ***Do data based questions on page 128***

    B Skill: Analysis of results from experiments involving measurement of respiration rates in germinating seeds or invertebrates using a respirometer.

    Lab Practical – Using a respirometer to measure the rate of respiration in germinating peas - Can use an online simulation for online learning http://www.phschool.com/science/biology_place/labbench/lab5/intro.html

    2.6 Structure of DNA and RNA

    Understandings:

    ∑ - The nucleic acids DNA and RNA are polymers of nucleotides.

    • Nucleotides are the monomers of the polymer DNA.
    • DNA nucleotides are made up of 3 components a phosphate group (PO4-3), a pentose sugar, and a nitrogenous base.
    • The phosphate, sugar and base are linked by covalent bonds
    • In DNA and RNA each nucleotide is linked to the next nucleotide between the phosphate of one and the pentose sugar of the other nucleotide

    ∑ - DNA differs from RNA in the number of strands present, the base composition and the type of pentose.

    DNA
    RNA
    Sugar is deoxyribose (carbon 2 - no oxygen attached)
    Sugar is ribose (carbon 2 has an –OH attached)
    Nitrogenous bases are guanine, adenine, cytosine and thymine
    Nitrogenous bases are guanine, adenine, cytosine and uracil
    Double-stranded molecule
    Single-stranded molecule

    ∑ - DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs.

    • DNA is double-stranded and shaped like a ladder, with the sides of the ladder made out of repeating phosphate and deoxyribose sugar molecules covalently bonded together. The two strands are antiparallel to each other.
    • The rungs of the ladder contain two nitrogenous bases (one from each strand) that are bonded together by hydrogen bonds.
    • The nitrogenous bases match up according to the Chargaff’s Rules in which adenine always bonds to thymine, and guanine always bonds with cytosine. These bonds are hydrogen bonds.
    • These base pairs, A-T and G-C, are considered to be complimentary.
    • Guanine and cytosine are held together by 3 hydrogen bonds.
    • Adenine and thymine are held together by 2 hydrogen bonds.

    β - Applications and skills:

    β - Application: Crick and Watson’s elucidation of the structure of DNA using model making.

    Go to http://www.dnai.org/a/index.html and click on Finding the Structure.

    Then click on the menu button players

    Watch the interviews for Erwin Chargoff, Rosalind Franklin and Watson and Crick
    Write a one page summary on how Watson and Crick used models to discover the structure of DNA

    B - Skill: Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentoses and bases.

    Draw and label your own simple structure of DNA using circles for phosphates, pentagons for pentose sugar and rectangles for bases.

    Condensation Reaction (formation of a triglyceride)

    ​Absorption Spectrum

    2.3 Carbohydrates and lipids

    ∑ - Monosaccharide monomers are linked together by condensation reactions to form disaccharides and polysaccharide polymers.

    • When two monomers combine together they form a dimer. When many monomers combine together they form a polymer.
    • Condensation Reactions: The building of large macromolecules (polymers) by the removal of water molecules when monomers combine. Each time two monomers combine, one water is removed.
    • For example, glucose is a monosaccharide that is used to build up large storage molecules (polysaccharides) in plants and animals. In plants, many glucose molecules combine through condensation reactions to form the polysaccharide starch. In animals, glucose molecules are combined to form the polysaccharide glycogen through condensation reactions.
    • When a plant or an animal needs to use energy stored in polysaccharide molecules, the opposite reaction to condensation takes place. This break down of larger polysaccharides into smaller monosaccharides through the addition of water is called hydrolysis (water split or separate)
    • Starch and glycogen are broken down by the addition of water into glucose molecules (the energy molecule used in aerobic respiration).
    • In lipids, the polymer is called a triglyceride.
    • Hydrolysis of a triglyceride uses water to break apart the lipid into glycerolC3 H 5 (OH) 3 and 3 fatty acids.


    β - Applications and skills:

    β - Application: Structure and function of cellulose and starch in plants and glycogen in humans.

    • Polysaccharides are long chains of monosaccharides held together with glycosidic linkages made by condensation reactions
    • Starch, cellulose and glycogen are all polysaccharides that are made from long chains of glucose however, they differ in their structure and the type of glucose, which leads to different functions
    • Starch -a long chain of α (alpha) glucose molecules used as glucose storage by plants
    • Starch consists of two types of molecules, amylose which linear and amylopectin which is branched
    • Since the bonds in starch are α-glucose, the –OH groups from the glucose molecules are always pointed down, causing the starch to have a curved appearance. This makes starch a good molecule for storing glucose in plants.
    • Even though glucose is hydrophilic, starch is too large to be soluble in water at room temperature
    • Cellulose are unbranched straight chains of β (beta) glucose molecules, held together with glycosidic bonds
    • Since the –OH groups point out in opposite directions and every other β glucose is flipped 180 degrees, cellulose forms a nice straight chain
    • These straight chains also allow cellulose to form bundles linked by H-bonds
    • This is essential for cellulose’s function, which is to provide strength for cell walls in plant cells (high tensile strength)
    • Notice the up and down alternating glycosidic bonds between the glucose molecules
    • Glycogen– Is a multi-branched energy storage polysaccharide for animals
    • Glycogen consists of many α (alpha) glucose molecules linked
    • It is highly branched, making the molecule more compact and a perfect molecule for energy storage
    • It is stored in the liver and some muscles of humans


    β - Skill: Use of molecular visualization software to compare cellulose, starch and glycogen.

    • Use the following link to analyze and compare the above polysaccharides.
    • http://biomodel.uah.es/en/model3/polisac.htm
    • Method to manipulate the molecules with the mouse is on the bottom right corner of the webpage

    ∑ - Fatty acids can be saturated, monounsaturated or polyunsaturated.

    Fatty Acids

    Fatty acids are non-polar and therefore hydrophobic

    Chains consist of covalently bonded carbon with hydrogen

    Saturated FA’s are all single bonds and are therefore saturated with hydrogen.

    ∑ - Unsaturated fatty acids can be cis or trans isomers.

    • If the hydrogen atoms are on the same side of the double bond then the isomer is “cis” (yellow H above) and if the hydrogens are on the opposite side of the double bond then the isomer is “trans”
    • “cis” fatty acids have a kink at the double bonds, causing the fatty acids to pack more loosely, lowering the melting point and making them liquid at room temperature
    • “trans” fatty acids do not have the kink at the double bond, can pack more tightly, have a higher melting point and are solid at room temperature.
    • Trans fats are partially hydrogenated oils found in some processed foods like margarine. They can cause health risks for humans.

    ∑ - Triglycerides are formed by condensation from three fatty acids and one glycerol.

    • Fatty acids have a long hydrocarbon (carbon and hydrogen) chain with a carboxyl (acid) group. The chains usually contain 16 to 18 carbons.
    • Glycerol contains 3 carbons and 3 hydroxyl groups. It reacts with 3 fatty acids to form a triglyceride or fat molecule through a condensation reaction, which gives off 3 water molecules and forms an ester bond

    Triglyceride or Fat

    http://www.hhmi.org/biointeractive/science-fat
    Check out the interactive video on the molecular structure of fats

    β - 1) Application: Scientific evidence for health risks of trans fats and saturated fatty acids.

    β - 2) Application: Evaluation of evidence and the methods used to obtain the evidence for health claims made about lipids

    Use the following links as examples and find one journal article and one web post on the health risks of trans or saturated fats. You need to find one article from what you would consider as a reputable source and one that is not a good source. You will present these articles to the class discussing the above two applications. Make sure you have a clear understanding of what trans fats and saturated fatty acids are and how they affect our bodies. Critically analyze the evidence for health risks and the methods used to obtain the evidence.

    β - Application: Lipids are more suitable for long-term energy storage in humans than carbohydrates.

    Energy Storage

    • One’s body requires energy to function, more specifically each cell relies on a source of energy to drive the chemical reactions involved in metabolism, growth and other physiological functions
    • Both carbohydrates and lipids (triglycerides) are a major source of energy in animals.
    • Fats contain about twice as much energy as carbohydrates. Each gram of carbohydrates stores about 4 calories of energy, whereas each gram of lipid stores about 9 calories.
    • Therefore, lipids serve as a more compact way to store energy, since it contains more energy per gram than carbohydrates. As a result, your body tends to use fat to store energy over long periods of time and uses carbohydrates to store energy short-term.
    • Glycogen (carb storage) can be quickly into glucose for energy.
    • Triglycerides (fats) contain glycerol and 3 fatty acids and is stored mainly in the body’s adipose tissue
    • Fats also provide thermal insulation, protection for organs (shock absorber) and hormones

    B - Skill: Determination of body mass index by calculation or use of a nomogram.

    https://www.webmd.com/men/weight-loss-bmi

    Use the nomogram on the following quick reference guide from Health Canada to calculate your family members' BMI. Ask your parents’ permission if they are willing to share the data.

    Metric BMI Formula BMI = weight (kg) / [height (m)]2

    2.2 Water

    Understandings: ∑

    ∑ - Water molecules are polar and hydrogen bonds form between them.

    • A water molecule consists of an oxygen atom covalently bound to two hydrogen atoms
    • Since O is more electronegative than H, an unequal sharing of electrons occurs
    • This creates a polar covalent bond, with H having a partial positive charge and O having a partial negative charge
    • Water is also bent so the positive charge exists more or less on one side and the negative charge from the O exists on the opposite side
    • The partial +ve charge is attracted to the partial –ve charge creating an intermolecular attraction between the water molecules called a “Hydrogen bond.”
    • H-bonds are the strongest of the intermolecular bonding, but is still considered a weak bond however, since there are so many H2O molecules they give water its unique properties and make it essential to life on this planet

    ∑ - Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties of water.

    Thermal Property

    Water has a high specific heat capacity (amount of energy needed to raise the temperature of a substance by a certain temperature level). Basically, water can absorb a lot of heat and give off a lot of heat without drastically changing the temperature of the water.
    Water’s high specific heat capacity results from the extensive hydrogen bonding between the water molecules.
    Water also has a high latent heat of vaporization which means it takes a lot of heat to evaporate water from a liquid to a vapour. This is very important as a cooling mechanism for humans. As we sweat, the water droplets absorb heat from our skin causing the water to evaporate and our bodies to cool down. Interesting Documentary on the

    ICEMAN: Man who can control his core body temperature (relates to metabolism as well) https://www.youtube.com/watch?v=VaMjhwFE1Zw

    Cohesive Properties

    • Water is a polar molecule, with a negative oxygen end and a positive hydrogen end.
    • Hydrogen bonds that exist between water molecules create a high level of attraction linking water molecules together. This attraction between two of the same molecules is called cohesion.
    • These cohesive forces allow water to move up vascular tissue in plants against gravity. It also creates surface tension on the water that allows some organisms to walk on water.

    Adhesive Properties

    • Not only does water bind strongly to itself, but it also forms H-bonds with other polar molecules. This is called adhesion.
    • This is an important property in transpiration as well, as water adheres to the cellulose in the walls of the xylem vessels
    • As water is evaporated from the stomata, the adhesion can help the water move up through the xylem

    Solvent Properties

    • Water is known as the “universal solvent” because of its ability to dissolve many substances because of its polarity.
    • Water is able to dissolve other polar molecules such as many carbohydrates, proteins and DNA and positively and negatively charged ions such as Na+.
    • This is essential because it allows water to act as a transport medium (blood and cytoplasm) of important molecules in biological organisms.

    ∑ - Substances can be hydrophilic or hydrophobic.

    • Essentially hydrophilic means “water-loving”
    • Any substances that dissolve in water including charged ions such as Na+ or polar molecules such as glucose and fructose are hydrophilic. Molecules that are attracted to water like phospholipid heads are also hydrophilic
    • Hydrophobic molecules are kind of “water-fearing” but basically, these are non-polar, insoluble in water or non-charged substances, such as lipids
    • Note: Don't use the terms "water-loving or water-fearing" to describe these properties on an exam, it should simply be a way to remember what hydrophilic and hydrophobic mean.

    Lab Activity – Water stations to demonstrate the different properties of water.

    β - Applications and skills:

    β - Application: Comparison of the thermal properties of water with those of methane.


    β - Application: Use of water as a coolant in sweat.

    • Water is essential to living organisms.
    • Water has a high latent heat of vaporization which means it takes a lot of heat to evaporate water from a liquid to a vapour.
    • This is very important as a cooling mechanism for living organisms. As humans sweat, the water droplets absorb heat from the blood flowing under our skin causing the water to evaporate and our blood to cool down. This will, in turn, cool our whole body down.
    • This cooling is controlled by negative feedback through receptors in the hypothalamus
    • If the body is overheated, receptors in the hypothalamus sense this and stimulate the sweat glands to secrete sweat
    • Some reptiles such as crocodiles cool by opening their mouths (gaping). Dogs also pant which causes water to evaporate from their upper respiratory tract.

    β - Application: Modes of transport of glucose, amino acids, cholesterol, fats, oxygen and sodium chloride in blood in relation to their solubility in water.

    • Blood transport many different substances to different parts of the body using a variety of methods
    • Water is critical both as a solvent in which many of the body's solutes dissolve
    • Due to its polarity water is a great solvent of other polar molecules and ions. This is vital because it allows water to act as a transport medium (blood and cytoplasm) of important molecules in biological organisms.
    • NaCl is an ionic compound that is very soluble in water. Na+ and Cl- dissolve and are carried in the blood plasma
    • Glucose is polar and is soluble in water and is therefore transported in the plasma
    • Amino acids have both a negative and a positive charge, but their “R” groups vary, therefore they can be hydrophilic or hydrophobic. They are all soluble enough to be carried in the plasma
    • Fats are non-polar and therefore insoluble in water. They are transported in a single layer sphere of phospholipids called a lipoprotein complex. The hydrophilic heads face outwards towards the water in the plasma and the tails face inwards towards the fats. Proteins are also embedded in the phospholipid layer.
    • Finally, cholesterol, which is mostly hydrophobic because it is a lipid, is also transported inside the lipoprotein complex with the small hydrophilic end facing the phospholipid heads

    2.1 Molecules to metabolism

    ∑ - Understandings:

    ∑ - Molecular biology explains living processes in terms of the chemical substances involved.

    • Involves the explaining of biological processes from the structures of the molecules and how they interact with each other
    • There are many molecules important to living organisms including water, carbohydrates, lipids, proteins, and nucleic acids
    • Proteins are one of the most varied macromolecules, performing many cellular functions, including catalyzing metabolic reactions (enzymes)
    • The relationship between genes and proteins is important as well
    • Molecular biologists break down biochemical processes into their component parts (reductionism)
    • When they look at the sum of all these reactions as a whole, they can study the emergent properties of that system

    Applications and skills: β

    β - Application: Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.

    Video on how the synthesis of urea was discovered

    • Urea is a component of urine which is produced when there is an excess of amino acids in the body way to secrete nitrogen
    • A series of enzyme-catalyzed reactions produce urea in the liver, where it is transported by the blood to the kidney, where it is filtered out and excreted in the urine.
    • Urea can be produced artificially through different chemical reactions however, the product is the same.
    • Urea is mainly used as a nitrogen source in fertilizers

    Read the following article http://humantouchofchemistry.com/urea-and-the-beginnings-of-organic-chemistry.htm. In groups of 3-4 discuss the “Falsification of Vitalism”, with respect to the synthesis of artificial urea. After you have discussed this concept in small groups, come back together for a class discussion on your findings and opinions.

    ∑ - Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.

    • Carbon has a few unique bonding properties - the most important of which is its ability to form long chains of carbon. No other element can bond as carbon does.
    • The reason carbon can do this is that carbon-carbon bonds are extremely strong. This allows carbon to make up many of the basic building blocks of life (fats, sugars, etc).
    • Since carbon-carbon bonds are strong and stable, carbon can form an almost infinite number of compounds
    • In fact, there are more known carbon-containing compounds than all the compounds of the other chemical elements combined except those of hydrogen (because almost all organic compounds contain hydrogen too).
    • Carbon can also form rings eg. glucose
    • The simplest form of an organic molecule is the hydrocarbon—a large family of organic molecules that are composed of hydrogen atoms bonded to a chain of carbon atoms. Eg. Methane
    • All bonding in hydrocarbons is covalent
    • Covalent Bonds are chemical bonds formed by the sharing of a pair of electrons between atoms. The nuclei of two different atoms are attracting the same electrons.
    • Carbon can form single, double and triple bonds

    Carbon has 4 valance electrons in its outer shell.

    ∑ - Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

    Carbohydrates

    • Carbohydrates are composed of carbon, hydrogen, and oxygen
    • The general formula for carbohydrates is (CH 2 O)n.
    • Many carbohydrates are used for energy or structural purposes
    • Lipids are compounds that are insoluble in water but soluble in nonpolar solvents.
    • Some lipids function in long-term energy storage. Animal fat is a lipid that has six times more energy per gram than carbohydrates.
    • Lipids are also an important component of cell membranes.
    • Some examples of lipids are triglycerides, steroids, waxes, and phospholipids
    • Animal fats (saturated) are solid at room temperature and plant fats (unsaturated) are liquid at room temperature
    • Proteins are composed of one or more chains of amino acids
    • All proteins are composed of carbon, hydrogen, oxygen, and nitrogen
    • Proteins are distinguished by their “R” groups. Some of these also contain sulphur

    Generalized amino acid

    Nucleic Acids

    • Nucleic acids are composed of smaller units called nucleotides, which are linked together to form a larger molecule (nucleic acid).
    • Each nucleotide contains a base, a sugar, and a phosphate group. The sugar is deoxyribose (DNA) or ribose (RNA). The bases of DNA are adenine, guanine, cytosine, and thymine. Uracil substitutes for Thymine in RNA
    • They are made from carbon, hydrogen, oxygen, nitrogen and phosphorus

    B - Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.

    • Composed of an amine (NH2) group, a carboxyl (COOH) group, and an R group.
    • 20 amino acids exist that compose all proteins
    • Each amino acid differs because the R groups are different
    • Is a reducing sugar that contains C 6 H 12 O 6
    • Most commonly found in a ringed structure and is the main product formed by photosynthesis
    • Energy molecule used in aerobic respiration
    • A monomer of starch, glycogen, and cellulose
    • Pentose (5 carbon) sugar of RNA and R U BP (Calvin cycle)
    • C 5 H 10 O 5
    • Differs from Deoxyribose (sugar in DNA) because it has an extra –OH group on the 2nd carbon of the ring

    Fatty Acids

    • The main component of triglycerides and phospholipids
    • Fatty acids are non-polar and therefore hydrophobic
    • Chains consist of covalently bonded carbon with hydrogen
    • Saturated FA’s are all single bonds and are therefore saturated with hydrogen.
    • Unsaturated FA’s contain a double bond or double bonds.


    Saturated Fatty Acid
    Unsaturated Fatty Acid

    £ - Skill: Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

    • The generalized formula for carbohydrates is CH2O. All carbohydrate contain C, H, and O
    • Proteins also contain C, H, O but they all have N. Some proteins also contain S in their R-groups
    • Lipids contain C, H, and O as well, but in different ratios and much less O then carbohydrates.

    ∑ - Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism.

    • Metabolism is the set of life-sustaining chemical reactions within the cells of living organisms.
    • These reactions are catalyzed by enzymes and allow organisms to grow and reproduce, maintain their structures, and respond to their environments.
    • Many of these reactions occur in the cytoplasm, but some are extracellular including digestion and the transport of substances into and between different cells
    • The word metabolism can refer to the sum of all chemical reactions that occur in living organisms

    ∑ - Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.

    • Metabolism is divided into two components anabolism (building large molecules from smaller ones) and catabolism (breaking down of large molecules into their component parts)
    • Anabolic reactions require energy as you are building large molecules from small ones (takes energy to build things)
    • Some anabolic processes are protein synthesis, DNA synthesis and replication, photosynthesis, and building complex carbohydrates, such as cellulose, starch, and glycogen
    • If you can’t remember which one is which, think anabolic steroids are used to build muscles in athletes and bodybuilders and catapults are used to break down walls in wars

    ∑ - Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

    • Catabolism is a reaction that breaks down larger molecules into smaller ones or their component parts
    • Catabolic reactions release energy (sometimes captured in the form of ATP)
    • Some examples of catabolic reactions are digestion of food, cellular respiration, and break down of carbon compounds by decomposers
    • Think of "catapults" used to break down enemy walls during wars


    **Note these reactions are condensation and hydrolysis which are outlined **

    2.4 Proteins

    ∑ - Understandings:

    ∑ - Amino acids are linked together by condensation to form polypeptides.

    • Amino acids are then combined to create large polypeptides through condensation reactions which produce many molecules of water (i.e. polypeptides - Hemoglobin and Insulin).

    B Skill: Drawing molecular diagrams to show the formation of a peptide bond.

    • A basic dipeptide is shown to the right. Students should practice drawing with a variety of different amino acids (different “R” groups)
    • Every peptide bond should be between the NH 2 (amine group) and the COOH (carboxyl group). One H comes from the NH2 and an –OH group comes from the –COOH group to produce H 2 O
    • Condensation reaction

    ∑ - There are 20 different amino acids in polypeptides synthesized on ribosomes.

    • Twenty different amino acids are used by the ribosomes to create polypeptides in our body
    • They all contain an amine (NH 2 ) group, a carboxyl (-COOH) group which combine to form the peptide bond and an “R” group
    • The different “R” groups are what makes the amino acids different and allow the proteins to form a wide array of structures and functions
    • Some are charged or polar, hence they are hydrophilic
    • Some are not charged and are non-polar, hence they are hydrophobic

    ∑ - Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.

    • Ribosomes link amino acids together forming a peptide bond according to the mRNA sequence copied from the gene or genes (DNA) for a particular polypeptide
    • Since there are 20 amino acids, an enormous variety of polypeptides can be produced
    • Basically, the number of different polypeptides that can be produced is 20^n, where 20 represents the number of amino acids that can be used and n represents the number of AA’s in a particular polypeptide.
    • So if a protein has 200 AA’s, the number of different combinations would be 20^200, which is an astronomically large number. Some proteins can be in the thousands or tens of thousand

    ∑ - The amino acid sequence of polypeptides is coded for by genes.

    • The sequence of amino acid in polypeptides is coded by the base sequence in an organism’s genes
    • Each 3 bases codes for 1 amino acid in a polypeptide
    • So if a polypeptide is 300 amino acids in length, 900 bases actually code for that polypeptide (not including the 3 base pairs that code for the stop codon). Also, the genes are actually longer as they contain non-coding regions that don't code for the polypeptide.
    • The actual coding region is called the reading frame

    ∑ - A protein may consist of a single polypeptide or more than one polypeptide linked together.

    • Some proteins consist of a single polypeptide, while some contain more than one polypeptide
    • Hemoglobin, for example, has 4 linked polypeptides, which are folded into a globular protein to carry oxygen in the blood
    • Collagen consists of 3 polypeptides wound together like a rope (a structural protein in tendons)
    • Keratin consists of 2 polypeptides twisted into a double helix (a structural protein in hair and fingernails). Insulin also has two polypeptides
    • Glucagon consists of only 1 alpha-helix polypeptide. Glucagon breaks down glycogen into glucose when the body needs sugar for energy

    ∑ - The amino acid sequence determines the three-dimensional conformation of a protein.

    • There are 4 levels of proteins, primary, secondary, tertiary and quaternary
    • How protein twists and folds to form secondary and tertiary structures is determined by the primary sequence of amino acids
    • Secondary structures for fibrous proteins such as collagen and keratin are determined by repeating sequences in the amino acid sequence. They are formed by the interactions between the amine and carboxyl groups
    • Tertiary structures that form globular proteins are still determined by the original amino acid sequence. They form from interactions between the different “R” groups causing them to fold to create an active protein

    ∑ - Living organisms synthesize many different proteins with a wide range of functions.

    Protein Functions

    Enzymes- catalyze biochemical reactions by lowering the activation energy needed for the reaction to take place

    Examples
    Pepsin – breaks down protein in the stomach

    Amylase – breaks down the starch in the mouth and small intestine

    Hormones– chemical messengers that help coordinate certain regulatory activities

    Example
    Insulin – regulates glucose metabolism by controlling blood sugar concentration

    Structural Proteins– fibrous proteins provide support and structure within the body

    Collagen – main protein in connective tissues such as tendons and ligaments

    Transport Proteins – move molecules from one place to another around the body

    Example
    Hemoglobin – transports oxygen throughout the blood system

    Muscle Contractions

    Example
    Actin and myosin – used in the contraction of a muscle in location and transport

    Cytoskeletons

    Example
    Tubulin– subunit of microtubules in the spindle to pull apart chromosomes and give animal cells their shape

    Example
    Binding sites in the membrane for hormones, neurotransmitters and light in the retina

    Example
    Antibodies– for defence against pathogens

    ∑ - Every individual has a unique proteome.

    • A proteome is all of the different kinds of proteins produced by a genome, cell, tissue or organism at a certain time.
    • This is completed by extracting mixtures of proteins and using gel electrophoresis with antibodies specific to those proteins with fluorescent markers
    • Proteomes vary in different cells (different cells make different proteins) and at different times within the same cell (cell activity varies)
    • Proteomes vary between different individuals because of not only cell activity but slight variations in amino acid sequences
    • Within a species, there are strong similarities between proteomes

    Applications and skills:

    β - Application: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.

    Rubisco

    - Catalyzes the reaction in the Calvin cycle that fixes CO2 into organic carbon to be used by living organisms to produce the carbon compounds need for life.
    - Full name is ribulose bisphosphate carboxylase
    - It is one of the most abundant and important enzymes in the world

    - a hormone produced by the beta cells of the pancreas that reduces the blood glucose levels by promoting the absorption of glucose from the blood to the skeletal muscles and tissue
    - Insulin binds reversibly to receptors in the cell membrane to promote uptake

    Immunoglobulins

    - these are also known as “antibodies”
    - They are Y shaped proteins produced by the plasma B cells to identify and neutralize foreign pathogens like bacteria and viruses
    - they act as markers to identify these pathogens for destruction by large white blood cells called Phagocytes
    - each antibody is specific for a specific pathogen

    - rhodopsin is a biological pigment in the photoreceptor cells of the retina
    - rhodopsin consists of a retinal molecule surrounded by an opsin polypeptide
    - When the retinal absorbs light through the eye, it changes its shape and the shape of the opsin. This sends a nerve impulse through the optic nerve to the brain
    - essential in low light

    - main structure molecule in various connective tissues such as skin, blood vessels, and ligaments
    - They are fibrous rope-like proteins made from 3 polypeptides

    Spider silk

    - spider silk consists of many different types with different functions
    Eg. dragline silk is stronger than steel and tougher than Kevlar used in bulletproof vests)
    - used in the spokes of web and when a spider suspends itself
    - very extensible and resistant to breaking

    β - Application: Denaturation of proteins by heat or by the deviation of pH from the optimum. (studied in further detail in enzyme section)


    Breakthrough Just around the Corner

    Prof. Namba believes that the 3D structure of not only proteins but also any of the other biomolecular complexes, including lipids and nucleic acids, will be visualized in 5 years.

    An especially important application is the analysis of membrane proteins on cell surfaces. These proteins are the target of actions of pharmaceutical reagents, and their 3D structural analysis will help reveal the mechanisms underlying their molecular function, dramatically improve therapy outcomes, and make possible the development of drugs with no side effects.

    In the future, there may even be a movement toward the industrial applications of biological molecular motors, such as super energy-saving machines that require a minimal power source and operate using ambient heat as the primary energy source. This paradoxical notion could defy the long-held belief about machinery and engineering.

    Although we are still a long way from realizing such inventions, their realization may prove to lie just around the corner.

    β-galactosidase 2.6 Å resolution CRYO ARM™


    • Sample:
      β-galactosidase with PETG
    • Microscope:
      CRYO ARM™ (Schottky 200 kV) / K2 summit
    • Number of Images:
      2,500 over 3 days by JADAS
    • Image pixel size:
      0.8 Å/pixel
    • Number of particle images:
      350,000(Initial pickup), 88,564 (for final 3D reconstruction)
    • Software:
      Motioncor2, Gctf, Gautomatch, Relion2.0
    • Total dose:
      70 e-/Å 2 (70 frames (0.2 sec/frames x 14 sec)

    Data: courtesy by Dr. T. Kato and Dr. K. Namba, Osaka University, August 2017


    Watch the video: Protein structure. Primary. Secondary. Tertiary. Quaternary (September 2022).


Comments:

  1. Diomedes

    I think you are not right. I'm sure. I can prove it. Write in PM, we will talk.

  2. Gozil

    I am ready to help you, set questions.

  3. Tobiah

    Very useful idea

  4. Amani

    wonderfully, the useful piece

  5. Struan

    This has already been discussed recently.



Write a message