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Amino Acids Flashcards

1
Q

How many letter words form the 20 unique letter

A

3 letter words( composed of 4 unique letters)

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2
Q

What are the main agents of protein

A

Catalysis
Transport
Structure
Motion

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3
Q

Example of protein acting as a catalysis

A

DNA polymerase in DNA replication
Enolase ( in glycolytic pathway)

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4
Q

Example of protein acting as a transport

A

hemoglobin (transporting oxygen in the blood)
Lactose permease (transports lactose across cell membrane)

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5
Q

Example of protein acting as a structure

A

collagen (connective tissue)
keratin ( hair, nails, feathers)

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6
Q

Example of protein acting as a motion

A

myosin (muscle tissue)
actin (muscle tissue, cell motility)

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7
Q

What are the general structure of protein

A

linear hetero-polymers of alpha amino acids

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8
Q

Proteins consist of amino acid linked by

A

peptide bonds

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9
Q

Each amino acid consists of

A

central carbon atom
amino group
carboxyl group
R side chain

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10
Q

What distinguishes each amino acid and their properites

A

R group

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11
Q

Most alpha amino acids are achiral/chiral

A

chiral (L & D isomer)

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12
Q

When you have the amino group on the right hand side which isomer is that

A

D isomer

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13
Q

When you have the amino group on the left hand side which isomer is that

A

L isomer

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14
Q

Most amino acid are kept in which isomer

A

L amino acid

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15
Q

Which amino acid is achiral

A

Glycine

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16
Q

How do you name amino acid in biochemistry

A

start from alpha carbon down to R-group

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17
Q

How do you identify an R group

A

name, three-letter code, one letter symbol

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18
Q

How many and what are the basic groups of amino acid based on R substituent

A

(5)
Non polar, aliphatic
Aromatic
Polar, uncharged
Positively charged
Negatively charged

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19
Q

Where in a protein would positively and negatively charged R groups be placed

A

on the outside

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20
Q

Where in a protein would you want to place an aromatic protein placed

A

inside, some are hydrophobic

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21
Q

What are the nonpolar Aliphatic side chain

A

Glycine
Alanine
Proline
Valine
Leucine
Isoleucine
Methionine

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22
Q

Why is Glycine the only group that is achiral

A

because it has an Hydrogen on the R group sid e

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23
Q

Which amino acid is not actually an amino acid but an IMINOacid

A

Proline, because of the ring structure

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24
Q

What are aromatic R groups

A

Phenylalanine
Tyrosine
Tryptophan

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25
What range do amino acid absorb UV light
270-280 nm
26
What structure allow amino acid to absorb light
Aromatic structure
27
WHich absorb more light phenylalamine , tryptophan
tryptophan absorb more light because they have a bigger ring
28
What are the polar uncharged R group
Serine Threonine Cysteine Asparagine Glutamine
29
what group does cysteine have
sulfur group
30
WHat bonds can the side chain of polar uncharged R group amino acid form
hydrogen bonds
31
oxidation of 2 cysteine molecules forms
a disulfide bond
32
What are the positively charged R group
Lysine Arginine Histidine
33
What are the negatively charged R group
Aspartate Glutamate
34
At the acidic pH, what is the ionization of carboxyl and amino acid
carboxyl is protonated, amino acid is in cationic form
35
At the neutral pH, what is the ionization of carboxyl and amino acid
carboxyl group is deprotonated, amino acid is protonated
36
What is the net charge of carboxyl and amino group at neutral pH? what are ions called
zero, zwitterions
37
At the alkaline pH, what is the ionization of carboxyl and amino acid
amino group is neutral, amino acid is in anionic form
38
when is an amino acid fully protonated
pH < pKa
39
What is the charges when fully protonated
NH3+, COOH
40
when is an amino acid half protnated/half deprotonated
pH=pKA
41
What is the charges when half protonated/half deprotonated
NH3+/NH2, COOH/COO-
42
When is an amino acid fully deprotonated
pH>pKa
43
What is the charge when fully deprotonated
NH2, COO-
44
What is the order of deprotonation in amino acid
Carboxyl group, R group, amino acid
45
is amino acid more /less soluble in water at isoelectric point
less soluble
46
Does amino acid migrate in electric field at isoelectric point? True/ false
True
47
What are the amino acid that are ionizable? know structures
Tyrosine Cysteine Lysine Histidine Arginine Glutamate Aspartate
48
How are peptides formed
condensation products of amino acids
49
Pepides are written in which orientation
left to right (N to C terminus)
50
10 to 100 amino acids are called
polypeptides
51
2 to 10 amino acids are called
dipeptide to decapeptide
52
>100 amino acids
proteins
53
several identitcal polypeptides
homoologomeric
54
several different polypeptides
heterrooligomeric
55
3 polypeptides are known as
trimer
56
average molecular weight of an amino acid rsidue in a peptide is
110
57
pkas can change depending on chemical environment in their immedicate vicinity TRUE/FALSE
TRUE
58
Many proteins (especially enzymes) require associated chemical constituesnts for function. This are called ?
cofactor
59
If the cofactor is attached covalently, the result is a
conjugated protein
60
The attached group in a conjugated protein is callled
prosthetic group
61
What is the first step of many analyses is usually
purification
62
Why do you purify protein
- determine its properties -structural studies -sequence analysis -pharmaceuticals
63
How do you divide and conquer in purofocation
fractionation
64
Ways to fractionate
1. Ammonium sulfate precipitation (salting out) 2. Column chromatography
65
How can a mixture of protein can be seperated
charge, size, affinity for a ligand, solubility, hydrophobicity, thermal stability
66
What is commonly used for preparative seperation
chromatography
67
In separation of charge, how can you use a resin?
the resin can have the opposite charge of what you are trying to seperate
68
How can we seperate by size?
the stationary phase has the smaller protein in polymer beads, so bigger protein comes out first
69
How can u seperate by affinity
the protein of interest binds to the ligand which seperates out the unwanted protein
70
Do you lose/gain protein with every stepyou carry out
you lose protein
71
What is the relationship with total protein and specific activity
as total protein goes down in mg then more protein goes up in specific activity
72
What is ur goal with protein purification
to maximize specific activity while losing as little protein as possible
73
When do you know when protein purification is complete
electrophoresis
74
Function of SDS page
alows seperation based on size only negates differences in mass/charge between different protein
75
How can isoelectric focusing be used to determine the pl of a protein
* sample applied to an ampholyte containing gel * when field applied, protein moved to the pH that matches their pL * at its pl, the protein has a net 0 charge and thus won't move further
76
In 2D electrophoresis what 2 things are combined
isoelectric focusing and SDS-Page
77
how do they do protein sequencing
sanger method or edman degradation
78
What labelling material was used in Sanger method
HCL
79
differences between sanger and edman degradation
uses lesser toxic reagant so reaction can continue
80
Edman degradation is good for how many amino acid
50
81
if you have more thann 50 amino acids, how do you sequence them
1. break it up into smaller pieces 2. sequence the small pieces 3. assemble resulting sequences to get full length
82
these days, what method is used for protein ID
mass spectrometry
83
Synthesis in peptide proceed in which direction
C to N terminal direction

Biochemistry (16 decks)

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