Protein

Question 1

Biochemical roles of proteins

Answer 1

Catalysts, signaling molecules, transporters, receptors, and cell shape/provide structural support

Question 2

Are proteins true polymers ?

Answer 2

Yes: it’s a large biomolecule, has multiple monomers, and they’re interlinked

Question 3

How does hydrophobic effect affect protein folding

Answer 3

If in an aqueous environment, polar amino acids (hydrophilic) on exterior and nonpolar AA on interior. If in nonpolar environment, vice versa composition.

Question 4

Where do ligand proteins bind

Answer 4

Extracellular receptors (7TM or dimeric)

Question 5

There are L amino acids and D amino acids, which form is incorporated into proteins

Answer 5

L amino acids

Question 6

Why is chirality important

Answer 6

For receptor binding

Question 7

What type of covalent bond attaches AAs

Answer 7

Peptide bonds

Question 8

From which end is AA sequence written

Answer 8

The alpha amine group (N-terminus)

Question 9

Are polypeptides folded

Answer 9

No, not yet

Question 10

What type of bonds stabilize a primary structure

Answer 10

Uncharged peptide bonds

Question 11

Which configuration are primary structures in

Answer 11

Trans- minimizes steric clashes of R groups

Question 12

What bonds are secondary structures stabilized by

Answer 12

Hydrogen bonds

Question 13

Do peptide bonds between AAs rotate in secondary structures

Answer 13

No

Question 14

T/F, most alpha helixes have a left handed screw sense

Answer 14

False; majority right handed cuz fewer steric clashes

Question 15

Which AAs cannot be used in alpha helixes

Answer 15

Proline, glycine, aspartate and cysteine

Question 16

T/F, all AAs can be used in beta sheets

Answer 16

Yes though distribution will vary within them

Question 17

What bonds stabilize tertiary structures

Answer 17

Noncovalent interactions between R groups

Question 18

How many polypeptides makeup tertiary structures

Answer 18

1

Question 19

What forms quaternary structures

Answer 19

Multiple polypeptide chains

Question 20

What is a glycoprotein

Answer 20

CHO monomer attached covalently to exterior

Question 21

What is a proteolipid

Answer 21

Lipid monomer attached covalently to exterior

Question 22

What is the only structure retained in denatured proteins

Answer 22

Primary structure

Question 23

What does sequence specifies conformation refer to

Answer 23

Order of AAs in polypeptide chain determines protein 3D shape

Question 24

Which proteins do not follow the central principle

Answer 24

Intrinsically unstructured proteins and metamorphic proteins

Question 25

How do intrinsically unstructured proteins assume a structure

Answer 25

From interactions w other molecules

Question 26

What is covalent catalysis

Answer 26

Active site contains a nucleophile that is briefly covalently modified

Question 27

What is general acid base catalysis

Answer 27

AAs with ionizable side chains act as general acids or bases

Question 28

What is metal ion catalysis

Answer 28

Ions serve as an electrophilic catalyst, generate a nucleophile, or bind to the substrate

Question 29

What is catalysis by approximation and orientation

Answer 29

Two substrates brought closely together to facilitate reaction

Question 30

Are cofactors permanently modified by enzymes

Answer 30

No

Question 31

What are metal ion cofactors called

Answer 31

Minerals

Question 32

What enzymes require metal ions

Answer 32

DNA polymerase, hexokinase, and adenylate cyclase

Question 33

Where are metal ions stored

Answer 33

Mainly in liver (Fe2+ and Cu2+) and bones (Ca2+ and P3+)

Question 34

Cofactors derived from vitamins are called…

Answer 34

Coenzymes

Question 35

T/F, enzymes assist chemical reactions by lowering delta G

Answer 35

False: by lowering EA

Question 36

What is the first law of thermodynamics

Answer 36

Energy cannot be created or destroyed

Question 37

What is the second law of thermodynamics

Answer 37

Entropy in the universe always increases

Question 38

What dictates if a reaction occurs

Answer 38

Gibbs free energy

Question 39

Does gibbs free energy provide information on reaction rate

Answer 39

No; just spontaneity of reaction

Question 40

Does a reaction proceed spontaneously if delta G is positive

Answer 40

No

Question 41

If Delta G =0 that means

Answer 41

Reaction is at equilibrium and forward reaction = reverse reaction

Question 42

What type of kinetics do most enzymes conform to

Answer 42

Michaelis-Menten kinetics

Question 43

T/F, Mich-Men enzymes catalyze irreversible reactions

Answer 43

False: readily reversible reactions

Question 44

T/F, MM enzymes have one active site

Answer 44

True

Question 45

Is Keq affected by enzymes

Answer 45

No

Question 46

Reactions proceed to equilibrium by going in what pathway direction

Answer 46

Higher -> lower

Question 47

If Keq is large, delta G is

Answer 47

Negative

Question 48

If Keq is small, delta G is

Answer 48

Positive

Question 49

T/F, Vmax AND KM are influenced by environmental conditions

Answer 49

True!

Question 50

KM in Mich-Ment model refers to…

Answer 50

Substrate affinity

Question 51

Does vmax depend on [E]

Answer 51

Yes

Question 52

T/F, KM depends on [E]

Answer 52

False

Question 53

T/F, the greater KM, greater affinity

Answer 53

False; the smaller greater affinity

Question 54

At 1/2 vmax, [S] is where

Answer 54

KM

Question 55

T/f, allosteric enzymes also have one active site

Answer 55

False, they have multiple

Question 56

How are MM enzyme activity governed

Answer 56

By mass action (if theres a substrate then enzyme reacts)

Question 57

How are allosteric enzyme activity governed

Answer 57

Environmental signals, more complex enzyme kinetics, quaternary structure

Question 58

What are effectors

Answer 58

Small molecules which bind and alter enzyme activity

Question 59

T/F, allosteric effectors bind to the enzymes active site

Answer 59

FALSE, they bind to a different distinct location

Question 60

Are most pharmaceutical drugs enzyme inhibitors or activators

Answer 60

Inhibitors

Question 61

How can competitive inhibitor binding be overcome

Answer 61

High concentrations of substrate

Question 62

Do inhibitors resemble substrate in uncompetitive inhibitor binding

Answer 62

Naur

Question 63

How do uncompetitive inhibitors prevent catalytic activity

Answer 63

By binding NEAR active sight and distorting it

Question 64

Where do noncompetitive inhibitors bind

Answer 64

Elsewhere on the enzyme to distort tertiary structure

Question 65

Type of Interaction in enzyme-complex …

Answer 65

Non covalent

Question 66

In digestion, what bonds get cleaved with water

Answer 66

Covalent bonds

Question 67

Does saliva contain protein specific digestive enzymes

Answer 67

Nope!

Question 68

What is the role of pepsin in the stomach

Answer 68

Cleaves proteins into fragments or oligopeptides (2-10 AA residues)

Question 69

Is pepsin a nonspecific or specific protease

Answer 69

Nonspecific because it cleaves randomly

Question 70

What do bile salts serve as

Answer 70

Protein-destabilizing agents by interfering w/ disulfide bonds

Question 71

Where are bile salts release from and who stimulates their release

Answer 71

Released from Gallbladder; stimulated by gastrin

Question 72

What does chymotrypsin do

Answer 72

Hydrolyzes oligopeptides

Question 73

Is chymotrypsin a specific or nonspecific protease

Answer 73

Specific; it cleaves by large hydrophobic AA residues

Question 74

What is the role of peptidases?

Answer 74

Cleaves remaining fragments which results in individual AAs, dipeptides and tripeptides

Question 75

T/F, AAs can be stored for later use

Answer 75

FALSEEEEE

Question 76

Which AAs can be directly deaminated

Answer 76

Glycine, Serine, and threonine

Question 77

What is the Urea cycle

Answer 77

Nitrogen metabolism pathway that converts toxic NH4+ into less toxic urea.

Question 78

Where does the urea cycle begin

Answer 78

Liver mitochondria

Question 79

What 7 keto acids are generated from 20 proteinogenic AAs

Answer 79

Pyruvate, a-ketoglutarate, fumarate, succinyl CoA, oxaloacetate, acetyl CoA and acetoacetyl CoA.

Question 80

What can keto acids be used for…

Answer 80

Synthesizing Nonessential AAs & lipid/CHO monomers

Question 81

Whats a major source of Nitrogen

Answer 81

The atmosphere

Question 82

Why is N2 unusable to most bio organisms

Answer 82

Very strong and unreactive; takes 16 ATPs to break

Question 83

Where do humans obtain most of their nitrogen

Answer 83

From their diet

Question 84

What are the 7 standard proteinogenic AAs that have readily ionizable side chains

Answer 84

Aspartate, glutamate, histidine, cysteine, tyrosine, lysine and arginine

Question 85

Can different enzymes performing similar reactions use the same cofactor

Answer 85

Yeth!

Question 86

Transition states differ from intermediate because their free energy is….(lower/higher??)

Answer 86

Higher

Question 87

What is a prosthetic group

Answer 87

cofactor permanently attached to enzyme

Question 88

What type of effectors are there

Answer 88

Inhibitors and activators

Question 89

rapid dissociation of enzyme-inhibitor complex occurs in what type of inhibition, reversible or irreversible

Answer 89

Reversible