Molecular Biology of the Cell Resumes and Schemes
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Chapter 3 Proteins
Proteins constitute most of a cell’s dry mass. They are not only the main building blocks from which cells are assembled but they also execute the majority of the cell’s functions.
o Enzymes: catalyse covalent bond breakage or formation
- Structural proteins: provide mechanical support to cells and tissues (collagen and
- Transport proteins: carry small molecules or ions (Haemoglobin; serum albumin:
elastin)
lipids)
o Motor proteins: generate movement in cells and tissues (Myosin)
- Storage proteins: store amino acids or ions (Ferritin: iron in liver)
o Signal proteins: carry extracellular signals from cell to cell (Insulin)
o Receptor proteins: detect signals and transmit them to the cell’s response
machinery (Rhodopsin: detects light)
- Gene regulatory proteins: bind to DNA to switch genes on or off (Lactose repressor
- Special-purpose proteins: highly variable and specialized proteins (Antifreeze
in bacteria)
proteins in fishes; fluorescent protein in jellyfish)
A protein in made up from:
- Amino acids (20 different types coded for directly); each
linked to its neighbour trough:
- Peptide bonds (amine linkages)
▪ Proteins= polypeptides, their chains are polypeptide chains
o Polypeptide backbone: the repeating sequence of atoms
along the core of the polypeptide chain. Attached to this repetitive chair are those portions the AAs that are not
involved in making a peptide bond:
- 20 different side chains that give each amino acid its
unique properties (uncharged polar, nonpolar, neg./pos.charged)
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A protein to be functional needs to fold into a particular 3D structure.The folding of a protein chain is determined by different sets of weak non covalent bonds: ▪ Hydrogen bonds ▪ Van der Waals attractions ▪ Electrostatic attractions ▪ Hydrophobic interaction= in an aqueous environment, hydrophobic side chains in a protein (leucine, valine etc…) cluster in the interior of the molecule to avoid contact with the water; hydrophilic side chains (arginine, histidine etc…) arrange themselves near the outside of the molecule, where they can form HB with water.
As a result of all these interactions most proteins have a particular three-dimensional
structure:
Conformation= final folded structure in which the free energy of any polypeptide chain is minimized.Protein folding in living cell is assisted by molecular chaperones proteins
- Bind to partially folded chains and help them to fold.
- Prevent the temporarily exposed hydrophobic regions in newly synthesized protein
chains from associating with each other to form protein aggregates (that can eventually spread causing the death of the cell).
When comparing the 3D structures of many different protein molecules, it becomes clear that, although the overall conformation of each protein is unique, two regular folding
patterns are often found within them:
- α- helix: found in α-keratin; generated when a single polypeptide chain twists
around on itself to form a rigid cylinder (right or left handed).▪ Hydrogen bond ( C=O→N-H) every fourth peptide bond ▪ Helix with a complete turn every 3.6 amino acids.
▪ Coiled coil: form when two/three (or more) α- helices have most of their
nonpolar (hydrophobic) side chain on one side, so that they can twist around each other with these side chain facing inward.
o β- sheet: found in fibroin (major constituent of silk)
▪ Parallel chains: form from neighbouring segments of the polypeptide
backbone that run in the same orientation
▪ Antiparallel chains: form from a polypeptide backbone that folds back and
forth upon itself, with each section of the chain running in the direction opposite to that of its immediate neighbours.Both (α- helix and β- sheet) formed by hydrogen bonds between the oxygen of the C=O group and H of the N-H group.
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Scientist distinguish four levels of organization in the structure of a protein:
o Primary structure: amino acid sequence.
- Secondary structure: stretches of polypeptide chain that form α- helices and β-
sheets.
o Tertiary structure: full three-dimensional organization.
o Quaternary structure: when a protein is formed of more than one polypeptide
chain.
Studies of the conformation of proteins also revieled the central importantance of a unit of organization distinct from there four. This is the protein domain, a substructure produced by any segment of a polypeptide chain that can fold independently of the rest of the protein into a stable structure. The different domains of a protein are often sssociated with different functions. For example the Src protein kinase, which function in signalling
pathways inside vertebrate cells, has three domains: SH2 and SH3 domains have
regulatory roles, while the C-terminal domain is responsible for the kinase catalytic activity.Most proteins are composed of a series of proteins domains; such multidomain proteins are believed to have originated from an evolutionary process called domain shuffling through which proteins have evolved through the joining of pre-existing domains in new combinations.
- Protein modules: especially mobile protein domains. Each of these domains have a
stable β- sheet core structure from which less-ordered loops (binding sites) protrude. Protein modules can easily integrate themselves into other proteins.Some domains have their N- and C- terminal ends at opposite poles of the domain (examples are the immunoglobulin and fibronectin type 3 domains).Domains with this “in-line” arrangement can be readily linked in series to form extended structures, either with themselves or with other in-line domains.Other frequently used domains (including the kringle domain and the SH2 domain), are of a “plug-in” type with their N- and C- termini close together. After genomic rearrangements, such domains are usually accommodated as an insertion into a loop region of a second protein.
Many proteins can be grouped into protein families, each family member having an amino acid sequence and 3D conformation that resembles those of the other family members, even though they have different functions.For example the serine proteases are a large family of protein-cleaving (proteolytic) enzymes that includes the digestive enzymes chymotrypsin, trypsin, and elastase, and several proteases involved in blood clotting. Their structure is basically identical, many different serine proteases nevertheless have distinct enzymatic activities, each cleaving 5 / 10
different proteins or the peptide bonds between different types of amino acids. Each therefore performs a distinct function in an organism.
The same weak bonds that enable a protein chain to fold into a specific conformation also allow proteins to bind to each other to produce larger structures in the cell.Binding site: any region of a protein’s surface that can interact with another molecule trough sets of non covalent bonds.Ligand: substance a protein can specifically bind to due to non covalent bonds + hydrophobic forces.▪ In the simplest case, two identical folded polypeptide chains bind to each other in a head-to-head conformation, forming a symmetric complex of two protein subunits (dimer), held together by interactions between two identical binding sites.
Subunit: a single polypeptide chain in such a protein.
Many of the proteins in cells contain two or more types of polypeptide chains.Hemoglobin, the protein that carries oxygen in red blood cells, for example, contains two identical α-globin subunits and two identical β-globin subunits, symmetrically arranged.
Protein can be distinguished in:
- Globular proteins: with a compact ball shape with an irregular surface; they can
form filaments that may span the entire cell.➢ An actin filament, for example, is a long helical structure produced from many molecules of the protein actin. Actin is a globular protein that is very abundant in eukaryotic cells, where it forms one of the major filament systems of the cytoskeleton.
o Fibrous proteins: they have an elongated 3D structure. Fibrous proteins are
particularly abundant in the extracellular matrix.➢ Collagen is the most abundant of these proteins in animal tissues. A collagen molecule consists of three long polypeptide chains, each containing the nonpolar amino acid glycine at every third position. This regular structure allows the chains to wind around one another to generate a long regular triple helix. Many collagen molecules then bind to on another side-by-side and end-to- end to create long overlapping arrays—thereby generating the extremely tough collagen fibrils that give connective tissues their strength.➢ In contrast to collagen, another abundant protein in the extracellular matrix, elastin, is formed as a highly disordered polypeptide. This disorder is essential for elastin’s function. Its relatively unstructured polypeptide chains are covalently cross-linked to produce an, elastic structure that can be reversibly pulled from one conformation to another. The elastic fibers that result enable skin and other tissues, such as arteries and lungs, to stretch and recoil without breaking.
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Enzymes Enzymes are molecules that cause the chemical transformations that make and break covalent bonds in cells.They bind to one or more ligands, called substrates, and convert them into one or more chemically modified products. Enzymes speed up reactions without themselves being changed—that is, they act as catalysts that permit cells to make or break covalent bonds in a controlled way.
Enzymes can be grouped into chemical classes:
Substrate molecules must pass through a series of intermediate states of altered geometry and electron distribution before they form the ultimate products of the reaction.
Transition state: most unstable intermediate state
o Activation energy: free energy required to attain the transition state
Enzymes have a much higher affinity for the transition state of the substrate than they have for the stable form. Because this tight binding greatly lowers the energy of the transition state, the enzyme greatly accelerates a particular reaction by lowering the activation energy that is required.
Enzymes not only bind tightly to a transition state, they also contain precisely positioned atoms that alter the electron distributions in the atoms that participate directly in the making and breaking of covalent bonds. Peptide bonds, for example, can be hydrolyzed in 7 / 10
the absence of an enzyme by exposing a polypeptide to either a strong acid or a strong base. Enzymes are unique, however, in being able to use acid and base catalysis simultaneously, because the rigid framework of the protein constrains the acidic and basic residues and prevents them from combining with each other, as they would do in solution
Proteins are regulated by more than the reversible binding of other molecules. A second method that eukaryotic cells use extensively to regulate a protein’s function is the covalent addition of a smaller molecule to one or more of its amino acid side chains. The most common such regulatory modification in higher eukaryotes is the addition of a phosphate group.Protein phosphorylation: consist in the transfer of a terminal phosphate group from ATP to a serine, threonine or tyrosine side chain of the protein. Aided by protein kinase
Dephosphorylation: protein phosphatase (removal of phosphate group-
dephosphorylation).
The hundreds of different protein kinases in a eukaryotic cell are organized into complex networks of signalling pathways that help to coordinate the cell’s activities, including the cell cycle. Individual protein kinases serve as input–output devices in the integration process. An important part of the input to these signal-processing proteins comes from the control that is exerted by phosphates added and removed from them by protein kinases and protein phosphatases, respectively.The Src family of protein kinases exhibits such behavior. The Src protein (pronounced “sarc” and named for the type of tumor, a sarcoma, that its deregulation can cause) was the first tyrosine kinase to be discovered. It is now known to be part of a subfamily of nine very similar protein kinases, which are found only in multicellular animals.
Src kinases can switch between:
➢ Inactive conformation: in which a phosphorylated tyrosine near the C-terminus is bound to the SH2 domain, and the SH3 domain is bound to an internal peptide in a way that distorts the active site of the enzyme and helps to render it inactive.➢ Active conformation: turning the kinase on involves at least two specific inputs: removal of the C-terminal phosphate and the binding of the SH3 domain by a specific activating protein.
Eukaryotic cells also have another way to control protein activ- ity by phosphate addition and removal. In this case, the phosphate is not attached directly to the protein; instead, it is a part of the guanine nucleotide GTP, which binds very tightly to a class of proteins
known as:
➢ GTP binding proteins (GTPase): generally they are active when GTP is bound and inactive when GDP is bound.They can hydrolyze GTP→GDP + P+ (released)→ causing a conformational change that inactivate the protein. The process is reversible.The Ras protein, for example, has an important role in cell signalling. In its GTP- bound form, it is active and stimulates a cascade of protein phosphorylations in the 8 / 10
cell. Most of the time, however, the protein is in its inactive, GDP-bound form. It becomes active when it exchanges its GDP for a GTP molecule in response to extracellular signals, such as growth factors, that bind to receptors in the plasma membrane
GTP binding proteins are controlled by regulatory proteins:
• GTPase-activating protein (GAP): inactivate the protein by triggering the
hydrolysis of the bound GTP to GDP.
• Guanine nucleotide exchange factor (GEF): activate the protein by
catalysing the exchange of GDP to GTP.
The most common type of enzyme control is feedback inhibition, in which a product produced late in a reaction pathway inhibits an enzyme that act earlier in the pathway.Thus, when large quantities of the final product begin to accumulate, this product binds to the enzyme and slows down its catalytic action, thereby limiting the further entry of substrates into that reaction pathway.
• Negative regulation: it prevents an enzyme from acting.
• Positive regulation: a regulatory molecule stimulates the enzyme’s activity rather than shutting the enzyme down.
Enzymes involved in feedback regulation have at least two different binding sites on their
surface:
• Active site that recognizes the substrates.• Regulatory site that recognizes a regulatory molecule.These two sites communicate so that the catalytic events at the active site can be influenced by the binding of the regulatory molecule at the regulatory site.
A stinking feature of both positive and negative regulation is that the regulatory molecule often has a shape totally different from the shape of the substrate. This is why the effect on a protein is termed allostery (from the Greek allos (other) and stereos (three-dimensional)).The interaction between separated sites on a protein molecule is now known to depend on a conformational change in the protein: binding at one of the sites causes a shift from one folded shape to a slightly different folded shape. It is thought that most proteins are allosteric as they can adopt two or more slightly different conformations.
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Chapter 4 DNA, Chromosomes and Genomes
The structure and function of DNA
Deoxyribonucleic acid (DNA):
Biologists in the 1940s had difficulty in conceiving how DNA could be the genetic material. The molecule seemed too simple: a long polymer composed of only four types of nucleotide subunits, which resemble one another chemically. Early in the 1950s, DNA was examined by x-ray diffraction analysis, a technique for determining the three-dimensional atomic structure of a molecule. The early x-ray diffraction results indicated that DNA was composed of two strands of the polymer wound into a helix. The observation that DNA was double-stranded provided one of the major clues that led to the Watson–Crick model for DNA structure that, as soon as it was proposed in 1953, made DNA’s potential for replication and information storage apparent.
A deoxyribonucleic acid (DNA) molecule consists of two long polynucleotide chains composed of four types of nucleotide subunits. Each of these chains is known as a DNA chain, or a DNA strand. The chains run antiparallel to each other, and hydrogen bonds between the base portions of the nucleotides hold the two chains together.
- Nucleotide: nitrogen-containing base + five-carbon sugar + 1 or more phosphate
groups. In the case of DNA the sugar is deoxyribose attached to a single phosphate
group. The bases may be:
Purine (2 rings) Pyrimidine (1 ring) Adenine A Thymine T Guanine G Cytosine C
The nucleotides are covalently linked together in a chain through the sugars and phosphates, which thus form a “back- bone” of alternating sugar–phosphate–sugar– phosphate. Because only the base differs in each of the four types of nucleotide subunit, each polynucleotide chain in DNA is analogous to a sugar-phosphate necklace (the backbone), from which hang the four types of beads (the bases A, C, G, and T).
The way in which the nucleotides are linked together gives a DNA strand a chemical polarity. We can distinguish between a 3’ end (the hole) and the 5’ end (the knob), names derived from the orientation of the deoxyribose sugar.