Lecture 3-4

Question 1

General amino acid formula

Answer 1

R group (amino acid side chain)
Carboxyl group (- charge)
Amino group (+ charge)
C (a-carbon atom)

Question 2

What happens to amino and carboxyl groups at pH 7?

Answer 2

They get ionized

Question 3

Optical isomers

Answer 3

Optical isomers occur because the a-carbon is asymmetric, which creates 2 mirror images (stereoisomers L and D)

Question 4

What is the optical isomers of proteins?

Answer 4

L-isomer

Question 5

Peptide bond

Answer 5

amide linkage that joins 2 amino acids (C-N bond)

Question 6

Why is there no rotation around the C-N bond?

Answer 6

peptide bonds form a rigid planar unit

Question 7

How can amino acids be more flexible?

Answer 7

single bonds allow rotation

Question 8

How are amino acid side chain properties grouped?

Answer 8

size, charge, polarity

Question 9

Protein shape is determined by?

Answer 9

amino acid sequence

Question 10

amino acid sequence referred to as?

Answer 10

primary structure

Question 11

Name 3 noncovalent bonds that help proteins fold?

Answer 11

Electrostatic attractions, van der Waals attraction, hydrogen bonds

Question 12

Common folding patterns of proteins

Answer 12

a helix b sheet

Question 13

Secondary structure

Answer 13

regular local structure of protein backbone stabilized by intramolecular bonding

Question 14

B-sheets can occur in what configurations?

Answer 14

Antiparallel vs parallel

Question 15

alpha helices can form what superstructure?

Answer 15

coiled coil

Question 16

Coiled-coil

Answer 16

In the helix, there are amino acids from a-g. The amino acids in a and d are often nonpolar. Proline breaks the helix.

Question 17

How does coiled-coil superstructure minimize exposure of hydrophobic amino acid side chains to aqueous environment?

Answer 17

alpha helices wrap around each other. Specifically, the hydrophobic amino acids in the a and d position of the alpha helices are wrapping around each other

Question 18

What is the structure of the Scr kinase?

Answer 18

SH2 and SH3 domains, ATP

Question 19

tertiary structure

Answer 19

full 3D organization of polypetide chain

Question 20

What stabilizes extracellular proteins?

Answer 20

covalent cross-linkage (disulfide bonds SH)

Question 21

What do intrinsically disordered regions often contain?

Answer 21

few hydrophobic amino acids and are relatively highly charged

Question 22

What are some functions of intrinsically disordered regions?

Answer 22

1) binding
2) signaling
3) tethering
4) diffusion barrier

Question 23

What determines protein chemistry?

Answer 23

Surface Conformation

Question 24

What are the 2 mechanisms to increase reactivity of active site?

Answer 24

Keep water out or cluster functional residues together

Question 25

What are 3 ways that proteins can bind to other proteins?

Answer 25

1) Surface-string 2) helix-helix 3) surface-surface

Question 26

equilibrium constant

Answer 26

measures binding strength (dissociation)

Question 27

How do enzymes speed up reactions?

Answer 27

By selectively stabilizing transition states

Question 28

Transition rate

Answer 28

Transition rate determines the activation energy, and is the most unstable intermediate in catalysis reactions.

Question 29

Why do enzymes selectively stabilize transition states during catalysis?

Answer 29

When they are stable, enzymes have a higher affinity for transition states than substrates

Question 30

Enzymes use acid and base catalysis simultaneously example

Answer 30

A) no catalysis

Question 31

Enzyme mechanisms

Answer 31

1) precise substrate orientation 2) distortions of electron clouds 3) forcing substrate into transition state

Question 32

Coenzymes are?

Answer 32

tightly bound small non-amino acid molecules that are often: 1) metal ions 2) small organic molecules 3) both in one molecule ex retinal heme

Question 33

Since enzymes are effective, many reactions in the cell are ____?

Answer 33

diffusion limited

Question 34

3 Cellular mechanism for increasing metabolism?

Answer 34

1) use membranes to compartmentalize 2) enzymes are localized into the cell and group with enzymes that share the same pathway 3) form multi enzyme complex

Question 35

Multi enzyme complexes increase?

Answer 35

metabolism rate

Question 36

multi-enzyme complexes increase?

Answer 36

metabolism rate (fatty acid synthase)

Question 37

Explain how fatty acid synthase works?

Answer 37

It has 5 enzyme domains, and the acyl carrier domain passes it off to each enzyme domain

Question 38

Pathway nodes?

Answer 38

Enzymes compete for the same substrate

Question 39

Enzyme regulation is achieved by?

Answer 39

1) expression regulation 2) regulation of subcellular distribution 3) PTM 4) enzyme degradation 5) small molecule binding

Question 40

Feedback regulation

Answer 40

allostery, sometimes competition

Question 41

Feedback inhibition

Answer 41

?

Question 42

Example of feedback activation?

Answer 42

ADP activates enzymes for sugar catabolism

Question 43

Allosteric enzymes have how many binding sites?

Answer 43

Allosteric enzymes have two or more interacting binding sites

Question 44

symmetric protein assemblies produce?

Answer 44

cooperative allosteric transitions (ligand stabilizes the protein conformation it binds to)

Question 45

phosphorylation can affect?

Answer 45

1) protein conformation 2) allow protein binding 3) mask binding site on protein

Question 46

Which amino acid side chains can be phosphorylated?

Answer 46

Serine (S), Threonine (T), Tyrosine (Y)

Question 47

PTMS and allosteric shape changes enable protein to function as?

Answer 47

microprocessor, assembly factor/scaffold/mechanic motor/ ion pump

Question 48

Protein that functions like a microprocessor

Answer 48

Src protein

Question 49

Src kinase mechanism

Answer 49

1) phosphate removal loosens structure 2) activating ligand binds to SH3 domain 3) kinase can now phosphorylate tyrosine to self-activate

Question 50

molecular input-output device of Src kinase (micropressor)

Answer 50

inputs= has this phosphate been removed, has this binding been disrupted? has this phosphate been added If yes to all three Src-type protein kinase activity turns on

Question 51

Proteins can be regulated by?

Answer 51

covalent addition of other proteins: Ubiquitin, SUMO (small ubiquitin-related modifier)

Question 52

Covalent modification of proteins can direct proteins to?

Answer 52

Covalent modifications can direct proteins to specific cell sites