MCAT > Biochem Chapter 1 > Flashcards

Biochem Chapter 1 Flashcards

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1
Q

What’s determines chemical properties in amino acids

A

The side chain , R groups

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2
Q

Amino acids have 2 functional groups, what are they

A

Amino - NH2
Carboxyl group - COOH

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3
Q

What are the 20 amino acids encoding our human genetic code called

A

Protein organic amino acids

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4
Q

The only amino acid that is optically inactive and does not have a chiral centre is

A

Glycine

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5
Q

All Amin acids have what configuration except which one

A

They all are S amino acids
Except cysteine which has R configuration

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6
Q

What does it Ean when amino acids mainly have L configuration, which side is NH2 on

A

Left usually

And COOH on top

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7
Q

How many amino acids are nonpolar, non aromatic side chains

A

7

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8
Q

Whcih amino acids are nonpolar, non aromatic side chains

A

Glycine
Leucine
Isoleucine
Valine
Alanine
Methionine
Proline

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9
Q

What is something special methionine has attached to it

A

Sulphur

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10
Q

Why is proline unique

A

Cyclic amino acid

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11
Q

What are the 3 Amino acids that have uncharged aromatic side chains

A

Tryptophan
Phenylalanine
Tyrosine

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12
Q

Is tyrosine polar or non polar and why

A

It’s basically phenylalanine with an OH, so this one is polar

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13
Q

Which 5 Amino acids have polar side chains

A

Serine
Threonine
Asparagine
Glutamine
Cysteine

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14
Q

What is the side chain for cysteine

A

Thiol (SH)

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15
Q

Which 2 Amino acids have negatively charged side chains

A

Aspartic acid (Aspartate)
Glutamic acid (Glutamate)

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16
Q

What does it mean by negatively charged side chains
Are they acidic or basic

A

Acidic

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17
Q

Most acids in cells exist in protonated or deprotonated form

A

Deprotonated

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18
Q

What are positively charged side chains
Acidic or basic

A

Basic

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19
Q

Which 3 amino acids have postitively charged side chains

A

Lysine
Histidine
Arginine

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20
Q

Histidine’s aromatic ring is called

A

Imidazole

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21
Q

How does long alkyl side chains affect if amino acid is hydrophilic or hydrophobic

Where they found ( in or out of proteins )

A

Long chain is strongly hydrophobic

Found in interior of proteins, away from water on protein surface

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22
Q

All Amino acids with positively or negatively charged side chains, are they hydrophilic or hydrophobic

Where can they be found

A

They are hydrophilllic

Going on surface of protein

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23
Q

Alanine abbreviation 1 letter and 3 letter

A

Ala A

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24
Q

Arginine abbreviation 1 letter and 3 letter

A

Arg R

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25
Asparagine abbreviation 1 letter and 3 letter
Asn N
26
Aspartuc acid abbreviation 1 letter and 3 letter
Asp D
27
Cysteine abbreviation 1 letter and 3 letter
Cys C
28
Glutamic acid abbreviation 1 letter and 3 letter
Glu E
29
Glutamine abbreviation 1 letter and 3 letter
Gln Q
30
Glycine abbreviation 1 letter and 3 letter
Gly G
31
Histidine abbreviation 1 letter and 3 letter
His H
32
Isoleucine abbreviation 1 letter and 3 letter
IIe I
33
Leucine abbreviation 1 letter and 3 letter
Leu L
34
Lysine abbreviation 1 letter and 3 letter
Lys K
35
Methionine
Met M
36
Phenylalanine abbreviation 1 letter and 3 letter
Phe F
37
Proline abbreviation 1 letter and 3 letter
Pro P
38
Serine abbreviation 1 letter and 3 letter
Serine S
39
Threonine abbreviation 1 letter and 3 letter
Thr T
40
Tryptophan abbreviation 1 letter and 3 letter
Trp W
41
Tyrosine abbreviation 1 letter and 3 letter
Tyr Y
42
Valine abbreviation 1 letter and 3 letter
Val v
43
At low Ph and High ph, do ionaizable compounds protontate or deprotonated
Low - protonated High - deprotonated
44
If pH is less than pKa, majority of species will be protonated or deprotonated
protonated
45
All amino acids have how many pKA
At least 2 because they have at least 2 groups that can be deprotonated
46
What are teh usual PKA values of amino acids
The carboxyl group is usually 2 The amino group is usually 9-10
47
How many ionizable side chains does glycine have
0
48
Why are amino acids usually positively charged in acidic pH
Because strong acid lets say is about 1. Then PKa of COOH and NH2 is higher than that, so because pH is lower than PKA, majority of the species will be protonated.
49
At intermediate pH , lets say about 7, how are amino acids protonation What are these called
The PKa of COOh is now lower than the pH So COOH chain will be deprotonated, and NH2 ones will be protonated. The molecule has positive and negative charge, but overall neutral ZEITTERIONS - HYBRIDS
50
What do amino acids do under basic conditions in terms of protonation
So pH lets say is 12 It is above the PKA of COOH and NH2 so they are both deprotonated Negatively charged now
51
What criteria is needed for a solution to be a buffer
PH of solution is about the same as PKa of solute
52
What is isoelectric point of an amino acid
PH at which the molecule is electrically neutral
53
For amino acids with no ionizable side chains the isoelectric point (pI) is
6
54
How do you calculate isoelectric point (pI) values for neutral amino acids
The first pKa value of NH group+ second PKa value of COOh group divided by 2
55
Among NH3 and COOH, which gets deprotonated frist
COOH first
56
How do you calculate the isoelectric point (PI) for acidic charged amino acids
PKa for the R group + PKa for teh COOh group / 2
57
How do you calculate the isoelectric point (PI) for basic charged amino acids
PKa for the NH3 group + PKa for the R group / 2
58
Amino acids with acidic and basic side chains have what type of pI values
Acidic is below 6 Basic is above 6
59
What is released during peptide bond formation
Water
60
In peptide bonds what is the N terminus and C terminus
N - amino end C-carboxy terminus
61
How are peptide bonds drawn from left to right , which terminus is it
Left N terminus to right C terminus
62
Where does trypsin cleave on amino acids
Carboxyl end of arginine and lysine
63
Where deos chymotrypsin cleave at amino acids
Carboxyl end of phenylalanine,, tryptophan and tyrosine
64
What are teh 4 levels of structures of proteins
Primary Secondary Tertiary Quaternary
65
What is the primary structure of a protein mean
The order of its amino acids
66
What is the secondary structure of amino acids Also what are the 2 common types of amino
Local folding that happens in neighbouring amino acids Due to hydrogen bonding Alpha helix and beta pleated sheets
67
What is alpha helix
Rodlike structure in which the peptide chain coils clockwise around a central axis
68
What is beta pleated sheets
Peptide chains lie alongside one another, forming rows or strands held together by hydrogen bonds
69
Alpha helix is the most important component in which structure
Keratin
70
Are beta pleated sheets parallel or anti parallel
Both
71
What is the Beta sheets the main component of
Fibroin
72
What role does proline serve in secondary structure
It’s rigid structure introduces kinks in the alpha helix and turns in beta pleated sheets
73
What are primary structure and secondary structure stabilizing bonds
Primary - peptide bonds Secondary - hydrogen bonding
74
In alpha helix, the hydrogen bond is between what and what
Carbonyl oxygen and amide hydrogen
75
In Beta sheets, the hydrogen bond is between what and what
Carbonyl oxygen atom and amide hydrogen atoms
76
How are the tertiary structure of a protein resulted
Result of moving hydrophobic amino acid side chains into the interior of the protein
77
Proline in a sequence signals what
A fold or a turn
78
What is tertiary structure of protein
The 3d shape of the protein
79
What is an important component of tertiary structure of proteins, like what bonds What does it do and for which amino acid
Disulfide bonds when 2 cysteine molecules come together to form cystine Extra stability
80
How do disulfide bonds relate to hair
They create loops in protein chain So the more disulfide bonds you have in your hair, the curlier it is
81
Forming a sullied bond requires the loss of which 2 things What type of reaction is this
2 protons and 2 electrons Oxidation
82
If a molecule loses tertiary structure it is called
Denaturation
83
Intermediate state during tertiary structures is called
Molten globules
84
What is the reason hydrophobic residues go interior of protein, and hydrophillic goes to surface
Entropy
85
Quaternary structures advantages
Increase stability Less DNA to encode protein complex Improve catalytic efficiency by bringing sites closer Cooperative or allosteric factors, better binding
86
Quaternary structure only found in
Proteins that have more than one polypeptide chain
87
Hemoglobin and immunoglobulin are what structures
Quaternary
88
Conjugated proteins deprive part of their function from cavoalenty attached molecules called
Prosthetic groups
89
Proteins with lipid carb and nucleic acid prosthetic groups are called
Lipoproteins Glycoproteins Nucleoproteins
90
How does the entropy get affected in hydrophobic interactions Gibbs free energy Entropy
Hydrophobic interactions push hydrophobic R groups to the interior of a protein, it increases entropy of surrounding water molecule and creates negative Gibbs free energy
91
Is denaturation of protein reversible
Usually irreversible
92
What are 2 main causes of denaturation
Heat and solutes
93
How deos heat denatures proteins
Increase kinetic energy and disrupting hydrophobic interaction
94
How deos solutes denature proteins
Disrupting elements of secondary,tertiary and quaternary structure.
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