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Biochemistry > Amino Acids > Flashcards

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
Q

What range do amino acid absorb UV light

A

270-280 nm

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26
Q

What structure allow amino acid to absorb light

A

Aromatic structure

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27
Q

WHich absorb more light phenylalamine , tryptophan

A

tryptophan absorb more light because they have a bigger ring

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28
Q

What are the polar uncharged R group

A

Serine
Threonine
Cysteine
Asparagine
Glutamine

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29
Q

what group does cysteine have

A

sulfur group

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30
Q

WHat bonds can the side chain of polar uncharged R group amino acid form

A

hydrogen bonds

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31
Q

oxidation of 2 cysteine molecules forms

A

a disulfide bond

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32
Q

What are the positively charged R group

A

Lysine
Arginine
Histidine

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33
Q

What are the negatively charged R group

A

Aspartate
Glutamate

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34
Q

At the acidic pH, what is the ionization of carboxyl and amino acid

A

carboxyl is protonated, amino acid is in cationic form

35
Q

At the neutral pH, what is the ionization of carboxyl and amino acid

A

carboxyl group is deprotonated, amino acid is protonated

36
Q

What is the net charge of carboxyl and amino group at neutral pH? what are ions called

A

zero, zwitterions

37
Q

At the alkaline pH, what is the ionization of carboxyl and amino acid

A

amino group is neutral, amino acid is in anionic form

38
Q

when is an amino acid fully protonated

A

pH < pKa

39
Q

What is the charges when fully protonated

A

NH3+, COOH

40
Q

when is an amino acid half protnated/half deprotonated

A

pH=pKA

41
Q

What is the charges when half protonated/half deprotonated

A

NH3+/NH2, COOH/COO-

42
Q

When is an amino acid fully deprotonated

A

pH>pKa

43
Q

What is the charge when fully deprotonated

A

NH2, COO-

44
Q

What is the order of deprotonation in amino acid

A

Carboxyl group, R group, amino acid

45
Q

is amino acid more /less soluble in water at isoelectric point

A

less soluble

46
Q

Does amino acid migrate in electric field at isoelectric point? True/ false

A

True

47
Q

What are the amino acid that are ionizable? know structures

A

Tyrosine
Cysteine
Lysine
Histidine
Arginine
Glutamate
Aspartate

48
Q

How are peptides formed

A

condensation products of amino acids

49
Q

Pepides are written in which orientation

A

left to right (N to C terminus)

50
Q

10 to 100 amino acids are called

A

polypeptides

51
Q

2 to 10 amino acids are called

A

dipeptide to decapeptide

52
Q

> 100 amino acids

A

proteins

53
Q

several identitcal polypeptides

A

homoologomeric

54
Q

several different polypeptides

A

heterrooligomeric

55
Q

3 polypeptides are known as

A

trimer

56
Q

average molecular weight of an amino acid rsidue in a peptide is

A

110

57
Q

pkas can change depending on chemical environment in their immedicate vicinity TRUE/FALSE

A

TRUE

58
Q

Many proteins (especially enzymes) require associated chemical constituesnts for function. This are called ?

A

cofactor

59
Q

If the cofactor is attached covalently, the result is a

A

conjugated protein

60
Q

The attached group in a conjugated protein is callled

A

prosthetic group

61
Q

What is the first step of many analyses is usually

A

purification

62
Q

Why do you purify protein

A
  • determine its properties
    -structural studies
    -sequence analysis
    -pharmaceuticals
63
Q

How do you divide and conquer in purofocation

A

fractionation

64
Q

Ways to fractionate

A
  1. Ammonium sulfate precipitation (salting out)
  2. Column chromatography
65
Q

How can a mixture of protein can be seperated

A

charge, size, affinity for a ligand, solubility, hydrophobicity, thermal stability

66
Q

What is commonly used for preparative seperation

A

chromatography

67
Q

In separation of charge, how can you use a resin?

A

the resin can have the opposite charge of what you are trying to seperate

68
Q

How can we seperate by size?

A

the stationary phase has the smaller protein in polymer beads, so bigger protein comes out first

69
Q

How can u seperate by affinity

A

the protein of interest binds to the ligand which seperates out the unwanted protein

70
Q

Do you lose/gain protein with every stepyou carry out

A

you lose protein

71
Q

What is the relationship with total protein and specific activity

A

as total protein goes down in mg then more protein goes up in specific activity

72
Q

What is ur goal with protein purification

A

to maximize specific activity while losing as little protein as possible

73
Q

When do you know when protein purification is complete

A

electrophoresis

74
Q

Function of SDS page

A

alows seperation based on size only
negates differences in mass/charge between different protein

75
Q

How can isoelectric focusing be used to determine the pl of a protein

A
  • 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
Q

In 2D electrophoresis what 2 things are combined

A

isoelectric focusing and SDS-Page

77
Q

how do they do protein sequencing

A

sanger method or edman degradation

78
Q

What labelling material was used in Sanger method

A

HCL

79
Q

differences between sanger and edman degradation

A

uses lesser toxic reagant so reaction can continue

80
Q

Edman degradation is good for how many amino acid

A

50

81
Q

if you have more thann 50 amino acids, how do you sequence them

A
  1. break it up into smaller pieces
  2. sequence the small pieces
  3. assemble resulting sequences to get full length
82
Q

these days, what method is used for protein ID

A

mass spectrometry

83
Q

Synthesis in peptide proceed in which direction

A

C to N terminal direction

Biochemistry (16 decks)

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