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Fundamentals > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

what happens to melting temperature of lipid membrane as you increase hydrocarbon chain length?

A

melting temperature increases

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2
Q

what does cholesterol do for lipid membrane fluidity?

A

it prevents it from being packed in to tightly, but also prevents it from being too loose

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3
Q

what is the ideal state for the lipid membrane?

A

liquid-crystalline

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4
Q

if you increase the number of double bonds in hydrocarbons of lipid membrane fatty acids, what happens to the melting temperature?

A

melting temperature decreases

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5
Q

what color is hemotaxin and what does it stain?

A

pink, protein

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6
Q

what color is eosin and what does it stain?

A

blue, DNA

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7
Q

what happens in sickle cell anemia?

A

a valine is put in place of a glutamate, creating a hydrophobic spot in the hemoglobin protein which causes it to congregate with the hydrophobic spots on other hemoglobin proteins to form fibers that then distort the RBC and prevent oxygen transport

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8
Q

what happens in osteogenesis imperfecta?

A

switch aspartate for glycine in collagen - so you can’t make collagen fibers

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9
Q

what happens in testicular feminization?

A

you can’t form zinc fingers because you lose a cysteine that typically coordinates a zinc ions, without this, you can’t bind to DNA and transcribe genes that lead to the production of male secondary sex characteristics

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10
Q

what is the pKa of aspartate? what is it’s charge at neutral pH?

A

4.0, negative

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11
Q

what is the pKa of glutamate? what is it’s charge at neutral pH?

A

4.0, negative

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12
Q

what is the pKa of histidine? what is it’s charge at neutral pH?

A

6.0, neutral

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13
Q

what is the pKa of cysteine? what is it’s charge at neutral pH?

A

8.4, neutral

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14
Q

what is the pKa of tyrosine? what is it’s charge at neutral pH?

A

10.5, neutral

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15
Q

what is the pKa of lysine? what is it’s charge at neutral pH?

A

10.5, positive

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16
Q

what is the pKa of arginine?what is it’s charge at neutral pH?

A

12.5, positive

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17
Q

what is the pKa of the carboxy terminal end? what is it’s charge at neutral pH?

A

2.0, negative

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18
Q

what is the pKa of the amino terminal end? what is it’s charge at neutral pH?

A

9.5, positive

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19
Q

what is special about glycine?

A

it is super flexible

20
Q

what is special about serine?

A

it is often present in the active sites of digestive proteins. it has a very high pka but can dissociate depending on what other amino acids it is surrounded by

21
Q

what is special about cysteine?

A

it can form disulfide bonds between amino acids chains - these will bury into the center of the protein because they are hydrophobic; they are the nucleophiles in caspases, and they coordinate metal ions

22
Q

what is special about methionine?

A

useful for radioactive dating

23
Q

what is special about proline?

A

it is good for bending and is very rigid

24
Q

what is special about phenylalanine?

A

it has a benzene ring so it can stack

25
Q

what is special about tyrosine?

A

it is a phosphorylation site and can act as a nucleophile; absorbs UV light

26
Q

what is special about tryptophan?

A

it absorbs UV light and has some polarity - so it will be found at the transition between hydrophobic and hydrophilic entities

27
Q

what is special about histidine?

A

it is a good buffer, can be a hydrogen donor or acceptor (acid or base)

28
Q

which two amino acid atoms make up the psi angle?

A

the alpha carbon and C’

29
Q

which two amino acid atoms make up the phi angle?

A

the alpha carbon and the nitrogen

30
Q

which atom in amino acids do the phi and psi angles flank?

A

the alpha carbon (the one with the R group attached to it)

31
Q

what are helix-loop-helix motifs?

A

two alpha helices connected by a a strand of amino acids - it functions to bind calcium ions

32
Q

what are helix-turn-helix motids?

A

two alpha helices connected by a very short strand of amino acids; it functions to bind DNA, inserting one helix into the major groove of DNA and turn transcription on or off

33
Q

what are leucine zipper motifs?

A

they function to dimerize two alpha helices so that they can go on to bind DNA (so the motif itself is not directly involved in DNA binding, it simply facilitates it) every seventh leucine binds

34
Q

what are zinc finger motifs?

A

they involve coordination f zinc by two cysteines and two histidines; functions as a DNA binder - present in a lot of transcription factors

35
Q

glycosylation: what amino acids does it occur on and what is its function?

A

get N-glycosylation on asparagine and O-glycosylation on the OH of serine or threonine
functions to target proteins for secretion and involved in folding

36
Q

lipid attachement: what amino acids does it occur on and what is its function?

A

palmitoylation occurs on cysteine and myristoylation occurs on Nterminal end of glycine
functions to attach proteins to lipid membrane (weakly though)

37
Q

phosphorylation: what amino acids does it occur on and what is its function?

A

occurs on serine, threonine, and tyrosine

functions to regulate protein activity

38
Q

acetylation: what amino acids does it occur on and what is its function?

A

occurs on lysine and on the N terminus of proteins;

alters DNA characteristics by binding to histones and prevents degradation

39
Q

carboxylation: what amino acids does it occur on and what is its function?

A

occurs on glutamate (so get two carboxy terminals)

functions in calcium ion binding

40
Q

hydroxylation: what amino acids does it occur on and what is its function?

A

occurs on proline

functions to permit maturation and secretion of collagen

41
Q

selenocysteine: what amino acids does it occur on and what is its function?

A

made from serine - contains selenium instead of sulfure in cysteine
functions in enzyme catalytic activity

42
Q

what are cofactors?

A

inorganic metal ions that aid in enzymatic activity - either help in substrate binding or have a critical role in catalysis

43
Q

what are coenzymes?

A

organic or metalloorganic molecules that help enzymes in substrate binding or catalytic activity

44
Q

what does thiamine pyrophosphate do?

A

it’s functional group is a reactive carbon and it transfers an aldehyde

45
Q

what does coenzyme A do?

A

it’s functional group is a thiol and it transfers an acyl group.

46
Q

what does pyroxidal phosphate do?

A

its function group is an aldehyde and it transfers an amino group

47
Q

what does NAD+ do?

A

its function group is a reactive carbon and it transfers a hydride ion

Fundamentals (11 decks)

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