Proteins 1 Flashcards
<p>What are the major steps of protein synthesis?</p>
<p>DNA to RNA (transcription)</p>
<p>RNA to protein (translation)</p>
<p>What is transcription?</p>
<p>The first step of gene expression where a particular section of DNA is copied onto RNA</p>
<p>What is translation?</p>
<p>The process where ribosomes synthesis proteins</p>
What does a diagram of DNA look like?
<p>What kind of bonds link the two bases of two DNA backbones?</p>
<p>Hydrogen bonds</p>
<p>What is the backbone of DNA called?</p>
<p>Deoxyribose-phosphate backbone</p>
<p>What are the four bases present in DNA?</p>
<p>Adenine (A)</p>
<p>Cytosine (C)</p>
<p>Thysine (T)</p>
<p>Guanine (G)</p>
<p>What is the base pairing of DNA?</p>
<p>Adenine pairs with thymine</p>
<p>Cytosine pairs with guanine</p>
<p>What is the double helix?</p>
<p>The double stranded molecule that DNA exists as</p>
What does the general structure of an amino acid look like?
<p>What are the sections of an amino acid?</p>
<p>Amino group</p>
<p>Side chain</p>
<p>Carboylic acid group</p>
<p>Does each amino acid have a unique side chain?</p>
<p>Yes</p>
<p>What is physiological pH?</p>
<p>7.4</p>
<p>What happens to an amino acid at physiological pH?</p>
<p>The carboxyl group dissosiates forming a negatively charged carboxylate ion (-COO^-) and the amino group is protonated (-NH3^-)</p>
<p>What does dissociate mean?</p>
<p>Molecule splits</p>
<p>What does protonated mean?</p>
<p>Transfer a proton to a molecule</p>
<p>What does the dissociation of amino acids at physiological pH allow them to do?</p>
<p>Amino acids join together with a peptide bond with the loss of 1 molecule of water</p>
What does the reaction of two amino acids joining together look like?
<p>Where does translation occur?</p>
<p>In the ribosome</p>
<p>What determines the properties of an amino acid/protein?</p>
<p>The side chain</p>
<p>What are different side chain properties</p>
<p>Aliphatic (organic compounds where carbon atoms form open rings, not aromatic rings)</p>
<p>Aromatic</p>
<p>Sulphur containing</p>
<p>Basic</p>
<p>Acidic</p>
<p>Uncharged polar</p>
<p>Other (such as proline)</p>
<p>What do non polar side chains not do?</p>
<p>Bind or give of protons</p>
<p>Participate in hydrogen or ionic bonds</p>
<p>Non polar side chains can be thought of as being hydrophobic, what interactions do they promote?</p>
<p>In aqueous solution (polar environment) they cluster in the interior to give 3D structure</p>
<p>In hydrophobic environments they are on the outside interacting with the lipid environment</p>
<p>What does hydrophobic mean?</p>
<p>Repels water, tends to have no charge</p>
<p>What does hydrophilic mean?</p>
<p>Attracted to water, dissolves in water</p>
<p>What are the properties of uncharged polar chains?</p>
<p>Have a net charge of 0</p>
<p>Contain partial charges that can form bonds</p>
<p>What are the properties of sulphur containing side chains?</p>
<p>Contains a sulfhydroxyl group (-SH) which is often important in the active site of enzymes</p>
<p>What are the properties of acidic side chains?</p>
<p>Side chains are fully ionised, containing a negatively charged carboxylate group (-COO-)</p>
<p>Negatively charged at physiological pH</p>
<p>Are orignially proton donors (before they are ionised)</p>
What does an amino acid with an acidic side chain look like?
<p>What are the properties of basic side chains?</p>
<p>Originally accept protons (before ionised)</p>
<p>Positively charged at physiological pH</p>
<p>Are fully ionised, containing a positively charged amino group (-NH3+)</p>
<p>How many kinds of amino acids are coded by DNA?</p>
<p>20</p>
<p>What are the four protein structures?</p>
<p>Primary</p>
<p>Secondary</p>
<p>Tertiary</p>
<p>Quarternary</p>
<p>What is the primary structure of a protein?</p>
<p>The sequence of amino acids in a polypeptide chain</p>
<p>What is the primary structure the source of?</p>
<p>Versitility and function due to there being 20 different occupants for each position an an enormous range of sequences</p>
<p>What is the secondary structure of a protein?</p>
<p>The spatial arrangement of amino acid residues that are near each other in the linear sequence</p>
<p>What are the three forms of secondary structures?</p>
<p>Alpha helix</p>
<p>Beta sheet</p>
<p>Beta bends</p>
<p>What is the alpha helix structure?</p>
<p>A coiled structure held in place by hydrogen bonds between every N-H group and the O of the C=O group in the next turn of the helix</p>
<p>What is the beta sheet structure?</p>
<p>Composed of two or more peptide chains which are almost fully extended, the hydrogen bond is perpendicular to the polypeptide backbone</p>
<p>What is the tertiary structure of a protein?</p>
<p>Spatial arrangment of amino acid recidues that are far apart in a linear sequence</p>
<p>What forces hold the tertiary structure in place?</p>
<p>van der Waals</p>
<p>Ionic interactions</p>
<p>Hydrogen bonds</p>
<p>Disulphide bridges</p>
<p>Hydrophobic interactions</p>
<p>What are van der Waals?</p>
<p>Non specific weak attraction between atoms 0.3-0.4nm apart</p>
<p>They are individually weak but collectively strong</p>
<p>What are ionic interactions?</p>
<p>Occurs between two oppositely charged side chains</p>
<p>These are strong</p>
<p>What are hydrogen bonds?</p>
<p>Occur when H is bonded to O, N or F and lone pair of electrons are present</p>
<p>Similar to van der Waal but are stronger and more permanent</p>
<p>They are 1/20 the strenth of covalent bonds</p>
<p>What are examples of molecules that form hydrogen bonds?</p>
<p>Water and ammonia</p>
<p>What is a disulphide bridge?</p>
<p>Strong covalent bond between two cysteine residues</p>
<p>Can occur within and between a polypeptide</p>
<p>What are hydrophobic interactions?</p>
<p>Intra-polypeptide interactions occuring in an environment with proteins which water is excluded</p>
<p>Where are hydrophilic and hydrophobic side chains found within a protein?</p>
<p>Hydrophillic side chains are found on the outside interacting with the environment (making the molecule soluble)</p>
<p>Hydrophobic side chains are found on the inside interacting with each other (giving 3D structure)</p>
<p>What is the quarternary structure of a protein?</p>
<p>Spatial arrangement of individual polypeptide chains in a multi sub unit protein</p>
<p>How are the subunits in the quarternary structure held together?</p>
<p>Non covalent interactions, they may function independently or in collaboration</p>
<p>What is denaturing?</p>
<p>Disruption and possible loss of both the secondary and tertiary structures</p>
<p>Leads to the loss of 3D structure and function</p>
<p>Are denaturing reactions enough to break the peptide bonds of the primary structure?</p>
<p>No</p>
<p>What is renaturation</p>
<p>Gaining of a proteins 3D shape and function after denaturation</p>
<p>It is rarely possible as the effects of denaturation are often permanent</p>
<p>What are some causes of denaturation?</p>
<p>Acids</p>
<p>Heat</p>
<p>Solvents (ethanol, methanol)</p>
<p>Cross linking reagents (formaldehydes)</p>
<p>Chaotropic agent (urea)</p>
<p>Disulphide bond reducers</p>
<p>What are some effects of denaturation?</p>
<p>Decreased solubility</p>
<p>Altered water binding capacity</p>
<p>Loss of biological activity</p>
<p>Improved digestability</p>
<p>What is protein digestion?</p>
<p>Cleavage of the peptide bonds within the primary structure</p>
<p>What are types of protein digestions?</p>
<p>Peptidases (cleavage of peptide bonds)</p>
<p>Endopeptidases (cleave of internal bonds)</p>
<p>Exopeptidases (cleavage of one amino acid at a time)</p>
<p>Carboxypeptidases (cleaves at the -COOH terminal)</p>
<p>Aminopeptidases (cleavage at the -NH2terminal)</p>
<p>What is protein structure dependent on?</p>
<p>DNA sequence coding for amino acids</p>
<p>Interactions of amino acids</p>
<p></p>
<p>structure determines function</p>
<p>What happens when proteins are denatured?</p>
<p>Structure and function are lost</p>
