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Cells created using differently aligned proteins

Cells created using differently aligned proteins


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I remember reading that scientist were making cells (I assume bacteria), that used differently oriented proteins to create a whole new class of life. Because apparently right and left aligned proteins don't interact in same way, cells made in such manner would behave similarly but couldn't be interacted with differently aligned bacteria/virus.

However I can't find any proof this story was true? I could be wrong about details. Is there a similar mechanism that would allow a whole case of twin (contain DNA, and most molecules that regular cells posses) cells that couldn't interact with existing bacteria?


The problem with this is something called the structure-function relationship. The function of a protein or enzyme is completely dependent on its structure. For example, take a look at this representation of the active site of chymotrypsin:

The side chains of D102, H57, and S195 all need to be in a perfect conformation in order for the enzyme to function properly, with the hydrogen bonds being essential. If any one of those amino acids was in the D-form, the enzyme would lose its activity completely. Having every single amino acid in the D-form wouldn't help either, as the entire protein's structure (and hence its function) would be altered.


  • The cell theory describes the basic properties of all cells.
  • The three scientists that contributed to the development of cell theory are Matthias Schleiden, Theodor Schwann, and Rudolf Virchow.
  • A component of the cell theory is that all living things are composed of one or more cells.
  • A component of the cell theory is that the cell is the basic unit of life.
  • A component of the cell theory is that all new cells arise from existing cells.
  • cell theory: The scientific theory that all living organisms are made of cells as the smallest functional unit.

Structural analysis of natural killer cell receptor protein 1 (NKR-P1) extracellular domains suggests a conserved long loop region involved in ligand specificity

Receptor proteins at the cell surface regulate the ability of natural killer cells to recognize and kill a variety of aberrant target cells. The structural features determining the function of natural killer receptor proteins 1 (NKR-P1s) are largely unknown. In the present work, refined homology models are generated for the C-type lectin-like extracellular domains of rat NKR-P1A and NKR-P1B, mouse NKR-P1A, NKR-P1C, NKR-P1F, and NKR-P1G, and human NKR-P1 receptors. Experimental data on secondary structure, tertiary interactions, and thermal transitions are acquired for four of the proteins using Raman and infrared spectroscopy. The experimental and modeling results are in agreement with respect to the overall structures of the NKR-P1 receptor domains, while suggesting functionally significant local differences among species and isoforms. Two sequence regions that are conserved in all analyzed NKR-P1 receptors do not correspond to conserved structural elements as might be expected, but are represented by loop regions, one of which is arranged differently in the constructed models. This region displays high flexibility but is anchored by conserved sequences, suggesting that its position relative to the rest of the domain might be variable. This loop may contribute to ligand-binding specificity via a coupled conformational transition.


Protein-folding forces

Proteins possess the remarkable ability to fold spontaneously into precisely determined three-dimensional structures. Refolding experiments have established that the information required to specify a protein’s folded conformation (its native state) is completely contained in its linear amino acid sequence 13,14,15 . According to Anfinsen’s thermodynamic hypothesis, this information is encoded in the shape of the energy landscape of the polypeptide: the native state is the one with the lowest free energy 16,17 . This hypothesis forms the basis for a general approach to protein structure prediction that combines sampling of alternative conformations with scoring to rank them by energy and identify the lowest energy state 18,19,20,21 . The chief obstacle to the success of this energy-guided approach, first identified by Cyrus Levinthal as a conceptual barrier to protein folding on biological timescales 22 , is the vast space of potential conformations: even supposing that each amino acid has only a limited, discrete set of possible backbone states, the total size of the conformational space that must be searched grows exponentially with chain length, and very quickly becomes astronomical. The solution to this dilemma lies in the recognition that it is not necessary to explore the entire conformational space in order to identify the native state: the energy landscape is not a flat ‘golf course’ with a single native ‘hole’ rather, directional cues impart an overall funnel shape to the landscape and guide sampling towards near-native conformations 19,23 (Fig. 1a). These directional cues can arise from sequence-local residue interactions that bias short stretches of the chain towards forming specific secondary structures, or from favourable long-range, non-local packing interactions that can be formed even before the global native fold is reached.

a | Simplified, two-dimensional representations of ‘golf course’ and ‘funnel’-shaped energy landscapes. Identifying the native energy minimum (‘N’) in the landscape on the left requires exhaustive exploration, whereas a simple downhill search from most starting points will locate the native state in the landscape on the right. b | Energetic features that distinguish the protein native state include: hydrophobic patterning (shown here in a cutaway view of the small protein ubiquitin), with burial of nonpolar side chains in the protein core backbone and side-chain hydrogen bonding (hydrogen bonds are shown as dotted green lines) tight side-chain packing (visible in a slice through a protein core) and restricted backbone and side-chain torsion angle distributions (evident in the highly focused two-dimensional probability distributions of backbone — phi angle versus psi angle — and side-chain — chi1 angle versus chi2 angle — torsion angles for the amino acid isoleucine). c | Computational models of protein energetics offer a trade-off between speed and accuracy. Coarse-grained models are computationally efficient and effectively smooth the energy landscape, permitting large-scale sampling however, they also introduce inaccuracies such as false minima (for example, the blue basin to the left of the native minimum in this part, highlighted with an arrow). High-resolution, atomically detailed energy functions are more accurate, but also slower to evaluate and sensitive to structural detail, which introduces bumpiness (many local minima) into the landscape and makes them harder to navigate efficiently.

The driving force favouring the folding of water-soluble, globular proteins is thought to be the burial of hydrophobic amino acid side chains away from water 24 folding is opposed by the loss of configurational entropy that accompanies the collapse of a flexible polypeptide chain into a defined 3D conformation. Tight packing of nonpolar side chains in the protein core enhances attractive van der Waals interactions and eliminates entropically unfavourable internal cavities (Fig. 1b). Moreover, this jigsaw puzzle-like packing is achieved while accommodating strong backbone and side-chain torsional preferences that restrict the observed torsion angle distributions (lower panels in Fig. 1b), effectively reducing side-chain flexibility to the neighbourhood of a discrete set of rotamers at each position. Intra-protein hydrogen bonds and salt bridges largely compensate for the loss of interactions with water, as polar groups are buried during folding and hence these interactions contribute less to the stability of the native state than to its specificity (that is, they help discriminate the native state from other compact states). Whereas hydrophobic burial and backbone hydrogen bonding can be detected from low-resolution structural models, the tight core packing and absence of buried, unsatisfied polar groups that distinguish the native state require explicit modelling of the side-chain degrees of freedom. As a result, molecular modelling approaches for structure prediction and design often employ multiple levels of resolution: large-scale conformational sampling is performed with a computationally efficient coarse-grained energy function that captures hydrophobic burial, formation of secondary structure, and avoidance of atomic overlaps 25,26,27 final protein model selection and refinement requires explicit modelling of the amino acid side chains using a more time-intensive, high-resolution atomistic energy function (Fig. 1c).


A new type of medicine

We need new medicines because there are still many diseases that we can’t treat with conventional small-molecule therapeutics. The prevailing approach in recent history has been to use small molecules to break apart protein-protein interactions. This approach has been effective, but researchers have learned that it only works with proteins that have special features.

It turns out that many proteins involved in disease don’t have these special features. Molecular glues, with their protein-pairing capabilities, provide an alternative: bringing proteins together and making new protein-protein interactions to interrupt disease biology.


Nucleotide

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Nucleotide, any member of a class of organic compounds in which the molecular structure comprises a nitrogen-containing unit (base) linked to a sugar and a phosphate group. The nucleotides are of great importance to living organisms, as they are the building blocks of nucleic acids, the substances that control all hereditary characteristics.

A brief treatment of nucleotides follows. For full treatment, see nucleic acids.

In the two families of nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA), the sequence of nucleotides in the DNA or RNA codes for the structure of proteins synthesized in the cell. The nucleotide adenosine triphosphate (ATP) supplies the driving force of many metabolic processes. Several nucleotides are coenzymes they act with enzymes to speed up (catalyze) biochemical reactions.

The nitrogen-containing bases of nearly all nucleotides are derivatives of three heterocyclic compounds: pyrimidine, purine, and pyridine. The most common nitrogen bases are the pyrimidines (cytosine, thymine, and uracil), the purines (adenine and guanine), and the pyridine nicotinamide.

Nucleosides are similar to nucleotides except that they lack the phosphate group. Nucleosides themselves rarely participate in cell metabolism.

Adenosine monophosphate (AMP) is one of the components of RNA and also the organic component of the energy-carrying molecule ATP. In certain vital metabolic processes, AMP combines with inorganic phosphate to form ADP (adenosine diphosphate) and then ATP. The breaking of the phosphate bonds in ATP releases great amounts of energy that are consumed in driving chemical reactions or contracting muscle fibres. Cyclic AMP, another nucleotide, is involved in regulating many aspects of cellular metabolism, such as the breakdown of glycogen.

A dinucleotide, nicotinamide adenine dinucleotide (NAD), participates in many oxidation reactions as an electron carrier, along with the related compound nicotinamide adenine dinucleotide phosphate (NADP). These substances act as cofactors to certain enzymes.


Cancer Cell Properties

STEVE GSCHMEISSNER/Getty Images

Cancer cells have characteristics that differ from normal cells.

  • Cell Reproduction: Cancer cells acquire the ability to reproduce uncontrollably. These cells may have gene mutations or chromosome mutations that affect the reproductive properties of the cells. Cancer cells gain control of their own growth signals and continue to multiply unchecked. They don't experience biological aging and maintain their ability to replicate and grow.
  • Cell Communication: Cancer cells lose the ability to communicate with other cells through chemical signals. They also lose sensitivity to anti-growth signals from surrounding cells. These signals normally restrict cellular growth.
  • Cell Adhesion: Cancer cells lose the adhesion molecules that keep them bonded to neighboring cells. Some cells have the ability to metastasize or spread to other areas of the body through the blood or lymph fluid. Once in the bloodstream, cancer cells release chemical messengers called chemokines that enable them to pass through blood vessels into the surrounding tissues.
  • Cell Specialization: Cancer cells are unspecialized and do not develop into cells of a specific type. Similar to stem cells, cancer cells proliferate or replicate many times, for long periods of time. Cancer cell proliferation is rapid and excessive as these cells spread throughout the body.
  • Cell Death: When the genes in a normal cell are damaged beyond repair, certain DNA checking mechanisms signal for cell destruction. Mutations that occur in gene checking mechanisms allow for the damages to go undetected. This results in the loss of the cell's ability to undergo programmed cell death.

10.2 The Cell Cycle

By the end of this section, you will be able to do the following:

  • Describe the three stages of interphase
  • Discuss the behavior of chromosomes during karyokinesis/mitosis
  • Explain how the cytoplasmic content is divided during cytokinesis
  • Define the quiescent G0 phase

The cell cycle is an ordered series of events involving cell growth and cell division that produces two new daughter cells. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages of growth, DNA replication, and nuclear and cytoplasmic division that ultimately produces two identical (clone) cells. The cell cycle has two major phases: interphase and the mitotic phase (Figure 10.5). During interphase , the cell grows and DNA is replicated. During the mitotic phase , the replicated DNA and cytoplasmic contents are separated, and the cell cytoplasm is typically partitioned by a third process of the cell cycle called cytokinesis . We should note, however, that interphase and mitosis (karyokinesis) may take place without cytokinesis, in which case cells with multiple nuclei (multinucleate cells) are produced.

Interphase

During interphase, the cell undergoes normal growth processes while also preparing for cell division. In order for a cell to move from interphase into the mitotic phase, many internal and external conditions must be met. The three stages of interphase are called G1, S, and G2.

G1 Phase (First Gap)

The first stage of interphase is called the G1 phase (first gap) because, from a microscopic point of view, little change is visible. However, during the G1 stage, the cell is quite active at the biochemical level. The cell is accumulating the building blocks of chromosomal DNA and the associated proteins as well as accumulating sufficient energy reserves to complete the task of replicating each chromosome in the nucleus.

S Phase (Synthesis of DNA)

Throughout interphase, nuclear DNA remains in a semi-condensed chromatin configuration. In the S phase , DNA replication can proceed through the mechanisms that result in the formation of identical pairs of DNA molecules—sister chromatids—that are firmly attached to the centromeric region. The centrosome is also duplicated during the S phase. The two centrosomes of homologous chromosomes will give rise to the mitotic spindle , the apparatus that orchestrates the movement of chromosomes during mitosis. For example, roughly at the center of each animal cell, the centrosomes are associated with a pair of rod-like objects, the centrioles , which are positioned at right angles to each other. Centrioles help organize cell division. We should note, however, that centrioles are not present in the centrosomes of other eukaryotic organisms, such as plants and most fungi.

G2 Phase (Second Gap)

In the G2 phase , the cell replenishes its energy stores and synthesizes proteins necessary for chromosome manipulation and movement. Some cell organelles are duplicated, and the cytoskeleton is dismantled to provide resources for the mitotic phase. There may be additional cell growth during G2. The final preparations for the mitotic phase must be completed before the cell is able to enter the first stage of mitosis.

The Mitotic Phase

The mitotic phase is a multistep process during which the duplicated chromosomes are aligned, separated, and move into two new, identical daughter cells. The first portion of the mitotic phase is called karyokinesis , or nuclear division. As we have just seen, the second portion of the mitotic phase (and often viewed as a process separate from and following mitosis) is called cytokinesis—the physical separation of the cytoplasmic components into the two daughter cells.

Link to Learning

Revisit the stages of mitosis at this site.

Karyokinesis (Mitosis)

Karyokinesis, also known as mitosis , is divided into a series of phases—prophase, prometaphase, metaphase, anaphase, and telophase—that result in the division of the cell nucleus (Figure 10.6).

Visual Connection

Which of the following is the correct order of events in mitosis?

  1. Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus reforms and the cell divides. Cohesin proteins break down and the sister chromatids separate.
  2. The kinetochore becomes attached to the mitotic spindle. Cohesin proteins break down and the sister chromatids separate. Sister chromatids line up at the metaphase plate. The nucleus reforms and the cell divides.
  3. The kinetochore becomes attached to the cohesin proteins. Sister chromatids line up at the metaphase plate. The kinetochore breaks down and the sister chromatids separate. The nucleus reforms and the cell divides.
  4. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. Cohesin proteins break down and the sister chromatids separate. The nucleus reforms and the cell divides.

Prophase (the “first phase”): the nuclear envelope starts to dissociate into small vesicles, and the membranous organelles (such as the Golgi complex [Golgi apparatus] and the endoplasmic reticulum), fragment and disperse toward the periphery of the cell. The nucleolus disappears (disperses) as well, and the centrosomes begin to move to opposite poles of the cell. Microtubules that will form the mitotic spindle extend between the centrosomes, pushing them farther apart as the microtubule fibers lengthen. The sister chromatids begin to coil more tightly with the aid of condensin proteins and now become visible under a light microscope.

Prometaphase (the “first change phase”): Many processes that began in prophase continue to advance. The remnants of the nuclear envelope fragment further, and the mitotic spindle continues to develop as more microtubules assemble and stretch across the length of the former nuclear area. Chromosomes become even more condensed and discrete. Each sister chromatid develops a protein structure called a kinetochore in its centromeric region (Figure 10.7). The proteins of the kinetochore attract and bind to the mitotic spindle microtubules. As the spindle microtubules extend from the centrosomes, some of these microtubules come into contact with and firmly bind to the kinetochores. Once a mitotic fiber attaches to a chromosome, the chromosome will be oriented until the kinetochores of sister chromatids face the opposite poles. Eventually, all the sister chromatids will be attached via their kinetochores to microtubules from opposing poles. Spindle microtubules that do not engage the chromosomes are called polar microtubules . These microtubules overlap each other midway between the two poles and contribute to cell elongation. Astral microtubules are located near the poles, aid in spindle orientation, and are required for the regulation of mitosis.

Metaphase (the “change phase”): All the chromosomes are aligned in a plane called the metaphase plate , or the equatorial plane, roughly midway between the two poles of the cell. The sister chromatids are still tightly attached to each other by cohesin proteins. At this time, the chromosomes are maximally condensed.

Anaphase (“upward phase”): The cohesin proteins degrade, and the sister chromatids separate at the centromere. Each chromatid, now called a single chromosome, is pulled rapidly toward the centrosome to which its microtubule is attached. The cell becomes visibly elongated (oval shaped) as the polar microtubules slide against each other at the metaphase plate where they overlap.

Telophase (the “distance phase”): the chromosomes reach the opposite poles and begin to decondense (unravel), relaxing once again into a stretched-out chromatin configuration. The mitotic spindles are depolymerized into tubulin monomers that will be used to assemble cytoskeletal components for each daughter cell. Nuclear envelopes form around the chromosomes, and nucleosomes appear within the nuclear area.

Cytokinesis

Cytokinesis , or “cell motion,” is sometimes viewed as the second main stage of the mitotic phase, during which cell division is completed via the physical separation of the cytoplasmic components into two daughter cells However, as we have seen earlier, cytokinesis can also be viewed as a separate phase, which may or may not take place following mitosis. If cytokinesis does take place, cell division is not complete until the cell components have been apportioned and completely separated into the two daughter cells. Although the stages of mitosis are similar for most eukaryotes, the process of cytokinesis is quite different for eukaryotes that have cell walls, such as plant cells.

In animal cells, cytokinesis typically starts during late anaphase. A contractile ring composed of actin filaments forms just inside the plasma membrane at the former metaphase plate. The actin filaments pull the equator of the cell inward, forming a fissure. This fissure is called the cleavage furrow . The furrow deepens as the actin ring contracts, and eventually the membrane is cleaved in two (Figure 10.8).

In plant cells, a new cell wall must form between the daughter cells. During interphase, the Golgi apparatus accumulates enzymes, structural proteins, and glucose molecules prior to breaking into vesicles and dispersing throughout the dividing cell. During telophase, these Golgi vesicles are transported on microtubules to form a phragmoplast (a vesicular structure) at the metaphase plate. There, the vesicles fuse and coalesce from the center toward the cell walls this structure is called a cell plate . As more vesicles fuse, the cell plate enlarges until it merges with the cell walls at the periphery of the cell. Enzymes use the glucose that has accumulated between the membrane layers to build a new cell wall. The Golgi membranes become parts of the plasma membrane on either side of the new cell wall (Figure 10.8).

G0 Phase

Not all cells adhere to the classic cell-cycle pattern in which a newly formed daughter cell immediately enters the preparatory phases of interphase, closely followed by the mitotic phase, and cytokinesis. Cells in G0 phase are not actively preparing to divide. The cell is in a quiescent (inactive) stage that occurs when cells exit the cell cycle. Some cells enter G0 temporarily due to environmental conditions such as availability of nutrients, or stimulation by growth factors. The cell will remain in this phase until conditions improve or until an external signal triggers the onset of G1. Other cells that never or rarely divide, such as mature cardiac muscle and nerve cells, remain in G0 permanently.

Scientific Method Connection

Determine the Time Spent in Cell-Cycle Stages

Problem: How long does a cell spend in interphase compared to each stage of mitosis?

Background: A prepared microscope slide of whitefish blastula cross-sections will show cells arrested in various stages of the cell cycle. (Note: It is not visually possible to separate the stages of interphase from each other, but the mitotic stages are readily identifiable.) If 100 cells are examined, the number of cells in each identifiable cell-cycle stage will give an estimate of the time it takes for the cell to complete that stage.

Problem Statement: Given the events included in all of interphase and those that take place in each stage of mitosis, estimate the length of each stage based on a 24-hour cell cycle. Before proceeding, state your hypothesis.

Test your hypothesis: Test your hypothesis by doing the following:

  1. Place a fixed and stained microscope slide of whitefish blastula cross-sections under the scanning objective of a light microscope.
  2. Locate and focus on one of the sections using the low-power objective of your microscope. Notice that the section is a circle composed of dozens of closely packed individual cells.
  3. Switch to the medium-power objective and refocus. With this objective, individual cells are clearly visible, but the chromosomes will still be very small.

Switch to the high-power objective and slowly move the slide left to right, and up and down to view all the cells in the section (Figure 10.9). As you scan, you will notice that most of the cells are not undergoing mitosis but are in the interphase period of the cell cycle.

Record your observations: Make a table similar to Table 10.1 within which to record your observations.

Phase or StageIndividual TotalsGroup TotalsPercent
Interphase
Prophase
Metaphase
Anaphase
Telophase
Cytokinesis
Totals100100100 percent

Analyze your data/report your results: To find the length of time whitefish blastula cells spend in each stage, multiply the percent (recorded as a decimal) by 24 hours. Make a table similar to Table 10.2 to illustrate your data.

Phase or StagePercentTime in Hours
Interphase
Prophase
Metaphase
Anaphase
Telophase
Cytokinesis

Draw a conclusion: Did your results support your estimated times? Were any of the outcomes unexpected? If so, discuss those events in that stage that may have contributed to the calculated time.

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    Actin as a mechanical framework

    Rather than affecting actin dynamics or regulating actin structure per se, an enormous number of ABPs use actin as a scaffold, physical support or track. Whilst some of these proteins may indirectly alter actin dynamics and structure, this is not their primary role in the cell. We have classified these proteins into three main categories myosins, anchors to membrane complexes, and linkers between actin and other cytoskeletal elements.

    Myosins

    Myosins are actin-dependent molecular motors that produce movement (and force) through the hydrolysis of ATP. As such, myosins simply use actin as a track along which to move. Most people are familiar with the two-headed myosin II involved in contractility and tension generation, but there are now over 17 different classes of myosins with various diverse functions (Hodge and Cope, 2000). Nonetheless, where tested, they all use actin as a track to move their specific cargo whether it be membranes or vesicles, actin filaments or a host of other proteins – and mostly but not exclusively from the pointed to the barbed end of the filament.

    Cytoskeletal linkers and membrane anchors

    The utility of F-actin as a structural framework within cells necessitates its connection to other cellular elements. Most of these individual proteins have quite specific functions relating to their (sub)cellular and organismal context. But as alluded to above they can be subdivided into two broad groups: proteins that connect actin to membranes or membrane proteins and those that interconnect different cytoskeletal elements. In the former category are proteins such as dystrophin and utrophin or talin and vinculin, which connect the actin cytoskeleton to the cell adhesion receptors dystroglycan or integrin, respectively and proteins that can bind directly to membranes and also interact with actin such as annexins. The latter category comprises a small but important group of proteins that can link actin to microtubules, actin to intermediate filaments or, in the case of plectin, actin to both microtubules and intermediate filaments. Clearly such proteins are of great importance to the cell in the integration of structure and signalling between the cytoskeletal elements and the maintenance of cell integrity.


    Watch the video: How Cells Become Specialized (January 2023).