Lecture 1 - AA & Proteins

Question 1

Acidic amino acid mnemonic

Answer 1

Erectile Dysfunction is a NEGATIVE thing to have

E = Glutamic Acid
D = Aspartic Acid

Question 2

Basic amino acid mnemonic

Answer 2

RHK

R = Arginine
H = Histidine
K = Lysine

Question 3

Neutral polar amino acid mnemonic

Answer 3

Polar bears are STNQY

S = Serine
T = Threonine
N = Asparagine
Q = Glutamine
Y = Tyrosine

Question 4

Nonpolar amino acid mnemonic

Answer 4

LIMPVAG For Winner Cock

L = Leucine
I = Isoleucine
M = Methionine
P = Proline
V = Valine
A = Alanine
G = Glycine

F = Phenylalanine

W = Tryptophan

C = Cysteine

Question 5

Most commonly phosphorylated amino acids mnemonic

Answer 5

Suck Your Toes

S = Serine
Y = Tyrosine
T = Threonine

Question 6

Peptide Bond Structure and Chemical Features

Answer 6

Structure:
- Rigid
- Planar
- Little freedom of movement

Chemical Features:
- Covalent bond b/t nitrogen of one amino acid and carboxylic acid of adjacent amino acid
- Resonance (causes little freedom of movement)

Question 7

Covalent forces that stabilize protein structure + function

Answer 7

Structure:
- Covalent peptide bond b/t nitrogen of one amino acid and carboxylic acid of adjacent amino acid

• Disulfide bonds b/t cysteine R group sulfurs

Function:
Enzymes change covalent bonds

Question 8

Noncovalent forces that stabilize protein structure + function

Answer 8

Structure:
- Hydrogen bonds (b/t neutral groups or b/t peptide bonds)
- Ionic interactions (attraction or repulsion depending on charges)
- Hydrophobic interactions (behavior in aqueous solvent like water)
- van der Waals interactions (any two atoms in close proximity)

Function:
- Protein folding
- Membranes
- Transport
- Substrate binding

Question 9

Polarity of polypeptides meaning? Direction of protein synthesis?

Answer 9

Proteins are read and synthesized from amino N to carboxyl C terminus

Question 10

The four levels of protein structure and examples of each covered in class

Answer 10

Primary: Amino acid sequence

Secondary: interactions b/t atoms of the backbone (alpha-helix, beta-pleated sheet)

Tertiary: 3D structure resulting from interactions b/t R groups of the amino acids that make up the protein

Quaternary: Interaction between 2 or more proteins (subunits)

Question 11

Alpha-helix general structure

Answer 11

• Tightly coiled
• Rod-like arrangement of amino acids
• “Backbone” consists of repeating units of amino group N-C
• R groups radiate OUTWARD
• All/most are “right handed” b/c energetically favored (less steric hindrance)

Question 12

How are alpha-helices stabilized? What is the “n+4” rule? Which amino acids sit on opposite sides of the helix?

Answer 12

Stabilized by extensive H bonding between the NH and CO groups

“n+4” rule -> 3.6 AA per turn: AA 3-4 residues apart in the linear sequence are spatially close to one another

AA two apart sit on opposite sides of the helix

Question 13

Alpha-helical supermolecular structures

Answer 13

• 2 or more a-helices can intertwine => “coiled coils”
• Found in keratin (hair), myosin (muscle), and fibrin (blood clots)

a-helix -> two-chained coiled coil -> protofilament -> protofibril

Question 14

Helix content varies significantly from protein to protein - hemoglobin vs chymotrypsin a-helix content?

Answer 14

Hemoglobin is high is a-helix content
Chymotrypsin lacks a-helix

Question 15

Beta-pleated sheet general structure

Answer 15

• Extended polypeptide chains
• Adjacent chains can run “parallel” (same direction), “antiparallel” (opposite direction), or “mixed” (strands running parallel and antiparallel)

Question 16

How are beta-pleated sheets formed?

Answer 16

Hydrogen bonding between NH and CO groups of same/different chains

Question 17

Definition & importance of protein domains. Discuss related proteins

Answer 17

Protein domain: functional structures formed from folded proteins (ex: catalytic function), typically in 3D/tertiary structure

Families of related proteins share conformational features such as similar domains and sequences (but may differ in substrate specificity), which implies similar/identical functions

Question 18

What are homeodomains?

Answer 18

DNA-binding domains, conserved b/t species separated by a billion years of evolution

Question 19

Some of the features governing protein-protein interactions (disulfide bonding, sheets/tubes, binding strength/specificity, proximity of AA binding, antibodies)

Answer 19

• Interchain disulfide bonding is more common than intrachain disulfide bonding (b/t cysteines) n/c extracellular environment is oxidizing
• Some protein subunits can form sheets or tubes through multiple points of contact w/ other subunits (ex: viral capsids)
• Interactions b/t two proteins or another molecule type and a protein involve specific non-covalent interactions that determine the specificity and strength of binding
• AA involved in binding are often far from one another in unfolded protein, but close together in folded state
• Modular approach of antibodies: when antibodies are generated, they assemble different genes together => different constant and variable region genes => light chains + heavy chains that provide specificity

Question 20

What does the structure of a protein depend on during protein assemblies?

Answer 20

The exact structure depends on orientation of binding sites on each subunit (ex: different binding sites could assemble dimers, helices, or rings)

Question 21

Another name for assemblies?

Answer 21

Polymer

Question 22

Some polymeric structures exhibit polarity (not electrical)? If true, give example?

Answer 22

True

Ex: actin microfilaments have a plus and minus end

Question 23

What type of structure is collagen?

Answer 23

Rigid

Question 24

What type of structure is elastin?

Answer 24

Elastic

Question 25

What are covalent modifications of proteins? Most common example?

Answer 25

The covalent attachment of a molecule(s) to proteins that can modify its function Ex: phosphorylation -> attaching phosphate group covalently to a protein -> activate or deactivate

Question 26

Kinetic properties of enzymes

Answer 26

- Increase rate of biological reaction w/o altering reaction equilibria - Decrease activation energy of a reaction - Accelerate reactions through stabilization of transition states i.e. lower activation energy (Ea) - The enzyme active site

Question 27

All chemical reactions can be described in terms of _________.

Answer 27

Equilibrium

Question 28

What is equilibrium in the context of enzymes and reactions?

Answer 28

The degree to which a reaction will proceed forward to yield a product or backwards to the starting point

Question 29

What are reaction equilibria linked to? What are reaction rates linked to?

Answer 29

Reaction equilibria are linked to the standard free energy change (ΔG'o) - Energy states of reactants and products remain unchanged in uncatalyzed vs enzyme-catalyzed reactions Reaction rates are linked to the activation energy, Ea -Enzymes increase reaction rate by decreasing Ea *refer to slide 68 lecture 1

Question 30

What is the relationship between K'eq and ΔG'o?

Answer 30

Inverse -> As K'eq increases, ΔG'o decreases

Question 31

Endergonic vs Exergonic reaction: ΔG and reaction progression plots

Answer 31

Endergonic: + ΔG, substrate energy < product energy Exergonic: -ΔG, substrate energy > product energy

Question 32

Is it better to have an enzyme complementary to substrate or an enzyme complementary to transition state? Explain

Answer 32

It is better to have an enzyme complementary to transition state. Otherwise, the enzyme-substrate complex would be more stable (has less free energy versus substrate alone), which results in an increased activation energy *refer to slide 70 lecture 1

Question 33

Features of the enzyme active/catalytic site?

Answer 33

- The catalytic site is relatively small and recessed compared with the rest of the enzyme to increase substrate specificity - Enzyme may also be big because of regulation and the presence of regulatory sites (allosteric effects, covalent modification, etc.) - The catalytic site is a three-dimensional entity - Substrates are bound to enzymes by multiple weak, non-covalent interactions (electrostatic bonds, hydrogen bonds, van der Waals forces, hydrophobic interactions)

Question 34

Catalytic sites form clefts or crevices - elaborate

Answer 34

- Substrate molecules bound within cleft - Water (unless involved in catalysis) is normally excluded - Overall nonpolar character of cleft can enhance binding of substrate - May also contain polar residues which may take on catalytic properties w/in this nonpolar environment (exception to the rule regarding hydrophobic "core" present in many globular proteins)

Question 35

Michaelis Menten saturation kinetics: what this means, what it says about how enzymes work

Answer 35

- At constant [enzyme], the rate of a reaction increases w/ increasing [S] until a Vmax is achieved => this saturation effect is an important distinction versus uncatalyzed reactions - Interpretation of enzyme kinetic curve: ES complexes formed until substrate saturation (Vmax) occurs at which point no more substrate binding sites (i.e. enzymes) are available

Question 36

What are factors affecting enzyme activity? What are we focused on?

Answer 36

Can have transcriptional, translational, posttranscriptional,, and posttranslational control Posttranslational Regulation: discussed in class - Allosteric Regulation - Covalent Modification - Proteolytic Modification

Question 37

What is allosteric regulation? Feedback inhibition?

Answer 37

Allosteric Regulation: When a positive/negative modulator binds to allosteric site of an enzyme, the enzyme conformationally change to become more/less active Feedback Inhibition: When a downstream product acts as a negative modulator, binds the allosteric site, making enzyme less active => way of regulating levels of synthesized endproduct

Question 38

What is covalent modification?

Answer 38

The covalent attachment of a molecule(s) to proteins that can modify its function Ex: phosphorylation -> attaching phosphate group covalently to a protein -> activate or deactivate

Question 39

What is proteolytic modification? Example?

Answer 39

The breakdown of proteins into smaller polypeptides or amino acids through the hydrolysis of peptide bonds by a protease => activating/deactivating Protease: enzyme that cleaves peptide bonds on other proteins Ex: Digestive enzymes