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Biochem 2 > Lecture 2 > Flashcards

Lecture 2 Flashcards

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1
Q

random coil

A

parts of polypeptide chain that don’t have discernible repeating pattern (ie alpha helix/beta sheets)
- structure determined by amino acid sequence

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2
Q

what are the two major types of tertiary structure?

A

globular and fibrous

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3
Q

globular tertiary structure

A

polypeptide folds into complex compact of shape like a ball
- water soluble
(ie enzymes, hemoglobin)

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4
Q

fibrous tertiary structure

A

simple, elongated 3D structure
- play role in cells that need molecules to travel far
(ie extracellular matrix protein: collagen, a-keratin)

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5
Q

subunit (quaternary structure)

A

polypeptide chain that makes up quaternary structure
- structure can be identical or different (dimer, trimer, tetramer, oligomer)

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6
Q

how are quaternary structure subunits hold together?

A

noncovalent forces

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7
Q

what exhibits allosteric properties?

A

multisubunit proteins
- subtle structure changes in one part of protein causing changes in function of another part

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8
Q

what can induce protein denaturation?

A

heat, high/low pH, detergents, urea and guanidine hydrochloride

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9
Q

what facilitates protein denaturation?

A
  • reducing agents —> they reduce disulfide bonds
  • urea improves accessibility of reducing agents to internal disulfide bonds
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10
Q

what are the consequences of protein denaturation?

A
  • decreased protein solubility = hydrophobic groups can lead to aggregation and precipitation
  • increased/decreased susceptibility to hydrolysis by proteolytic enzymes
  • total loss of biological activity
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11
Q

what is the anfinsen experiment?

A

determined all information necessary to determine the tertiary structure of a protein is provided by its amino acid sequence

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12
Q

molecular chaperones (chaperonins)

A

proteins that assist in living cells for protein folding

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13
Q

heat-shock proteins

A

major class of chaperonins, that are synthesized in response to heat shock or other stresses

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14
Q

does chaperones require energy?

A

yes, they bind in ways that are most energetically favored

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15
Q

why are chaperones used in the protein folding process?

A

b/c they make the folding process more reliable (even if shape is based on primary sequence)

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16
Q

what other factors facilitate protein folding?

A

ionic environment, enzymes (protein disulfide isomerase), cofactors (metal ions, organic compounds)

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17
Q

example of conformational disease

A

marfan’s syndrome

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18
Q

what characteristics does conformational diseases have?

A

-does not function or assemble
- “toxic folds” that trigger harmful protein aggregates
- defects in cellular trafficking

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19
Q

what gene mutation causes marfan syndrome?

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A

fibrillin –> elastin to elastic fibers

20
Q

what causes conformational diseases?

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A
  • change in amino acid sequence
  • defect in parents
  • nutrition deficiencies (vit C –> scurvy)
21
Q

amyloid

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A

deposits of protein aggregates that happen in and around cells

21
Q

common properties of aggregating proteins

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A
  • rich in b-sheets
  • transformation of helical structure to b-sheet
22
Q

amyloidosis

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A

accumulation of amyloid deposits –> alzheimer’s disease, prion disease

23
Q

prion proteins are responsible for what type of disease?

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A

neurodegenerative disease

24
examples of neurodegenerative diseases that are caused by prions
- CJD (humans) - mad cow disease - scrapie (sheep)
25
where are prions found?
outer surface of plasma membrane (most abundant in neurons)
26
normal prion is in what form? what about mutated form?
normal = a helix abnormal = b sheet, aggregates and protease resistant
27
who discovered prions?
stanley B. prusiner
28
what causes fetal familial insomnia (FFI)?
genetic mutation taht results in substitution of asparagine for aspartic acid in PrPc - affects the thalamus
29
what is the most common cause of blindness?
cataracts --> aggregation of partially unfolded lens proteins
30
crystallin proteins
structural and chaperone proteins in lens of eye - reduction in chaperone function = leads to increases in denatured proteins - alterations in a-crystallin oligomeric structure = leads to co-aggregation of a-crystallin and substrates
31
what is the most abundant protein in mammals?
collagen --> 25% of total protein mass in mammals
32
what is collagen?
fibrous protein that forms very stiff and strong cables - secreted by connective tissue cells
33
what is the structure of collagen molecules?
tropocollagen: 3 polypeptide chains wrapped forming superhelix
34
what is the amino acid composition of collagen?
1/3 --> glycine rich in proline hydroxyproline and hydroxylysine
35
what is the purpose of proline in collagen?
- stabilizes helical conformation through steric repulsion of pyrrolidone rings on the outside of chains - hydroxyl groups of hydroxyproline form interchain H bonds and H bonds with water, stabilizing the triple helix
36
what is the purpose of glycine in collagen?
smallest amino acid, only reside that can fit in middle of triple helix
37
what vitamin is required to form hydroxylproline and hydroxylysine?
vitamin C -->reducing agent that maintains enzymes in active form, keeping iorn atoms in reduced ferrous state
38
what disease is caused by vitamin c deficiency?
scurvy --> a chains are not hydroxylated failing to form triple helix
39
collagen cross links
intramolecular and intermolecular covalent cross links form between modified lysine residues that further stabilize collagen fibril
40
what is the major source of ATP in aerobic organisms?
oxidative phosphorylation
41
what are the two major mechanisms for delivering oxygen?
circulatory system --> oxygen to cells oxygen carrying proteins --> myoglobin and hemoglobin
42
where is myoglobin found? what is its function?
- found in muscle - reserve supply of oxygen, facilitates movement of oxygen within muscle
43
function of hemoglobin
- increase oxygen transporting capacity of blood - transport of CO2 and hydrogen ions in blood
44
prosthetic groups
non protein components that are tightly bound to many proteins and contribute to their biological activities
45
apoprotein
protein without prosthetic group

Biochem 2 (5 decks)

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