Biochemistry

Question 1

At physiological pH, what is the charge of the amino and carboxyl group of an amino acid?

Answer 1

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)

Question 2

Which amino acids have non polar side chains??

Answer 2

Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, proline, and tyrosine

Question 3

Which amino acids have polar side chains

Answer 3

Serine, threonine, cysteine, asparagine, glutamine

Question 4

What type of reaction is the formation of a peptide bond?

Answer 4

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)

Question 5

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?

Answer 5

Dehydration reaction

Question 6

Why are peptide/amide bonds said to have partial double bond character?

Answer 6

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)

Question 7

How are peptide bonds broken?

Answer 7

Peptide bond hydrolysis - broken by water molecules

Question 8

What level of protein structure is defined solely by the identity of the amino acids within it?

Answer 8

Primary structure

Question 9

What kind of bonding is characteristic of secondary protein structure, and between what components does it occur?

Answer 9

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)

Question 10

How do R groups contribute to the hydrogen bonding forming the alpha helix?

Answer 10

They do not

Question 11

What are interactions that arise between side chains of amino acids?

Answer 11

Concerns tertiary structure – ionic interactions, hydrophobic interactions

Question 12

When do post-translational modifications occur and what are some examples?

Answer 12

Occur after the protein has completely been translated from RNA. Phosphorylation, formation of disulfide bonds, ubiquitination, glycosylation

Question 13

Where in a protein would glycine be found and why?

Answer 13

Least sterically hindered amino acid - found in areas that require a high amount of flexibility and rotation

Question 14

What amino acid is involved in disulfide bond?

Answer 14

Cysteine

Question 15

How does proline contribute to protein structure and why?

Answer 15

Most sterically hindered – creates a kink – found in areas that need a bend or should be immobile

Question 16

What is the hydrophobic effect and how does it relate to entropy?

Answer 16

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

Question 17

What are some factors that can disrupt protein folding?

Answer 17

High/low pH, high salt concentration, high temperature

Question 18

What is the process by which proteins unfold/lose their correct 3D structure and how can this be mediated?

Answer 18

Called denaturation – chaperones can fold them back into their native state

Question 19

What structures serve as a scaffold for a) cell and b) tissue and what proteins are they composed of?

Answer 19

a) Cytoskeleton (actin, tubulin)
b) ECM (collagen, keratin, elastin)

Composed of five primary proteins: actin, keratin, elastin, collagen, and tubulin

Question 20

Where do actin monomers attach/detach to microfilments?

Answer 20

Attach at (+) end and detach at (-) end – Association and dissociation of actin molecules is regulated by ATP (cycle is known as tread milling)

Question 21

What enables myosin to generate its power stroke and generate force.

Answer 21

Dissociation of phosphate

Question 22

What structure is vital in mitosis and meiosis to ensure that chromosomes are separated?

Answer 22

Microtubules (recall that they have polarity which allows kinesins and dyenins to walk along microtubules).

Question 23

How to kinesins and dyenins move in the cell?

Answer 23

They are motor proteins - move by hydrolyzing ATP. Polarity allows them to travel in opposite directions. Kinesin - positive end. Dyenin - negative end.

Question 24

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?

Answer 24

Hormones

Question 25

What subunit of a GPCR is responsible for hydrolyzing GTP?

Answer 25

Alpha subunit

Question 26

Why are GPCRs referred to as 7-transmembrane receptors?

Answer 26

Span cell membrane with 7 different hydrophobic regions.

Question 27

What are some examples of peptide hormones and how do they exert their effects?

Answer 27

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)

Question 28

Where are peptide hormones particularly important (what axis)

Answer 28

HPG axis (Hypothalamic-pituitary-gonadal axis)

Hypothalamus (GnRH) –> Anterior pituitary (LH & FSH) –> Gonads (Testosterone, estrogen, progesterone)

Question 29

What is the difference between the two types of response systems within the immune system.

Answer 29

Innate immune system consists of nonspecific defenses against pathogens encountered by body.

Adaptive immune system provides more specific defenses against foreign bodies (antigens).

Question 30

How is the adaptive immune system able to provide specific defense against antigens/pathogens?

Answer 30

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.

Question 31

How do enzymes affect the kinetics but not the thermodynamics of a reaction?

Answer 31

Lower the activation energy of a reaction (speed it up) but do not affect delta G or equilibrium constant of a reaction.

Question 32

Why is it important that enzymes can be regenerated?

Answer 32

Reduces the amount of protein that a cell has to make in order to carry out biochemical reactions.

Question 33

Describe the difference between the lock and key model and induced fit model of E-S binding.

Answer 33

Lock and key - fit without any change in conformation

Induced fit - not rigid binding may undergo some conformational change to facilitate binding

Question 34

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

Answer 34

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

Question 35

Describe the difference between a holoenzyme and an apoenzyme

Answer 35

Holoenzyme — enzyme + cofactor/enzyme

Apoenzyme — enzyme without cofactor/enzyme

Question 36

What are prosthetic groups?

Answer 36

Cofactors/coenzymes tightly bound to an enzyme

Question 37

What is the difference between cofactors/coenzymes?

Answer 37

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+

Question 38

Is arginine or valine more likely to be catalytically important amino acid?

Answer 38

Arginine - polar (basic, positively charged) – more likely to be involved in reactions

Question 39

What is squalene a precursor for?

Answer 39

Fused four-ring system common to cholesterol & all steroid hormones