Amino Acids and Enzymes Flashcards
Amino Acids
Building blocks of proteins
Contain side groups with varying physical and chemical properties
Multitude of functions of protein formed by the different properties amino acids have due to their side groups
Polypeptide
Chain of amino acids linked together by peptide bonds; a protein
Primary, Secondary, Tertiary and sometimes Quaternary structure
Amide
Amine connected to a carbonyl Carbon
Amine formed by peptide bonds between two amino acids
Hydrolysis of a Peptide Bond
Peptide reacts with water (and usually an enzyme) to form two separate amino acid chains
Separates the peptide bond on a peptide
Reverse reaction is dehydration reaction of amino acid chains
What are some factors in causing the partial double bond character of the peptide bond?
- Nitrogen is most stable with four bonds
- Oxygen attracts electron density (partial negative charge of O in carboxylic acid on amino acid)
These two factors mean that electrons delocalize to give the peptide bond a partial double bond character (more rigid bond which does not rotate freely)
What are alpha amino acids?
20 amino acids in which most proteins in all species are made from
Amine is attached to the carbon in the alpha position to the carbonyl
Essential amino acids
Amino acids that cannot be manufactured and must be ingested directly
For humans 9/20 amino acids are essential
Side Chain of Amino Acid
AKA R group, attached to alpha Carbon
R group makes amino acid distinct
Divided into four categories based on distinct chemical properties: (1) acidic, (2) basic, (3) polar, and (4) nonpolar
What is Sickle Cell Disease caused by?
An acidic glutamate is replaced with a nonpolar valine
- Changes structure of hemoglobin chain and causes it to polymerize, bending the cell into a sickle shape under low oxygen conditions
Chirality of amino acids
Alpha carbon of alpha amino acids has four chemically distinct groups attached to it except in the case of Glycine, whose R group is a H
Therefore, 19/20 of alpha amino acids are chiral at alpha C
Nonpolar Amino acids
Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Phenylalanine (Phe, F), Tryptophan (Trp, W), Methionine (Met, M), Proline (Pro, P)
Polar Amino Acids
Serine (Ser, S), Threonine (Thr, T), Cystein (Cys, C), Asparagine (Asn, N), Tyrosine (Tyr, Y), Glutamine (Gln, Q)
Acidic Amino Acids
Aspartic acid (Asp, D), Glutamic acid (Glu, E)
Basic Amino Acids
Histidine (His, H), Lysine (Lys, K), Arginine (Arg, R)
Primary structure of protein
Number and sequence of amino acids in a polypeptide
Secondary structure of protein
Single chain of protein forms into distinct shapes such as twisting into an alpha helix or lying along itself in a beta-pleated sheet
Beta-pleated sheet segments can lie in parallel or antiparallel directions
Secondary structure reinforced by H-bonds between carbonyl O of AA and Hydrogen on N group of another
Tertiary structure of protein
Large proteins with three-dimensional shape formed by curls and folds of peptide chain
Five forces of Tertiary structure
Five forces:
- Covalent disulfide bonds btwn 2 cysteine AAs
- Electrostatic interactions between acidic and basic chains
- H-bond
- Van der Waals forces
- Hydrophobic/nonpolar side chains aggregating away from water
How does proline shape protein structure
Proline has a more rigid structure due to it’s side group bonding with the amine, causing kinks in alpha or beta sheets (turns)
Quaternary structure of a protein
Very large proteins have quaternary structure when two or more polypeptide chains bind together
Solvation Layer
Organized structures that force hydrophobic groups towards center of proteins and hydrophilic groups towards outside
Hydrophobic groups organizing towards the center allows decrease in size of highly ordered solvation layer, increasing entropy of the system
Denatured Protein
Native conformation of a protein is disrupted, causing a loss of functionality
Caused by a denaturing agent, sometimes removal of the agent will cause spontaneous reformation of the protein’s native conformation
Denaturing Agents
Urea disrupts H-bonds
Salt or change in pH disrupts Electrostatic bonds
Mercaptoethanol disrupts Disulfide bonds
Organic solvents disrupt Hydrophobic forces
Heat disrupts All forces
Two types of proteins
Globular: function as enzymes (e.g. pepsin), hormones (e.g. insulin), membrane pumps and channels (e.g. Na+/K+ pump), membrane receptors, intercellular and intracellular transport and storage, osmotic regulators, immune reponse
Structural: Made from long polymers, maintain and add strength to cellular and matrix structure
Structural Protein Example
Collagen: Structural protein made from unique type of helix
Most abundant protein in the body
Add great strength to the skin, tendons, ligaments, and bone
What’s an example of a Globular protein that can be a structural protein under certain conditions?
Tubulin can make up eukaryotic flagella and cilia, because can polymerize under right conditions
Glycoproteins
Proteins with carbohydrates attached
E.g. AB antigens on red blood cells
Generally more than 50% protein
Proteoglycans
Major component of extracellular matrix
Generally more than 50% carbohydrates
Cytochrome
Proteins which require a prosthetic heme group in order to function
They usually add color to the cell
E.g. hemoglobin and cytochromes of ETC in inner membrane of mitochondria
Conjugated proteins
Proteins which require nonproteinaceous components to function
Minerals
Dissolved inorganic ions inside and outside the cell
Create electrochemical gradients across membranes- assist in transport of substances entering and exiting the cell
Solidify: hydroxyapatite in bone
Cofactors: assisting enzymes
Enzyme
Globular protein or nucleic acid that acts as a catalyst for a chemical reaction, in other words by lowering the activation energy, thus increasing the rate of the reaction
Increase reaction rate by 1000-1 trillion times initial rate
Regulatory role: Cause necessary chemical reactions to occur and prevent unnecessary ones
How does an enzyme effect quantity of products and reactants at equilibirum
Enzyme does not alter this quantity and does not change the Gibbs Free Energy change of a reaction
Substrate
Reactant(s) upon which an enzyme works. Generally smaller than the enzyme
Substrate binds to enzyme at active site, forming enzyme-substrate complex
Enzyme specificity
Enzymes are designed to work on a specific group of substrate or substrates
Lock-and-key model: example of substrate locking into active site on enzyme and enzyme active site only fits specific substrate
Induced Fit Model
Model of enzyme-substrate complex in which after binding of the substrate, the enzyme and the substrate change shape to tighten the bond and increase the specificity. This can destabilize the substrate and allow reaction to proceed faster.
Saturation Kinetics
As concentration of substrate increases, relative rate of reaction increases until maximal rate (V_max) is reached
Substrates must eventually wait in line for a free enzyme to be ready to convert the substrate to the product
V_max is proportional to enzyme concentration
Turnover Number (k_cat)
Number of substrates that can be converted to products in a given unit of time given the concentration of substrate is saturated
Rough measure of catalytic efficiency of an enzyme
K_cat = V_max / [E]_t where [E] is conc of enzyme at time t
Michaelis Constant (K_m)
Substrate concentration in which rate of reaction is equal to 1/2 V_max
Indicates how highly concentrated the substrate must be to speed up the reaction
Inversely proportional to enzyme-substrate affinity
Is not affected by enzyme concentration
Michaelis-Menten curves
Plot reaction velocity as a function of substrate concentration
Show enzyme’s V_max and K_m
Explain Glucokinase and hexokinase in terms of K_m and glucose concentrations
Glucokinase and hexokinase phosphorylate glucose, converting it to glucose-6-phosphate, however Glucokinase has a higher K_m and requires higher concentrations of glucose to start working. Glucokinase is in the liver and only responds once glucose is very high to convert glucose to glycogen and fatty acids, while other cells can phosphorylate glucose at lower conc.
What is the effect of temperature and pH on reaction rate of an enzyme?
As temperature and pH increase, enzyme reaction rate increases until denaturing begins and then the rate drops off
Cofactor
Many enzymes require a non-protein cofactor to reach optimal activity
Coenzymes or Metal Ions
Coenzymes
Organic molecules that are cofactors
- Need to be present in excess quantities to catalyze reaction
- Water-soluble vitamins
Two types: Cosubstrates and Prosthetic groups
Cosubstrates
A Coenzyme that reversibly binds to a specific enzyme, and transfers some chemical group to another substrate
- reverts to original form via another enzymatic reaction
- ATP is an example
Prosthetic Groups
Remain covalently bound to enzyme throughout the reaction
- emerge from reaction unchanged
- e.g. heme which binds with catalase in peroxisomes to degrade hydrogen peroxide
Metal Ions
Second type of cofactor; inorganic small molecules required for some enzyme activities
- Can act alone or with a prosthetic group
- present in stoichiometric amounts, not consumed in the processes
- e.g. iron, copper, manganese, magnesium, calcium, zinc
What is an enzyme without its cofactor called?
Apoenzyme
What is an enzyme with its cofactor called?
Holoenzyme
