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Biochemistry > Exam 2: Proteins > Flashcards

Exam 2: Proteins Flashcards

1
Q

What are the parts of the GroES-GroEL complex

A

GroES: is a co chaperonin hsp10, it is a 7 subunit ring that can be on top of or underneath
GroEL: a chaperonin hsp60, made of two stacked 7 ring subunits that have a cavity (pot)

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2
Q

What are the 4 classes of molecular chaperones

A

ribosome associated chaperones
Hsp70- heat shock proteins
Hsp 90-heat shock proteins
molecular chaperonins

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3
Q

What do chaperonins do?

A

They help fold nascent (new) proteins and refold preexisting proteins, help assemble multi subunit proteins and any structures containing proteins, and they can target misfolded proteins

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4
Q

What do ribosome associated chaperones do

A

Help nascent/ denovo (never been folded) polypeptides exiting from the ribosome, binds to them to prevent them from folding unit needed for translation.

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5
Q

What do Hsp70 chaperones do?

A

fold denovo and misfolded proteins, need ATP to refold from ATP hydrolysis. Have hydrophobic portion on outside that attracts misfolded proteins (attracts np mols ie no charge), so they don’t always need heat to activate ATPase

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6
Q

Explain what Hsp refers to

A

heat shock proteins, named this way because they tend to be in high temperature environments,

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7
Q

Where are Hsp70 chaperones found?

A

transmembrane transfer of organelles: ER mitochondria and chloroplasts.

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8
Q

What do Hsp90 chaperones do?

A

finalize the folding of client proteins aka partially unfolded, can work together with Hsp70 to refold damaged proteins or destroy permanently denatured ones

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9
Q

Where are Hsp90 chaperones found

A

can be from bacteria to eukaryotes. in eukaryotes: nucleus, cytoplasm and mitochondria, chloroplasts in plants

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10
Q

What do molecular chaperonins do?

A

faster more efficient refolding of denatured proteins with an internal compartment

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11
Q

What are the steps of refolding with molecular chaperonins

A
  1. denatured protein binds to hsp70, stabilizing it.
  2. misfolded protein goes into pot (GroEL rings) because of hydrophobic attraction.
  3. Lid (GroES hsp10) binds to the pot and ATP hydrolysis causes conformation change inside of it, making it hydrophilic inside.
  4. This makes protein hide its hydrophobic R groups inside of it, refolding it.
  5. (7) ATPs are used in ATP hydrolysis, once they are all used up the protein is released.
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12
Q

Describe primary structure proteins

A

dictated by DNA. simple AA chain

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13
Q

What kind of illness can a mistake in primary structure cause explain

A

sickle cell anemia: Hemoglobin the first AA is out of place, hydrophobic Val is switched for glutamic acid, creates hydrophobic pocket causing aggregation.

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14
Q

Describe secondary structure proteins

A

Alpha helices: commonly right handed, R groups stick out of heliz
Beta pleated sheets can be parallel or antiparallel
both: backbone with non covalent bonds create phi and psi angles

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15
Q

What are secondary proteins stabilized by

A

alpha and beta parallel: N-H (H bond) and and C=O of backbone
beta antiparallel: N to C terminus go in opposite direction, OH bonds closer more stable

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16
Q

What AA are incompatible with alpha helices

A

Gly: too small
Pro: too rigid prevents NC from rotating
Asp, Glu- charged
Trp: too bulky

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17
Q

name the super secondary structures

A

beta-alpha-beta (heart shape), beta meander (up and down), B barrel (barrel of beta), Greek key (up down beta attached intercalated, alpha alpha unit (ribbon with two spirals).

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18
Q

Describe Tertiary structure proteins

A

3D, exclude water from inside of structure, have some or multiple domains (compact conserved structure unit with a specific function)

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19
Q

What are the 5 ways tertiary proteins are stabalized

A

1) hydrophobic effect: hydrophobic R groups inside, hydrophilic outside.
2) electrostatic interactions: salt bridges, +/- R gorups and dipole dipole effects
3) H bonds: create water bridges, are also all over inside and outside of structure
4) Covalent bonds: like disulfide bonds
5) Hydration shell: water surrounds protein creating bubble, allows protein to move inside bubble, helps overcome entropy because water is less organized and the universe wants disorder

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20
Q

Describe Quaternary Structure proteins

A

2+ polypeptides together to form a single functional protein.

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21
Q

What are the 3 types of quaternary proteins

A

sub unit: 1 pp chain with a protein that has multiple chains

oligomer: protein with multiple subunits where 1+ sub units are identical
protomer: single pp with an oligomer

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22
Q

What is the purpose of 4 structure

A

translation accuracy, easier to replace subunits independently than to replace an entire protein (saves energy), protein function is regulated by subunit association.

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23
Q

What bonds stabilize 4 structure

A

non covalent interaction: hydrophobic and electrostatic interactions. H bonds, covalent cross links: sometimes disulfide bonds but rarely.

24
Q

What is an IUP

A

intrinsically unstructured protein, denatured or unfolded.

25
Q

What are the functions of IUPs

A

regulation of signal transduction, transcription, translation and cell proliferation, multiprotein complex assembly.

26
Q

What makes a irreversible denatured protein

A

when bonds are broken, the new structure can be stabilized by external forces

27
Q

Under what conditions can proteins become denatured?

A
  • change in pH: addition of acids or bases, changes ionization state in R groups.
  • addition of an organic solvent: could interfere with hydrophobic effect
  • detergent: SDS sodium dodeoxylsulfate interferes with hydrophobic effect
  • reducing agents: BME (b merpto ethanol) breaks disulfide bonds
  • addition of salt: removes water, water leaves to dissolve salt. If salt levels are too high the protein can precipitate, if too low, protein becomes more soluble and salt bridges are interrupted
  • heavy metal ions: disrupt salt bridges and other electrostatic interactions
  • Rise in temp: created vibration, breaks weaker interactions, usually reversible.
  • Mechanical stress: trauma breaks weak bonds: like batting eggs. Irreversible
28
Q

What are the characteristics of fibrous proteins. name 2 examples

A

usually made of 2 structures, often have structural functions. ex: collagen and keratin

29
Q

Describe the structure of collagen

A

3 pp chains wrapped around each other in a triple helix. a right-handed triple helix of 3 polypeptides each in a left handed alpha helix. Its fibers are crosslinked with covalent bonds.

30
Q

What is the primary sequence of collagen

A

Gly-X-Y
X= pro or hydroxyproline
Y: Lys or hydroxylysine
Gly because its the only one small enough to fit in triple helix

31
Q

Where is collagen found?

A

In your skin, when stretched out over time causes wrinkles. Also in tendons

32
Q

What are the components of collagen fibers

A

enzymes cross link collagen that forms fiber

33
Q

What are the characteristics of alpha keratin

A

hair, double helix coiled coil structure (two alpha helices wrapped around each other). protofilament made of 2 coiled coiled wrapped. filament made of 4 right handed twisted protofilaments (rope)

34
Q

What makes hair curly or straight

A

depends on how many crosslinks are in alpha helix, more disulfide bonds makes it curlier.

35
Q

What are the characteristics of beta keratin

A

keratin in beta pleated sheets, has small R groups (lot of Ala and Gly, stacks of antiparallel beta sheets together which make H bonds

36
Q

What are 2 examples of globular proteins, what do they have in common

A

myoglobin Mb in muscles and hemoglobin Hb in blood, both are hemoproteins (have a prosthetic group called heme)

37
Q

What is the function of the heme in Mb and Hb

A

to reversibly bind to O2.

38
Q

What are the chemical properties of a heme

A

depend on iron Fe in the center of the heme. Fe has 6 binding positions. 4 are to N in protoprophyrin ring in covalent bond. 5th position is bound to a N-His.
6th position is reversibly bound to O2 (noncovalent bond) due to oxi-red rxns.

39
Q

What is the main function of Mb

A

stores O2 in muscle for aerobic metabolism

40
Q

What is the main function of Hb

A

deliver O2 from lungs to tissues in blood

41
Q

Describe the structure of Mb

A

single sub unit (pp chain) globin made of 8 alpha helices labelled from A to H, Folded structure has crevice that binds to heme.

42
Q

What keeps iron from oxidizing in Mb?

A

Distial histidine

43
Q

What is the structure of Hb

A

4 subunits (pp chains) 2 alpha and 2 beta.
Each subunit has 2/ 3 structure
each subunit can binds to a heme
4 hemes total ie 4 O2 binding sites

44
Q

How is Hb different in different environments

A

HbA 2 alpha and 2 beta are identicla
embryonic = 2 alpha 2 E
fetal: 2 alpha 2 gamma (r)
different because mom to baby transfer wouldnt be possible if they were the same

45
Q

What are the 2 stable conformations for Hb

A

deoxyhemoglobin/ T tense conformation

oxyhemoglobin/ R relaxed conformation

46
Q

What kind of oxidation curves to Hb and Mb have?

A

Hb: sigmoidal
Mb: hyperbolic

47
Q

Explain the steps of cooperative binding

A

1) O2 binds to 1st subunit in Hb and causes conformation change from T to R state
2) T subunit interacts with 2 other subunits and begins to force them towards the R conformation without the O2 bound.

48
Q

When does hb have a higher and lower affinity for O2

A

in dexoy/ T: lower affinity

In oxy/ R : higher affinity

49
Q

What are the 2 allosteric regulators of Hb

A

H+ and 2,3 bisphosphoglycerate (BPG) are allosteric regulators, do not bind at iron binding site in heme.

50
Q

What is an allosteric regulator

A

mols that bind to a protein at an alternative site, cause change conformation thus change in function. can activate or inhibit a protein

51
Q

How does H+ act as a regulator for Hb, what is this effect called

A

more H+= lower pH more acidic
less H+= higher pH more basic.
an increase in H+ causes decrease in pH, curve shifts to right, decrease in Hb affinity for O2
a decrease in H+ causes increase in pH, curve shifts to left, increase in Hb affinity for O2.
The more H+ present, the lower the affinity for O2. (allosteric inhibition of Hb). This is because the conformation changes to deoxy state.
Called Bohr effect

52
Q

Why is the allosteric regulation of Hb important

skip

A

at tissue: cellular respiration makes CO2 which diffuses into blood through capillaries, body compensates with allosteric regulation, produces H+, decreasing pH raising affinity for O2 to deliver more O2 to tissues. Shift toward T state
Lungs: breathing out decreases CO2 levels, body produces??????

53
Q

How does BPG regulate Hb

A

it is a negative allosteric regulator, when bound to Hb, BPG shifts the conformation to T state. Causes affinity for O2 to decrease. Binds to Hb at central cavity in the middle of the 4 subunits (not where iron binds). Causes right shift in graph

54
Q

Where does BPG come from

A

produced in blood cells as a side product of glycolysis.

55
Q

How is BPG production regulated

A

At a high altitude: lower O2 pressure, BPG production goes up, decreases affinity for O2. In graph causes shift to Right

56
Q

Give an example of when O2 in Hb has competition

A

carbon monoxide poisoning, CO competes with O2 to bind at iron binding site in heme. CO is 250x more attracted to iron. If CO binds to Hb, it blocks O2 from binding and kills you.
The same can happen with cyanide CN

57
Q

The shape of a Hb saturation curve indicates that O2 binding is..

A

cooperative

Biochemistry (7 decks)

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