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Mcat biochem > Mcat biochem > Flashcards

Mcat biochem Flashcards

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MCAT flashcards
1
Q

A- all chiral amino acids used in eukaryotes are what type of amino acids?
B- and where are they drawn in a fischer projection?
C-also what absolute configuration does this translate to in the cahn-ingold-prelog system?
D- what is the exception and why?

A

A-all chiral amino acids used in eukaryotes are L-amino acids
B-this translates to being drawn on the left in a fischer projection
C- this translates to an S absolute configuration for almost all chiral amino acids
D- the exception is cysteine; even though its still an L-amino acid it has an R absolute configuration cuz the CH2SH group has priority over the COOH group

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2
Q

what are the seven amino acids that have nonpolar, nonaromatic side chains?

A

they are alanine, valine, leucine, isoleucine, methionine, proline, and glycine

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3
Q

what special atom does methionine have in its side chain? why is methionine considered relatively nonpolar?

A

methionine has a sulfur atom in its side chain. bcuz the sulfur has a methyl group attached it is considered relatively nonpolar.

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4
Q

A- how is proline unique?
B- why is its amino group different from in the other amino acids?
C- what does the amino nitrogen become a part of, and what does it form?
D- what places constraints on the flexibility of proline and what does this limit?

A

A- proline is unique becuz it forms a cyclic amino acid
B- in all the other amino acids, the amino group is attached only to the alpha-carbon
C- in proline, though, the amino nitrogen becomes a part of the side chain, forming a five-membered ring
D- the five membered ring places constraints on the flexibility of proline which limits where it can appear in a protein and can have significant effects on proline’s secondary structure.

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5
Q

draw and know the 7 amino acids with nonpolar, nonaromatic side chains.

A

confirm their structures here

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6
Q

describe the structure of tryptophan

A

a double ring system that contains a nitrogen atom

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7
Q

describe the structure of phenylalanine

A

a benzyl side chain( a benzene ring plus a -CH2 group)

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8
Q

describe the structure of tyrosine

A

a benzyl side chain(a benzene ring plus a -CH2 group with an OH group attached to the ring

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9
Q

draw and know the three amino acids with aromatic side chains

A

confirm their structures after drawing

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10
Q

what are the five amino acids with polar side chains?

A

they are serine, threonine, asparagine, glutamine, and cysteine.

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11
Q

what makes serine and threonine polar and able to participate in a certain type of bonding?

A

they both have OH groups in their side chains which makes them highly polar and able to participate in hydrogen bonding

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12
Q

what type of side chain do asparagine and threonine have?

A

they have amide side chains

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13
Q

A- whats the difference between the amino group in all amino acids and the amide nitrogens in asparagine and glutamine?
B- do the amide nitrogens become charged?

A

A- unlike the amino group in all amino acids, the amide nitrogens DO NOT gain or lose protons with changes in PH
B- amide nitrogens DO NOT become charged

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14
Q

what sort of group does cysteine have in its side chain?

A

it has a thiol -SH group in its side chain

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15
Q

what are two characteristics of the sulfur and what fact does this contribute to and what does this leave the thiol group prone to?

A

the sulfur is larger and less electronegative than oxygen, the s-h bond is weaker than the o-h bond. this leaves the thiol group in cysteine prone to oxidation

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16
Q

draw and know the structures of the five amino acids with polar side chains

A

confirm them

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17
Q

what are the two amino acids with negative charges on their side chains at physiological pH?

A

they are aspartic acid(aspartate) and glutamic acid(glutamate) at 7.4(physiological pH).

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18
Q

how are glutamic acid and aspartic acid different from asparagine and glutamine?

A

glutamic acid and aspartic acid are different from asparagine and glutamine because glutamate and aspartate have carboxylate COO- groups in their side chains, rather than amides.

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19
Q

A- what is the deprotonated form of aspartic acid?

B- what is the deprotonated form of glutamic acid?

A

A- aspartate

B- glutamate

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20
Q

on the mcat, why are you likely to see anion names instead of acid names?

A

this is because most acids in cells exist in the deprotonated form

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21
Q

draw and know the amino acids with negatively charged side chains(also draw the deprotonated forms)

A

confirm them

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22
Q

what are the three amino acids with basic side chains?

A

lysine, histidine and arginine

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23
Q

these three amino acids have side chains with positively charged “what” atoms?

A

they have side chains with positively charged nitrogen atoms.

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24
Q

describe the structure of lysine

A

lysine has a terminal primary amino group

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25
Q

describe the structure of arginine; and wat charge is delocalized and how?

A

arginine has three nitrogen atoms in its side chain; the positive charge is delocalized over all three nitrogen atoms

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26
Q

describe the structure of histidine`

NOW KNOW HOW TO DRAW ALL THREE AMINO ACIDS WITH BASIC SIDE CHAINS

A

histidine has an aromatic ring with 2 nitrogen atoms(this ring is called an imidazole)
CONFIRM THEM ON PAGE 9

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27
Q

how can histidine acquire a positive charge

A

histidine can acquire a positive charge becuz the pKA of the side chain is close to 7.4(its about 6) so at physiologic pH, one nitrogen atom is protonated and the other isnt. Under more acidic conditions, the second nitrogen atom can become protonated, giving the side chain a positive charge.

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28
Q

where are amino acids with long alkyl side chains more likely to be found?

A

inside the protein

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29
Q

where are amino acids with polar and charged side chains more likely to be found?

A

surface of the protein

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30
Q

study the one letter and tree letter abbrev’s of the amino acids

A 
Alanine Ala  A
Arginine Arg R
Asparagine Asn N
Aspartic acid Asp D
Cysteine Cys C
Glutamic acid Glu E
Glutamine Gln Q
Glycine Gly G
Histidine His H
Isoleucine Ile I 
Leucine Leu  L
Lysine Lys K
Methionine Met M
Phenylalanine Phe F
Serine Ser S
Threonine Thr T
Tryptophan Trp W
Tyrosine Tyr Y
Valine Val V
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31
Q

when do ionizable groups gain or lose protons

A

they gain them in acidic conditions and lose them in basic conditions

32
Q

what happens when the pH is less than the pKa? greater than the pKa?

A

when the pH is less than the pKa the majority of the species will be protonated
when the pH is greater than the pKa the majority of the species will be deprotonated

33
Q

at a pH of 1 what happens to the amino acid in regards to whats protonated/deprotonated?

A

they exist as pos charged under acidic conditions
at a pH of 1, there are lots of protons in solution
we are far below the pKa of the amino group will be fully protonated NH3 and thus positively charged
we are also below the pKa of the carboxylic acid group, it will be fully protonated COOH and neutral
At very acidic pH values, amino acids tend to be positively charged

34
Q

at physiologic pH how do amino acids exist?

A

they exist as zwitterions at intermediate pH
at a pH of 7.4 we have moved above the pKa of the carboxyl group
the carboxyl group will be in its conjugate base form and be depronated, becoming COO-
we are also well below the pKa of the basic amino group so it will be fully protonated and its conjugate acid form NH3
so we will have a molecule that has a pos and negative charge but overall the molecule is elec neutral
these moles are called zwitterions
the charges neutralize each other and zwitterions exist in water as internal salts

35
Q

know how to draw when carboxylic acids become deprotonated at neutral PH?

A

know how to draw it and check it with the drawing on page `13

36
Q

at basic conditions how do amino acids exist?

A

amino acids are neg charged under basic conditions

37
Q

know how to draw when amino groups become deprotonated at basic pH forming an anion

A

know how to draw it and compare with the drawing on page 14

38
Q

if a side chain is charged, how many titration curves does it have?
how does glycine exist at low pH values? protonated/deprotonated? with what charge?
when the soln is titrated with NaOH, what group is deprotonated first and why?

A

3 curves
fully protonated
positively charged
the carboxyl group is deprotonated first becuz it is more acidic than than the amino group

39
Q

what happens when 0.5 equivalents of base have been added(what concs are equal?)
at this point, what does the PH equal?
what happens when the pH is close to the pKa(and what happens to the curve?)

A

when 0.5 equivalents have been added, the concs of the fully protonated glycine and its zwitterion are equal

  • at this point the pH=pKa 1
  • when the pH is close to the pKa the soln is acting as a buffer, and the titration curve is flat
40
Q

what happens to the concs, what 2 things happen just to the pH, and every molecule when you add 1.0 equivalents of base?
how does the molecule exist?
what is the pI?
how to calc pI for a neutral amino acid?

A

at 1.0 equivs of base, the amounts of glycine soln and base are now equal
the pH starts to go up fast(soln stops acting like a buffer); the pH equals the pI of glycine
every molecule is electrically neutral
the molecule exists exclusively as a zwitterion
the pI is the point at which the molecule is electrically neutral
the pI for a neutral amino acid is calculated by adding the pKas for the amino and carboxyl group and divided by 2

41
Q

what happens to the pH(2 things) and concs when we add more base(1.5 equivs)?
what phase does it go thru?

A

the pH is constant
the pH equals the pKa2
the concs of the fully deprotonated and zwitterion are equal
it goes thru a second buffering phase

42
Q

what happens to the amino acid when you add more base (2.0 equivs)?
what happens to the pH?

A

at 2.0 equivs, the amino acid is fully deprotonated

any more base will only increase the PH

43
Q

what charge does the amino acid have at very acidic pH values?
what charge does the amino acid have at very basic pH values?

A

at very acidic pH values, the amino acid tends to be positively charged
at very acidic pH values, the amino acid tends to be negatively charged

44
Q

how many amino and carboxyl groups does glutamic acid have?
what is glutamic acid’s charge in it fully protonated state?
describe the process of titration for glutamic acid.

A

glutamic acid has 2 carboxyl groups and one amino group
the charge in its fully protonated state is +1
during titration, it undergoes the first deprotonation, losing the proton from its main carboxyl group, just like glycine does; then it becomes electrically neutral
when it loses it second proton its overall charge will be -1(the second proton that is removed in this case comes from the side chain carboxyl group, NOT THE AMINO GROUP !!!!

45
Q

what is the pI for amino acids with non ionizable side chains

A

the pI for amino acids with non ionizable side chains, the pI is usually around 6

46
Q

how many amino and carboxyl groups does lysine have
what is its charge in its fully protonated state?
describe the titration of lysine

A

2 amino groups and 1 carboxyl group
the charge in its fully protonated state is +2
losing the carboxyl proton happens around a pH of 2, brings the charge down to +1
lysine doesnt become electrically neutral until it loses the proton from its main amino group, which happens around 9
it gets a negative charge when it loses the proton from the amino group in its side chain which happens at pH 10.5

47
Q

what pI do amino acids with acidic side chains have?

what pI do amino acids with basic side chains have?

A

amino acids with acidic side chains have pI values well below 6
amino acids with basic side chains have pI values well above 6

48
Q

how are residues in peptide chains made(what is the bond and how does it form?)
what func group does it form?

A

residues in peptide chains are made from peptide bonds, which is a specialized amide bond that forms between the COO- group of one amino acid and the NH3 group of another amino acid
the func group formed is C(O)NH-

49
Q

what type of reaction is a peptide bond formation

A

this is an example of a condensation or dehydration reaction, becuz it results in the loss of a water mole

50
Q

how does a peptide bond form specifically(what attacks what?)

A

in the peptide bond, the electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophilic amino group on the second amino acid
after the attack, the hydroxyl group of the carboxylic acid is kicked off

51
Q

know how to draw peptide bond formation and cleavage

A

confirm it on page 18

52
Q

where do amino groups have delocalizable pi electrons AND what do these electrons help the amino acid exhibit?
what character does the C-N bond have?
as a result of all this what happens to rotation of the protein backbone around C-N amide bonds, which makes the protein more what?
describe rotation around the remaining bonds in the backbone?

A

amino groups have delocalizable pi electrons in the carbonyl and in the lone pair on the amino nitrogen, so they can exhibit resonance
the C-N bond has partial double bond character
rotation of the protein backbone around its C-N amide bonds is restricted which makes the protein more rigid
rotation around the remaining bonds in the backbone is not restricted, as they remain single bonds

53
Q

how are proteins broken down?in living organisms?

A

proteins are broken down by acid or base catalysis

in living orgs, hydrolysis is catalyzed by hydrolytic enzymes like chymotrypsin and trypsin

54
Q

how does hydrolysis really work

A

hydrolysis- they break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon

55
Q

how is a proteins secondary structure made(also what bonds are involved)

A

its made of the local structure of neighboring amino acids(it is the result of hydrogen bonding btween nearby amino acids)

56
Q

describe the structure of the alpha helix(what does it look like and what else?)
how is the helix stabilized
where do the side chains point
what protein is associated with alpha helix

A

it looks like a rod and the peptide chain coils clockwise around a central axis
the helix is stabilized by intramolecular hydrogen bonds btween a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain
the side chains of the amino acids point away from the helix core
keratin

57
Q

describe the structure of the b-pleated sheet
how do the sheets lie and what do they form
what bonds are involved specifically

A

they can be parallel or anti parallel
the sheets lie alongside one another, forming rows or strands held together by intramolecular hydrogen bonds btween carbonyl oxygen atoms on one chain and amide hydrogen atoms on the chain next to it

58
Q

how do the r groups point?

A

the r groups of amino residues point above and below the plane of the b-pleated sheet

59
Q

what feature of proline causes a kink and where?

A

becuz of its rigid cyclic structure proline will introduce a kink in the peptide chain when its found in the middle of an alpha helix

60
Q

where is proline found

A

proline is found between the chains of a beta pleated sheet and it is often found at the start of an alpha helix

61
Q

what are the two categories of proteins and how do they look?

A

fibrous like collagen which looks like long strands

and globular like myoglobin which looks like a globe

62
Q

what is a protein’s tertiary structure? and how are tertiary structures determined?

A

this is its 3d shape

they are det’d by hydrophilic and hydophobic interactions btween r groups

63
Q

are c=o and n-h bonds philic or phobic

A

they are philic

64
Q

what bonds are 3d prot struc also helped by?

what interactions btween amino acids with “what” are also a factor, creating what?

A

3d prot strucs are also helped by hydrogen bonds, acid base interactions btween amino acids with charged r groups creating salt bridge

65
Q

what other bonds are apart of tertiary structure? and how do they form? what do they create in the protein chain

A

disulfide bonds, they form when two cysteine molecules become oxidized to form cystine
they create loops in the protein chain

66
Q

know how to draw disulfide bond formation

A

confirm it by page 23

67
Q

hydrocarbons are more stable in what than what?

A

more stable in aqueous solns than in organic ones(H<0)

68
Q

what happens when hydrophobic side chains are placed in aqueous soln,

A

the water moles in the solvation layer cant form H bonds with the side chain

69
Q

quaternary structures exist for proteins that contain more than one what

A

more than one polypeptide chain

70
Q

what kind of specific effects can quaternary structures induce
what are quats made of and what is 2 of their possible functions

A

they can induce allosteric effects or cooperativity

they are made of subunits and they pretty much reduce either DNA needed to encode the prot or reducing surface area

71
Q

where do conjugated proteins derive part of their function from “what”
give examples of “what”

A

they derive part of their function from covalently attached molecules called prosthetic groups
prosthetic groups could be organic molecules like vitamins or metal ions like iron

72
Q

give a popular example of a prosthetic group, what does it contain, bind and carry?

A

heme group. contains an iron atom in its core and binds to and caries oxygen

73
Q

how does heat denature a protein?

A

heat denatures a protein by overcoming hydrophobic interactions that hold a protein together causing the protein to unfold

74
Q

how do solutes denature a protein?

A

solutes denature a protein by disrupting tertiary and quaternary structures, by breaking disulfide bridges, by turning cystine back to two cysteine moles, they can overcome hydrogen bonds, even by breaking apart forces that hold alpha helices and beta pleated sheets together

75
Q

how do detergents denature proteins, and what does this disrupt?

A

detergents solubilize protein which disrupts noncovalent bonds

Mcat biochem (3 decks)

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