Biochemistry Flashcards
At physiological pH, what is the charge of the amino and carboxyl group of an amino acid?
Amino group is protonated (+) and carboxyl group is deprotonated (-)
At physiological pH amino acids are zwitterions (contain positive and negative charge on the same molecule)
Which amino acids have non polar side chains??
Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, proline, and tyrosine
Which amino acids have polar side chains
Serine, threonine, cysteine, asparagine, glutamine
What type of reaction is the formation of a peptide bond?
Peptide bond forms between two amino acids – type of a nucleophilic substitution reaction (carbonyl group of carboxylic acid acts as the electrophile and nitrogen of the amino group is the nucleophile)
Note that the carbonyl group of the carboxylic acid is an electrophile. The nucleophile is the nitrogen of the amino group. The nitrogen of the second amino acid has a free lone pair that can attack the carbonyl group, forming an N-C bond.
In the process, electrons from the second bond of the C=O are sent to the carbonyl oxygen. These electrons then reform a second bond, and the leaving group (-OH) leaves with a lone pair of electrons to form a molecule of water.
What kind of reaction is this?
Dehydration reaction
Why are peptide/amide bonds said to have partial double bond character?
Carbon of the amide bond is also double-bonded to oxygen atom. Nitrogen has a lone pair (partial double bond cannot freely rotate like a single bond)
How are peptide bonds broken?
Peptide bond hydrolysis - broken by water molecules
What level of protein structure is defined solely by the identity of the amino acids within it?
Primary structure
What kind of bonding is characteristic of secondary protein structure, and between what components does it occur?
Hydrogen bonding – between atoms forming the backbone of the protein chain NOT between side chains of each amino acid (H of N-H of one amino acid and carbonyl O of another amino acid)
How do R groups contribute to the hydrogen bonding forming the alpha helix?
They do not
What are interactions that arise between side chains of amino acids?
Concerns tertiary structure – ionic interactions, hydrophobic interactions
When do post-translational modifications occur and what are some examples?
Occur after the protein has completely been translated from RNA. Phosphorylation, formation of disulfide bonds, ubiquitination, glycosylation
Where in a protein would glycine be found and why?
Least sterically hindered amino acid - found in areas that require a high amount of flexibility and rotation
What amino acid is involved in disulfide bond?
Cysteine
How does proline contribute to protein structure and why?
Most sterically hindered – creates a kink – found in areas that need a bend or should be immobile
What is the hydrophobic effect and how does it relate to entropy?
Consequence of polar and non polar interactions – hydrophobic amino acids typically found within interior of a protein – surrounding water molecules therefore have more area to bind to surface of protein
What are some factors that can disrupt protein folding?
High/low pH, high salt concentration, high temperature
What is the process by which proteins unfold/lose their correct 3D structure and how can this be mediated?
Called denaturation – chaperones can fold them back into their native state
What structures serve as a scaffold for a) cell and b) tissue and what proteins are they composed of?
a) Cytoskeleton (actin, tubulin)
b) ECM (collagen, keratin, elastin)
Composed of five primary proteins: actin, keratin, elastin, collagen, and tubulin
Where do actin monomers attach/detach to microfilments?
Attach at (+) end and detach at (-) end – Association and dissociation of actin molecules is regulated by ATP (cycle is known as tread milling)
What enables myosin to generate its power stroke and generate force.
Dissociation of phosphate
What structure is vital in mitosis and meiosis to ensure that chromosomes are separated?
Microtubules (recall that they have polarity which allows kinesins and dyenins to walk along microtubules).
How to kinesins and dyenins move in the cell?
They are motor proteins - move by hydrolyzing ATP. Polarity allows them to travel in opposite directions. Kinesin - positive end. Dyenin - negative end.
In addition to nonenzymatic proteins providing structure within the cell and transmembrane proteins embedded in the cell membrane, there are also nonenzymatic proteins circulating in our blood. What are these called?
Hormones
What subunit of a GPCR is responsible for hydrolyzing GTP?
Alpha subunit
Why are GPCRs referred to as 7-transmembrane receptors?
Span cell membrane with 7 different hydrophobic regions.
What are some examples of peptide hormones and how do they exert their effects?
Oxytocin, insulin, FSH – Bind to receptors on the cell and cause conformational changes to the receptor. (Compare to steroid hormones which can directly pass through the cell)
Where are peptide hormones particularly important (what axis)
HPG axis (Hypothalamic-pituitary-gonadal axis)
Hypothalamus (GnRH) –> Anterior pituitary (LH & FSH) –> Gonads (Testosterone, estrogen, progesterone)
What is the difference between the two types of response systems within the immune system.
Innate immune system consists of nonspecific defenses against pathogens encountered by body.
Adaptive immune system provides more specific defenses against foreign bodies (antigens).
How is the adaptive immune system able to provide specific defense against antigens/pathogens?
Because of antibodies (aka immunoglobulins) - two heavy chains and two light chains - at the tip of the Y structure contain paratopes - enable foreign substances to be flagged as invasive – constant region (stem of the Y) recruits other antibodies/immune system cells to help destroy the antigen.
How do enzymes affect the kinetics but not the thermodynamics of a reaction?
Lower the activation energy of a reaction (speed it up) but do not affect delta G or equilibrium constant of a reaction.
Why is it important that enzymes can be regenerated?
Reduces the amount of protein that a cell has to make in order to carry out biochemical reactions.
Describe the difference between the lock and key model and induced fit model of E-S binding.
Lock and key - fit without any change in conformation
Induced fit - not rigid binding may undergo some conformational change to facilitate binding
List the kind of enzyme described by the examples below
An enzyme that converts a cis double bond into a trans double bond
An enzyme that seals the gap between two adjacent Okazaki fragments
A kinase that adds a phosphate group from ATP to a protein substrate
An enzyme that breaks a bond between two nucleotides without using water
An enzyme that breaks a bond between two nucleotides by adding water
An enzyme that transfers extra electrons from an NADH electron carrier to a protein substrate
Isomerase - Catalyzes an isomerization reaction (intramolecular rearrangement of bonds in a molecule)
Ligase - Catalyzes the joining of two molecules
Transferase - Catalyzes the transfer of a functional group from one molecule to another molecule
Lyase - Catalyzes the breaking of a molecule without the use of water
Hydrolase - Catalyzes the breaking of a molecule by adding water
Oxidoreductase - Catalyzes the transfer of electrons between molecules
Describe the difference between a holoenzyme and an apoenzyme
Holoenzyme — enzyme + cofactor/enzyme
Apoenzyme — enzyme without cofactor/enzyme
What are prosthetic groups?
Cofactors/coenzymes tightly bound to an enzyme
What is the difference between cofactors/coenzymes?
Both bind to enzyme’s active site and assist in catalyzing a reaction. Coenzymes are proteins whereas cofactors can be ions e.g. Mg 2+
Is arginine or valine more likely to be catalytically important amino acid?
Arginine - polar (basic, positively charged) – more likely to be involved in reactions
What is squalene a precursor for?
Fused four-ring system common to cholesterol & all steroid hormones
