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proteins
biol 1210
| Question | Answer |
|---|---|
| 4 classes of biological molecules | carbohydrates, lipids, proteins, nucleic acids |
| term for monomers & polymers of proteins | amino acids; polypeptides |
| amino acid structure - draw an amino acid | organic molecules w carboxyl & amino groups, differ in their properties due to differing side chains (R groups). See drawing in notes |
| 4 types of amino acids & their differences | based on the properties of their side chains. Nonpolar, uncharged polar, charged - acidic & basic. (-) charge in side chain = acidic; (+) charge in side chain = basic; uncharged with O atom = uncharged polar; uncharged & no O atom in side chain = nonpolar |
| ionization of amino acid in water | amino & carboxyl groups ionize to NH3+ & COO-. These charges help the amino acids stay dissolved in solution & make them more reactive |
| peptide bond | the resulting C-N bond formed between a carboxyl group of one amino acid and the amino group of another amino acid. Forms amino acids into polymers. Has characteristics of a double bond due to electron sharing - inflexible |
| describe N-terminus v. C-terminus end of amino acid chain | N-terminus refers to the open amino group and C-terminus refers to the open carboxyl group, it is where the dehydration synthesis takes place & amino acids are added to a chain |
| describe oligopeptide, polypeptide, protein, peptide, dipeptide & tripeptide | dipeptide - 2 amino acids; tripeptide - 3 AAs; peptide - 4+ AAs; oligopeptide - <50 AAs; polypeptide - >50 AAs; protein refers to any amino acid chain in its complete, functional form, and each is unique, linear sequence of AAs |
| briefly describe protein structure & the tiers | proteins have unparalleled diversity of size, shape & chemical properties, and their shape is entirely related to their function. Sequence of AAs determines a protein's 3D structure. Incl. primary, secondary, tertiary & quaternary structure |
| primary structure | the unique sequence of AAs in a protein. 2D from N-terminus to C-terminus. Determined from the mRNA template from DNA. Fundamental to higher levels of protein structure |
| backbone of protein | made of & H carboxyl on one side of the C-N bonds, the side chains stick out the other side |
| how can the change in a single amino acid affect the function of a protein? | amino acid's R-groups affect a polypeptide's properties, structure and function, so a single amino acid change (change in R group) can radically alter the protein's function |
| secondary structure | formed by hydrogen bonds btwn the carboxyl group of one amino acid & the amino group of another amino acid. This only occurs when a polypeptide bends so that C=O and N-H groups of the backbone are close together (no R chain interaction) |
| types of secondary structure | alpha-helix and beta-pleated sheet |
| tertiary structure | formed from interactions btwn R-groups or btwn R-groups and the peptide backbone. These contacts cause backbone to bend & fold, making distinctive 3D shape of polypeptide |
| 5 important types of R-group interactions | hydrogen bonds; hydrophobic interactions clustering away from water + Van der Waals interactions from proximity of polar molecules; covalent disulfide bonds btwn S on one R group & S on another; ionic bonds btwn acidic & basic R groups |
| quaternary structure | forms from 2+ polypeptide chains combine into one macromolecule (become subunits) |
| do all proteins have quaternary structure? | no, proteins can function with only 1 polypeptide chain (just tertiary structure) while some proteins require more than 1 polypeptide to function (ex. hemoglobin) |
| describe protein folding | each protein has characteristic folded shape necessary for its function |
| inactive v active proteins & structure | many proteins have disordered shape when they r inactive & when the active protein is needed, it folds into an ordered, active conformation. Some proteins are regulated by controlling when/where they r folded into active shapes |
| protein denaturation | occurs when protein unravels & loses its shape. The intermolecular bonds in quaternary, tertiary & secondary structures of proteins r broken & denatured protein is biologically inactive, but the peptide bonds are not broken (primary structure intact) |
| causes of protein denaturation | alterations in pH, salt concentration, temperature or other environmental factors (ex. toxins) |
| protein renaturation | some proteins can renature after denaturation once they are back in suitable environmental conditions |
| 8 functions of proteins | enzymatic proteins; storage of energy; defense - antibodies; transporters - carriers, pumps; hormonal - coordinate organism activity; receptor - respond to chemical stimuli; contractile/motor proteins - movement; structural support - keratin, collagen |
| why does shape (folding) of protein matter? give ex | ex. antibodies - have a specific shape to fit the antigen they search for (marker of pathogen) and need to maintain this shape in order to detect it (do their job) |
| catalyst | something that accelerates/speeds up a reaction |
| enzyme | protein that acts as a catalyst for its substrate (reactants). Each enzyme is specific to a particular chemical reaction & they r neither consumed nor changed by the chemical reaction |
| active site on enzyme | where substrates bind & react |
| describe how chemical reaction works | for a reaction to work, some or all chemical bonds in reactants must be broken so new bonds, btwn products, can form. To get bonds into state that allows them to break, molecule must be contorted into transition state |
| transition state | the unstable point during a reaction where there is the most amount of free energy and reactants' bonds r breaking. Reactants must have enough kinetic energy to reach it |
| activation energy | some amount of energy that must be added for a reactant to reach the transition state. When the activation energy is low, the reaction is faster |
| free energy in a reaction | the energy that is available to be used (to do work) in a reaction |
| enzymes & activation energy | enzymes r able to reduce the activation energy by stabilizing the transition state, hence increasing the rate of reaction. Most biological chemical reactions r only fast in presence of enzyme |
| does an enzyme the change in free energy btwn the reactants & products (deltaG)? | no, the same amount of energy is still needed to go from reactants -> products, just the rate is increasing by lowering the activation energy |
| enzyme shape | substrates bind to the active site via hydrogen bonding or interactions with amino acids residues |
| induced fit | a conformational change that occurs in many enzymes when the substrates are bound to the active site |
| describe enzyme sensitivity - 4 conditions that affect them | enzymes' structures are extremely picky to their function and may be affected by temperature, pH, interactions w other molecules, or modifications to an enzyme's primary structure |
| enzymes & temperature | each enzyme has an optimal temperature it functions at. As temp rises, reacting molecules have more & more kinetic energy -> increase in reaction rate. This peaks at optimal temp, then beyond peak point, enzyme denatures ->sudden decrease in reaction rate |
| enzymes & pH | each enzyme has optimal pH it functions at. In excess H+ (acidic) or OH- (basic), ionic & hydrogen bonding in tertiary enzyme structure r broken -> enzyme denaturation -> decrease in reaction rate. |
| describe decrease & increase in pH on enzyme's tertiary structure | increase in pH - more H+ ions that pull at the slightly (-) partners of hydrogen & ionic bonds. Decrease in pH - more OH- ions that pull at the slightly (+) partners of hydrogen & ionic bonds, disrupting them |
| enzyme activators | most enzymes r made of a protein (apoenzyme) + non-protein component (co-factor) that activates it by complementing final 3D structure of enzyme. |
| co-factor v. co-enzyme | co-factors may inorganic or organic substances. Organic co-factors r called co-enzymes ex. vitamins |
| competitive enzyme inhibitors | bind to active site of enzyme, competing w the substrate. Look structurally similar to an enzyme's substrate & its effect can be overcome by adding more substrate |
| non-competitive enzyme inhibitors | bind to another part of an enzyme (allosteric site) that causes the enzyme to change shape & make active site less effective/completely inactive. Do not look structurally similar to substrate & cannot be overcome by adding more substrate. |
| examples of enzyme inhibitors | heavy metals, toxins, poisons, pesticides, antibiotics |
| feedback inhibition in enzymes | when an enzyme pathway is inhibited by final product of the pathway - hence, end product of metabolic pathway shuts down the whole pathway |
| why would feedback inhibition be important in a cell? | to avoid over producing a product & spending resources unnecessarily/wasting reactants |
Created by:
AntBanana
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