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biochem > chapter 2 > Flashcards

chapter 2 Flashcards

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1
Q

proteins

A

linear, heteropolymers of amino acids

variable size and physcial properties
-accounts for diversity of structrue and biological function

final product of most genes
-means of expressing of genetic info

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2
Q

What is the most abundant macromolecules in cells

A

proteins

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3
Q

amino acids

A

An amino group and a carboxylate group covalently attached to a tetrehedral alpha carbon

-only differ at R group (side chain)

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4
Q

zwitterions

A

amino acids that have both a negative and a postive charge

(ampholytes)

can act as either an acid or a base

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5
Q

amino acids are -

A

zwitterions

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6
Q

zwitteroin alpha carboxyl groups have a pka near

A

2.2

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7
Q

zwitterion alpha amino groups have a pka near

A

9.4

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8
Q

at physiological pH (5-8), the alpha carboxyl and alpha amino groups of amino acids are-

A

completley ionized

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9
Q

Chirality

A

CO-R-N

looking down H-C bond, corn spelled clockwise indicates the L stereoisomer

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10
Q

amino acids are optically active or chiral becasue

A

of the tetrahedral Calpha bonded to 4 different groups

expection is Glycine

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11
Q

common amino acids found in proteins are all -

A

stereoisomers

(based on Fischer projections)

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12
Q

how are amino acids classified?

A

by the physiochemical properties of their R-groups

(polarity)

only 20 amino acids are commonly incoporated into proteins

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13
Q

non-polar amino acids

A

aliphatic and aromatic side chains

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14
Q

polar amino acids

A

hydroxyl, thiol, or carboxyanmide functional groups)

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15
Q

charged amino acids

A

neg and pos charged

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16
Q

non-polar amino acids

A

R-group is a hydrocarbon

includes aliphatic amino acids, 2 aromatic amino acids, Glycine, methionine and proline

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17
Q

aromatic amino acids in non polar

A

absorb UV light

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18
Q

proline R-group is-

A

covelently bonded to alpha amine

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19
Q

Glycine can also be

A

classsified as polar uncharged

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20
Q

Glycine structure

A

[G] (Gly)

achiral

very small -> flexible

weakly polar (Non-polar)

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21
Q

Alanine structure

A

[A] (Ala)

aliphatic R group

nonpolar

Hydrophobic interactions

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22
Q

Valine sturcture

A

[V] (Val)

aliplatic R group

highly hydrophobic R group

hydrophobic interactions

non-polar

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23
Q

Leucine structure

A

[L] (Leu)

aliphatic R group

highly hydrophobic R group

hydrophobic interactions

non-polar

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24
Q

isoleucine structure

A

[I] (Ile)

aliphatic R group

highly hydrophobic R group

hydrophobic interactions

non-polar

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25
Phenylalanine structure
[F] (Phe) aromatic R group -absorbs UV light (280 nm) very weakly highly hydrophobic R group hydrophobic interactions non-polar
26
Tryptophan structure
[W] (Trp) Aromatic R group -absorbs UV ligh (280) strongly -heterocyclic hydrophoic interactions bulky forms hydrogen bonds (donor) non-polar
27
methionine structure
[M] (Met) hydrophobic interactions sulfur containing side group (thioether) non-polar
28
Proline structure
[P] (Pro) Aliphatic side chain with distinctive cyclic structure -secondary amino group hydrophobic interactions non-polar
29
polar uncharged amino acids contain
hydroxyl, thiol or carboxyamide functional groups
30
All the nonpolars
alanine valine proline leucine isoleucine methionine glycine tryptophan phenylalanine
31
all the polar amino acids
serine cystenine threonine tyrosine glutamine asparagine
32
serine, threonine, and cysteine are often incolved in
enzymatic reactions
33
cysteine can form-
disulfide bridges (cystine)
34
serine structure
[S] (ser) polar, uncharged contains hydroxyl group -forms hydrgogen bonds (donor and acceptor) -R group can be modified
35
Threonine structure
[T] (Thr) polar, uncharged contains hydroxyl group -forms hydrgogen bonds (donor and acceptor) -can be phosphorylated
36
Tyrosine structure
[Y] (Tyr) weakly polar, uncharged aromatic R group -absorbs UV light (280nm) -phenol can participate in hydrophobic interactions but not classified as hydrophobic contains hydroxyl group -forms hydrgogen bonds (donor and acceptor) -can be phosphorylated
37
Cystenine stucture
[C] (Cys) polar, uncharged sulfur containing side group (sulfhydryl group - SH) -can form hydrogen bonds (usually donates) -can form a thiolate anion (S-) forms disulphide bonds with another Cys
38
Cystine
sulfihydrls in neighbouring cysteine residues undergo oxidation to form a disulphide bridge (covalent bond) relativily hydrophobic (non-polar)
39
asparagine stucture
[N] (Asn) amide containing side chain -carboxamide functional group -polar, noncharged -forms hydrogen bonds (donor(N) and acceptor (O)
40
Glutamine stucture
[Q] (Gln) amide containing side chain -carboxamide functional group polar, uncharged forms hydrogon bonds (donor and acceptor)
41
All the polar charged amino acids
histidine lysine arginine aspartate glutamate
42
charged amino acids \
partially or fully ionized at neutral pH, containing carboxylate or amine functional groupsh
43
histidine has a pka near
neutral
44
amines are-
neutral or + charged
45
carboxylates are -
neutral or - charged
46
histidine stucture basic form
[H] (His) -in the free amino acid the side chain uncharged at neutral pH 7 -imidazole ring -aromatic- abs weakly at 280 nm polar, in protiens may be charged/ uncharged at neutral pH His residues important in many enzymes catalyzed reactions -proton donor (acid)/acceptor (base)
47
histidine can act as an
acid or a base has a pka near 6.0 its ionization state depends upon its chemical environment it can accept or donate a proton (as well as form H-bonds)
48
aspartate stucture
[D] (Asp) - charged R group at pH 7 -second carboxyl group -acidic amino acid Very polar forms hydrogen bonds -H-bonds acceptor at pH called aspartic acid
49
glutamate stucture
[E] (Glu) - charged R group at pH 7 -second carboxyl group -acidic amino acid very polar forms hydrogen bonds (acceptor) at pH 1 called glutamic acid
50
Lysine stucture
[K] (lys) + charged side group at pH 7 -basic amino acid -side group contains an amino group -contains 2 primary amino groups alpha-amino group and the R group forms hydrogen bonds (donor) very polar
51
arginine structure
[R] (Arg) + charged side group at pH 7 -guanido group -basic amino acids -never deprotonated under physiological conditions very polar forms hydrogen bonds (donor)
52
residues
an amino acid in a peptide
53
cysteine pka
8.4
54
tyrosine pka
10.5
55
HISTIDINE pka
6.0
56
lysine pka
10.5
57
arginine pka
12.5
58
aspartate pka
3.9
59
glutamate pka
4.1
60
ionization state depends on
pH =complex acid/base titration curves
61
isoelctric point (pI)
pH at which the total charge of the amino acid (peptide or protein) is 0
62
for amino acids without ionizable side groups-
the pI is the average of the pkas
63
for amino acids with ionizable side groups, the pI is the
average of the 2 pkas bounding the molecular soecies with a net charge of 0
64
peptide bonds
covalent bond between amino acids formed in condensation reaction carboxylate group of residue 1 reacts with amine group of residue 2 form an amide bond allows for polymerization of amino acids into long peptides Linear polymers of amino acids have an amino (N) and carboxyl (C) terminus
65
what is a residue
an amino acid in a protein or polypeptide or peptide; a peptide unit
66
dipeptide/tripeptide
2/3 amino acid peptides
67
peptides
a short string of amino acids/ residues ~30 or less
68
polypeptides
longer polymers of residues: up to 33,000 residues or more
69
protein
one or more polypeptide chains

biochem (9 decks)

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