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Biochemistry - 730A > Protein Structure and Function > Flashcards

Protein Structure and Function Flashcards

1
Q

the most abundant and functionally diverse molecules in living organisms

A

Proteins

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2
Q

what are proteins the polymer of?

A

Amino acids (monomers)

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3
Q

What is weird about Proline?

A

proline’s side chain actually forms a RIGID RING structure which doesn’t allow it to form alpha helices common in globular proteins - therefore it is commonly found in fibrous proteins.

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4
Q

What bonds connect amino acids to each other?

A

Peptide bonds

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5
Q

what properties make amino acids amphoteric?

A

in amino acids, the amino group can have a positive charge and the carboxyl group can have a negative charge. This allows amino acids to behave as an acid or base

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6
Q

what is a zwitterion?

A

zwitterions are neutral molecules that have an equal amount of positive and negative charges on them

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7
Q

what is the physiological pH of amino acids?

A

pH = 7.4

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8
Q

What are the 4 classes of amino acids?

A

Nonpolar, Uncharged Polar, Acidic, and Basic

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9
Q

What group of amino acids is associated with Sickle Cell Anemia?

A

Nonpolar AAs

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10
Q

What causes sickle cell anemia?

A

instead of there being a polar glutamate at the 6th position in the b-subunit of hemoglobin A, there is a nonpolar valine instead.

this substitution causes an aggregation of hemoglobin which causes the sickle cell shape

this is bad long term- SCRBCs die faster than normal RBCs (hemolysis). because the hemolysis rate is faster than the renewal rate, this causes hemolytic anemia.

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11
Q

What are the Essential AAs?

A

Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine

His Imagination Lets Loose Many Possibilities To Try Verbalizing

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12
Q

What are the Nonessential AAs?

A

Alanine
Arginine (essential for infants)
Asparagine
Aspartate
Cysteine
Glutamate
Glutamine
Glycine
Proline
Serine
Tyrosine

As, Cs, Gs, PST

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13
Q

Which AA does NOT have a different L and D enantiomer?

A

Glycine (not chiral)

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14
Q

What configuration are all mammalian AAs in?

A

L-config

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15
Q

Why can AAs act as buffers?

A

AAs contain weakly acidic carboxyl groups and weakly basic amino groups

Because of this, they are able to easily neutralize a solution they are put in and retain the same pH.

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16
Q

What is the Bronsted-Lowry Theory

A

HA <–> H+ + A-

HA = conjugate Acid (proton donor)
H+ = proton
A- = conjugate Base (Proton Acceptor)

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17
Q

What is Ka?

A

Ka is the dissociation constant - it tells how strong an acid is

Larger Ka = stronger acid
Smaller Ka = weaker acid

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18
Q

What is pKa?

A

pKa is the number that tells how strong an acid is

Smaller pKa = stronger acid
Larger pKa = weaker acid

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19
Q

what are the relationships between Ka, pKa, and Acid strength?

A

the larger the Ka, the smaller the pKa, the stronger the acid

the smaller the Ka, the larger the pKa, the weaker the acid

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20
Q

if pH is < pKa = protonated acid form predominates

A

COOH and NH3+

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21
Q

if pH is > pKa DEprotonated base form predominates

A

COO- and NH2

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22
Q

What is the point where a molecule has no net charge?

A

Isoelectric point = pI
this is when form II predominates and there are equal amounts of form I and III

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23
Q

Primary Protein Structure

A

single sequence of amino acids

held together by peptide bonds

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24
Q

Secondary Structure of AAs

A

alpha helices or beta pleated sheets

held together by hydrogen bonds

coiling and folding

the C=O and the N-H groups bind together

myoglobin is an alpha helix

proteins that contain alpha helices include keratins (components of hair, nails, skin)

*proline is not compatible because of its ring structure causing a kink

beta pleated sheets can be parallel or antiparallel

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25
Q

Tertiary Structure of AAs

A

3D shape

held together by H-bonds, Disulfide bonds, Hydrophobic interactions, Ionic interactions

Ex: chaperones - proteins that help fold other proteins

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26
Q

Quaternary Structure of AAs

A

3D structure formed by more than one polypeptide chain

held together by H-bonds, ionic bonds, hydrophobic interactions

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27
Q

Peptidases (proteases)

A

enzymes that hydrolyze peptide bonds
- breaks down polypeptide into smaller fragments

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28
Q

exopeptidases

A

cut ends of proteins
N terminus - aminopeptidase
C terminus - carboxypeptidase

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29
Q

Endopeptidases

A

cleaves the inner portions of the proteins

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30
Q

Why are peptide bonds always in the trans formation?

A

it is because if they were in the cis formation there would be steric hinderance

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31
Q

What are the agents that cause Denaturation?

A

heat
strong acids/bases
organic solvents
detergents
mechanical mixing
heavy metal ions (lead, mercury)

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32
Q

is denaturation reversible?

A

Denaturation may or may not be reversible

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33
Q

Isoforms

A

proteins that do the same function but have different structures

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34
Q

isozymes

A

protein isoforms that function as enzymes

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35
Q

What happens to proteins as we age?

A

proteins can get misfolded and they can aggregate

this can cause amyloid diseases and prion diseases

36
Q

amyloid disease

A

accumulation of insoluble, aggregated misfolded proteins (called amyloids) made out of beta pleated sheets

seen in alzheimers and parkinsons

37
Q

Prion disease

A

caused by prion protein PrP

PrP is very resistant to degradation and forms insoluble aggregates of fibrils

causes TSE (transmissible spongiform encephalopathies

38
Q

TSE

A

Scrapie in sheep
Creutzfeld-Jakob in humans
mad cow disease in cattle

39
Q

PrPc -

A

prion protein cellular - normal and important role in the brain

when PrPsc comes, it causes a conformational change in PrPc resulting in resistance to degradation which means more aggregation which means disease

40
Q

What are the 2 globular hemeproteins

A

Hemoglobin and Myoglobin

41
Q

What are the key points about hemoglobin?

A

function - transport O2 from lungs to capillaries of tissues via RBCs

heme reversibly binds oxygen

hemoglobin transports 4 molecules of O2

it also transports H+ and Co2 from the tissues to the lungs

hemoglobin A has 4 polypeptide chains (2a and 2B) - each chain is alpha helical

42
Q

Myoglobin

A

myoglobin is present in the heart and skeletal muscle

it is an oxygen reservoir and it is an oxygen carrier/transporter

it can only hold 1 O2

myoglobin is a single polypeptide chain

43
Q

What are the 2 forms of hemoglobin?

A

Oxygenated form - R relaxed state

Deoxygenated form - T taut state

44
Q

On a graph what are the curves of myoglobin and hemoglobin?

A

myoglobin has a hyperbolic shape - 1 O2

Hemoglobin has a sigmoidal shape - 4 O2
- cooperative binding

45
Q

What is cool about myoglobin?

A

myoglobin is found in the heart and skeletal muscle

Myoglobin has a greater affinity for O2 causing O2 to move from the blood to the muscle

myoglobin releases O2 only when O2 is very low in muscle cells (during exercise)

46
Q

What is the Bohr effect

A

the binding affinity of O2 changes when other ligands bind to Hemoglobin

other ligands include
H+
2,3-bisphosphoglycerate
CO2

these ligands are helpful because they stabilize the deoxygenated taut state of Hb.

47
Q

effect of other ligands on the oxygen affinity of hemoglobin

A

increased H+ –> decreased affinity for O2 hemoglobin

increased 2,3-bisphosphoglycerate –> decreased affinity for O2

increased CO2 –> decreased affinity for O2

48
Q

What happens when CO (carbon monoxide) binds to a heme site?

A

Hb shifts to the R state - this causes other heme sites to bind O2 tightly - causes us to not absorb any O2 = death

Increased CO –> increased affinity for O2

49
Q

What are Hemoglobinpathies

A

genetic disorders caused by structurally abnormal Hb + insufficient amounts of Hb

Sickle Cell Anemia (Hb S)- glutamate subd with valine

Hemoglobin C (Hb C) - glutamate substituted with lysine

Hemoglobin SC - (Hb S + Hb C)

Thallassemia syndromes - decreased production of normal hemoglobin

50
Q

What are Fibrous Proteins

A
  • mainly secondary protein structure

Ex: collagen, elastin, alphakeratin

51
Q

Collagen - what about it?

A

it is the MOST ABUNDANT protein in the body

long, rigid

52
Q

Type I collagen

A

found in TEETH, bone, skin, tendons

53
Q

What proteins make up glycine?

A

Glycine, proline, 4-hydroxyproline, 3-hydroxyproline, 5 hydroxylysine

54
Q

What is the path of biosynthesis of Collagen?

A

Nucleus (DNA -> mRNA) - RER (mRNA-> polypeptide chain) - Golgi (procollagen) - ECM (tropocollagen)

multiple tropocollagens form collagen

55
Q

2 types of defects in collagen synthesis lead to

A

EDS: Ehler-Danlos syndrome

fragile and stretchy skin - loose joints

OI: Osteogenesis imperfecta - easy to bend and fracture bones

56
Q

Elastin

A

elastin has RUBBER like properties

elastin fibers are found in the LUNGS, walls of arteries, elastic ligaments

very stretchy

57
Q

Keratin

A

keratin is composed of alpha helices

found in hair, wool, skin, horns, fingernails

58
Q

What does a synthase do?

A

it catalyzes a synthesis process

59
Q

phosphatase

A

REMOVES phosphate group

60
Q

Phosphorylase

A

cleaves bond by substituting with an inorganic phosphate

61
Q

kinase

A

ADDS phosphate group (taking from ATP making it ADP)

62
Q

oxidase

A

catalyzes OXRED reactions using O2 as electron acceptor (O is NOT part of the end result

63
Q

oxygenase

A

oxidizes substrates by transferring oxygen atoms to it (O is part of the end result)

64
Q

active site

A

where substrate binds and catalyzing occurs

65
Q

efficient

A

10^3 - 10^8 times faster than UNcatalyzed reactions

66
Q

specific enzymes

A

interacts with certain substrates and catalyzing only ONE type of rxn

67
Q

Can enzyme activity be regulated?

A

yes - based on cellular need of the enzyme

68
Q

enzyme location?

A

enzymes are usually local to certain places -

69
Q

HOloenzyme

A

enzyme WITH nonprotein component - ACTIVE

70
Q

apoenzyme

A

enzyme WITHOUT nonprotein component - INACTIVE

71
Q

cofactor

A

nonprotein component of enzyme (inorganic)

72
Q

coenzyme

A

nonprotein component of enzyme (organic)

EX: NAD+ (niacin) and FAD (riboflavin) from the B Vitamins

73
Q

prosthetic group

A

coenzymes PERMANENT with enzyme

74
Q

COsubstrate

A

coenzymes that SOMETIMES are with enzyme

75
Q

allosteric enzymes

A

enzymes that change conformation with binded by a molecule at a site other than the active site

can cause activation or inactivation

there can be changes in binding affinity and different binding sites on the enzyme

76
Q

Enzymes and activation energy

A

enzymes lower the activation energy so that the reaction can happen without spending so much energy

77
Q

what factors affect the speed of an enzyme catalyzed reaction?

A

substrate concentration

temperature

pH

78
Q

Michaelis menton

A

rate of a reaction based on the concentration of the enzyme and the substrate

ALLOSTERIC ENZYMES DO NOT FOLLOW MM

79
Q

pH

A

different enzymes can work at different pH

EXTREMES of pH values can cause denaturation

80
Q

MM equation

A

E + S = ES –> E + Product

E is never used up or incorporated with product, it is always separate.

81
Q

Km

A

Km = 1/2Vmax / substrate concentration

enzyme affinity for substrate

large Km = low affinity of enzyme for substrate

small Km = high affinity of enzyme for substrate

82
Q

1st order

A

substrate concentration is less than Km

V is proportional to [S] - direct relationship

83
Q

0 order

A

substrate concentration is greater than Km

V is constant - straight horizontal line

84
Q

lineweaver-burk plot

A

double reciprocal plot

can calculate Km and Vmax

85
Q

reversible inhibitors

A

these inhibitors bind to enzymes with noncovalent bonds

2 types: competitive + noncompetitive

86
Q

irreversible inhibitors

A

bind to enzymes through COValent bonds

Biochemistry - 730A (4 decks)

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