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BMSC 200 > Chapter 3-theory > Flashcards

Chapter 3-theory Flashcards

1
Q

what are amino acids

A

the building blocks of proteins

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2
Q

what are proteins

A

linear polymers of amino acids

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3
Q

what are all proteins produced from

A

20 standard amino acids

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4
Q

what do all living organisms make there proteins from

A

the same pool of amino acids

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5
Q

how does 20 building blocks enable sequence diversity

A

for example a peptide of three residues could be produces 8000 ways

a protein on 100 residues has 1.3x10130 possible sequences

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6
Q

what is the advantages of making biomolecules as polymers of smaller, simpler building blocks

A

1) simplicity of chemistry
(one type of reaction for polymerization, a second type of reaction for degration)

2) recycling
(biomolecs can be digested back to component building blocks which are reusable for production of other biomolecs)

3) diversity
(the vast number of varying lengths and sequences)

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7
Q

what are the common features of amino acids

A

a hydrogen
central alpha C
Amino group
carboxyl group
side R chain

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8
Q

how do amino acids differ

A

the side chain group

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9
Q

how are amino acids constructed except glycine

A

the alph carbon is bonded to four different groups, this creates chiral caneter

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10
Q

how do amino acids have stereoisomers

A

the four different groups occupy unique spatial arrangements giving stereoisomers labelled as the L and D isomers

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11
Q

what stereoisomer are proteins made from

A

biologically proteins are made almost exclusively from L amino acids

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12
Q

what are the groups that amino acids are grouped into based off there properties

A

non-polar aliphatic
aromatic
polar, uncharges
polar, positively charges
polar, negatively charged

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13
Q

what are some characteristics of the non-polar, aliphatic amino acids

A

-mainly hydrocarbon side chains
-residues with non-polar chains are often buried in the core of the protein

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14
Q

what are the amino acids that fit into non-polar, aliphatic amino acids (7)

A

glycine
alanine
valine
leucine
isoleucine
proline
methionine

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15
Q

what are some unusual amino acid characteristics of nonpolar, aliphatic amino acids

A

glycine-only one thats not a cyro C and smallest acid
proline-has a ring
methionine-has a S group present

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16
Q

what amino acids are in the aromatics

A

tyrosine
phenylalanine
tryptophan

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17
Q

what is the largest amino acid

A

tryptophan

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18
Q

what is a phosphoralation

A

it is a type of post-translational modification
-phosphoryl groups are added by kinases to specific, hydroxyl-group containing amino acids (tyr, ser, thr)

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19
Q

what is post translation modification phosphorylation

A

phosphorylation is when certain amino acids can be covalently modified after their incorporation into a protein (post-translation)

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20
Q

in post translational modification what removes the phosphatases

A

phosphoryl

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21
Q

in post translational modification what adds the phosphatases

A

kinase

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22
Q

are post translational modifications reservable

A

yes

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23
Q

what amino acids are in the polar, uncharged group

A

cysteine
asparagine
glutamin
serine
threonine

24
Q

what can two cystines do

A

they can form covalent linkages called disulphide bond

25
Q

disulfide bonds important…

A

for stabilization of some protein structures

26
Q

why can cystine form a disulphide bond

A

because the S is at the end of the amino acid

27
Q

what polar, uncharged amino acids can be modified through phosphoralation

A

serine
threonine

28
Q

how do disulphide bonds form

A

through the oxidation of the sulfhydryl groups of two cysteine residues to for, a covalent linkage

29
Q

what do disulphides do

A

they stabilize protein structures

30
Q

cystine residue forming a disulphide bond must…

A

be within close proximity in space within the protein structure

31
Q

are disulphide bonds intra or inter-molecular

A

they can be both

32
Q

what is the effects of cooking an egg

A

heat+protein=protein starting to unfold and get tangled and ppt out of solution

33
Q

what amino acids are in the positively charged group

A

lysine
arginine
histidine

34
Q

what is the most polar group

A

the positively charged group

35
Q

what amino acids in the polar group carry a + charge at physiological pH

A

lysine
arginine

36
Q

if histidine isnt + charges at biological pH why is in the + group

A

-because it has the potential to carry a + charge
-its imidazole has a pKa of 6 (near physiological pH) (that fraction will be +1 and the rest will carry a net 0 charge)
-cell pH=7
-10:1=90% unprotinated

37
Q

what does histidine do in enzymatic reactions

A

it serves as a proton accepter/donor

38
Q

what amino acids are in the negatively charged group

A

aspartate
glutamate

39
Q

what is is glutamate responsible for

A

-for one of the five basic tastes (umami)
-it is used for a flavor enhancer (monosodium glutamate (MSG))

40
Q

what can aspartate and glutamate also be called

A

glutamic acid
aspartimic acid

41
Q

what does it mean that every amino acid has diprotic

A

every amino acid has at least two groups that accept and donate protons

42
Q

what do triprotic amino acids have

A

ionizable groups in their side chains (lys, arg, his, asp, glu, cys and tyr)

43
Q

what do diprotics have

A

two buffering groups

44
Q

what do triprotics have

A

three buffering regions

45
Q

what are the ionizable groups in the amino acids

A

carboxyl group
amino group
side chains off the triprotic amino acids

46
Q

what does each ionizable group have

A

a specific pKa

47
Q

what is the pKa

A

the pH at which that group changes its protonation state

48
Q

when pH is below the pKa…

A

the protonated form predominates (HA)

49
Q

when pH is above pKa…

A

the unprotonated form predominates (A-)

50
Q

what groups do all amino acids have and what are there pKa

A

carboxyl (pKa=2.0)
amino (pKa=10.0)

51
Q

at a pH of 7.4 what form will carboxyl and amine group be in

A

COO- and NH3+ forms

52
Q

what is the acids and conj base forms of carboxyl

A

COOH (acid)
COO- + H+ (conj base)

53
Q

what is zwitterion

A

dipolar ion of and amino acid

54
Q

what is the isoelectric point (pI) of an amino acid

A

it is the average of the pKas on either side of where the net charge is equal to zero
it is the pH at which the net charge on the molecule is equal to 0

55
Q

how do you calculate the pI

A

it is the average of the pKas on either side of where the net charge is equal to zero
pI=(pKa 1 + pKa 2) /2

BMSC 200 (10 decks)

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