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Biochemistry - 730A > Protein Structure and Function > Flashcards

Protein Structure and Function Flashcards

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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
Tertiary Structure of AAs
3D shape held together by H-bonds, Disulfide bonds, Hydrophobic interactions, Ionic interactions Ex: chaperones - proteins that help fold other proteins
26
Quaternary Structure of AAs
3D structure formed by more than one polypeptide chain held together by H-bonds, ionic bonds, hydrophobic interactions
27
Peptidases (proteases)
enzymes that hydrolyze peptide bonds - breaks down polypeptide into smaller fragments
28
exopeptidases
cut ends of proteins N terminus - aminopeptidase C terminus - carboxypeptidase
29
Endopeptidases
cleaves the inner portions of the proteins
30
Why are peptide bonds always in the trans formation?
it is because if they were in the cis formation there would be steric hinderance
31
What are the agents that cause Denaturation?
heat strong acids/bases organic solvents detergents mechanical mixing heavy metal ions (lead, mercury)
32
is denaturation reversible?
Denaturation may or may not be reversible
33
Isoforms
proteins that do the same function but have different structures
34
isozymes
protein isoforms that function as enzymes
35
What happens to proteins as we age?
proteins can get misfolded and they can aggregate this can cause amyloid diseases and prion diseases
36
amyloid disease
accumulation of insoluble, aggregated misfolded proteins (called amyloids) made out of beta pleated sheets seen in alzheimers and parkinsons
37
Prion disease
caused by prion protein PrP PrP is very resistant to degradation and forms insoluble aggregates of fibrils causes TSE (transmissible spongiform encephalopathies
38
TSE
Scrapie in sheep Creutzfeld-Jakob in humans mad cow disease in cattle
39
PrPc -
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
What are the 2 globular hemeproteins
Hemoglobin and Myoglobin
41
What are the key points about hemoglobin?
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
Myoglobin
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
What are the 2 forms of hemoglobin?
Oxygenated form - R relaxed state Deoxygenated form - T taut state
44
On a graph what are the curves of myoglobin and hemoglobin?
myoglobin has a hyperbolic shape - 1 O2 Hemoglobin has a sigmoidal shape - 4 O2 - cooperative binding
45
What is cool about myoglobin?
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
What is the Bohr effect
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
effect of other ligands on the oxygen affinity of hemoglobin
increased H+ --> decreased affinity for O2 hemoglobin increased 2,3-bisphosphoglycerate --> decreased affinity for O2 increased CO2 --> decreased affinity for O2
48
What happens when CO (carbon monoxide) binds to a heme site?
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
What are Hemoglobinpathies
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
What are Fibrous Proteins
- mainly secondary protein structure Ex: collagen, elastin, alphakeratin
51
Collagen - what about it?
it is the MOST ABUNDANT protein in the body long, rigid
52
Type I collagen
found in TEETH, bone, skin, tendons
53
What proteins make up glycine?
Glycine, proline, 4-hydroxyproline, 3-hydroxyproline, 5 hydroxylysine
54
What is the path of biosynthesis of Collagen?
Nucleus (DNA -> mRNA) - RER (mRNA-> polypeptide chain) - Golgi (procollagen) - ECM (tropocollagen) multiple tropocollagens form collagen
55
2 types of defects in collagen synthesis lead to
EDS: Ehler-Danlos syndrome fragile and stretchy skin - loose joints OI: Osteogenesis imperfecta - easy to bend and fracture bones
56
Elastin
elastin has RUBBER like properties elastin fibers are found in the LUNGS, walls of arteries, elastic ligaments very stretchy
57
Keratin
keratin is composed of alpha helices found in hair, wool, skin, horns, fingernails
58
What does a synthase do?
it catalyzes a synthesis process
59
phosphatase
REMOVES phosphate group
60
Phosphorylase
cleaves bond by substituting with an inorganic phosphate
61
kinase
ADDS phosphate group (taking from ATP making it ADP)
62
oxidase
catalyzes OXRED reactions using O2 as electron acceptor (O is NOT part of the end result
63
oxygenase
oxidizes substrates by transferring oxygen atoms to it (O is part of the end result)
64
active site
where substrate binds and catalyzing occurs
65
efficient
10^3 - 10^8 times faster than UNcatalyzed reactions
66
specific enzymes
interacts with certain substrates and catalyzing only ONE type of rxn
67
Can enzyme activity be regulated?
yes - based on cellular need of the enzyme
68
enzyme location?
enzymes are usually local to certain places -
69
HOloenzyme
enzyme WITH nonprotein component - ACTIVE
70
apoenzyme
enzyme WITHOUT nonprotein component - INACTIVE
71
cofactor
nonprotein component of enzyme (inorganic)
72
coenzyme
nonprotein component of enzyme (organic) EX: NAD+ (niacin) and FAD (riboflavin) from the B Vitamins
73
prosthetic group
coenzymes PERMANENT with enzyme
74
COsubstrate
coenzymes that SOMETIMES are with enzyme
75
allosteric enzymes
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
Enzymes and activation energy
enzymes lower the activation energy so that the reaction can happen without spending so much energy
77
what factors affect the speed of an enzyme catalyzed reaction?
substrate concentration temperature pH
78
Michaelis menton
rate of a reaction based on the concentration of the enzyme and the substrate ALLOSTERIC ENZYMES DO NOT FOLLOW MM
79
pH
different enzymes can work at different pH EXTREMES of pH values can cause denaturation
80
MM equation
E + S = ES --> E + Product E is never used up or incorporated with product, it is always separate.
81
Km
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
1st order
substrate concentration is less than Km V is proportional to [S] - direct relationship
83
0 order
substrate concentration is greater than Km V is constant - straight horizontal line
84
lineweaver-burk plot
double reciprocal plot can calculate Km and Vmax
85
reversible inhibitors
these inhibitors bind to enzymes with noncovalent bonds 2 types: competitive + noncompetitive
86
irreversible inhibitors
bind to enzymes through COValent bonds

Biochemistry - 730A (4 decks)

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