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BIOCHEMISTRY S.Y. 2022-2023 (LAB&LEC) FLASHCARDS > Amino Acids & Proteins (Lec) > Flashcards

Amino Acids & Proteins (Lec) Flashcards

1
Q

most abundant biomolecule in the cell

A

Proteins

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2
Q

polymers made of monomers

A

amino acids

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3
Q

atoms or small molecules that bond together to form more complex structures such as polymers

A

Monomers

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4
Q

four main types of monomer

A

sugars, amino acids, fatty acids, and nucleotides

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5
Q

a process by which a polypeptide chain folds to become a biologically active protein in its native 3D structure.

A

Protein folding

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6
Q

T/F - Proteins may be rigid or flexible to various degrees as required for optimum function

A

T

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7
Q

Number of peptides possible for a chain of n amino
acids

A

20^n (ex. 100 residue protein has 20^100)

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8
Q

Hierarchy of Protein Structure

the amino acid sequence

A

primary structure

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9
Q

Hierarchy of Protein Structure

frequently occurring substructures
or folds

A

secondary structure:

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10
Q

Hierarchy of Protein Structure

three-dimensional arrangement of all
atoms in a single polypeptide chain

A

tertiary structure

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11
Q

Hierarchy of Protein Structure

overall organization of non-covalently
linked subunits of a functional protein.

A

quaternary structure

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12
Q

tendency for non-polar solutes to aggregate in
aqueous solution to minimize the hydrocarbon-water
interface

A

Hydrophobic Effects [important in the binding of substrates (ligands) into protein receptors and enzymes]

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13
Q

RATIONALE BEHIND PROTEIN FOLDING

A

Proteins fold to minimize their surface contact with wate

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14
Q

hydrocarbon on the inside, polar group on the outside

A

micelle structure

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15
Q

unfolding of the native three-dimensional structure of a protein by chemical influences

A

Protein Denaturation

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16
Q

unfolding of the native three-dimensional structure of a protein by chemical influences

A

Protein Denaturation

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17
Q

Common secondary structures:

A

α-helix (amino acids wound into a helical structure)
β-sheet
β-turn
disulfide bonds

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18
Q

hydrophobic sidechains form an interface between
α-helices (de novo protein design)

A

Helical Bundles

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19
Q

covalent structural scaffolds, redox active, reversible

A

Disulfide bonds

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20
Q

FUNCTIONS OF PROTEIN (8)

A

Structural – for support (ex. collagen, elastin)

Catalytic – for hastening biochemical reactions (ex. amylase)

Storage – for storage of amino acids (ex. casein, ovalbumin)

Transport – for transport of other substances (ex. hemoglobin)

Regulation – for regulation of bodily activities (ex. insulin, glucagon)

Receptor – for response of cell to external stimuli (ex. neuron receptors)

Contractile – for movement (ex. myosin, actin)

Defensive – for protection against disease (ex.
antibodies)

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21
Q

a specific three-dimensional conformation that is essential for the biological function in proteins

A

Native conformation (3-D folded conformation with active function)

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22
Q

T/F - Loss of structure 🡪 loss of biological function

A

T

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23
Q

spatial arrangement of atoms in a protein

A

Conformation

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23
Q

building blocks or unit of proteins

A

amino acids

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24
Q

FOUR FEATURES OF AMINO ACIDS

A
  1. central/ α carbon atom linked to an amino group
  2. carboxyl group
  3. hydrogen atom/Amino group
  4. side chain (R group)
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25
Q

gives the amino acid a
unique identity and property

A

R group

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26
Q

T/F - Amino acids are chiral

A

T (chirality - existing in left and right-handed forms)

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27
Q

T/F - Amino acids can
exist as either the D or the L isomer (orientations that are mirror image of each other)

A

T (Most amino acids exist in nature in
the L isomer.)

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28
Q

the only cyclic amino acid

A

Proline (Usually a D isomer; does not have both free α-amino and free α-carboxyl groups)

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29
Q

the only achiral amino
acid

A

Glycine (has a hydrogen atom as its sidechain)

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30
Q

T/F - Proteins can be differentiated and classified according to type of side chain, R group

A

T (it specifies which class of amino acids it belongs to)

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31
Q

Non-polar amino acids (9): - hydrophobic

A

glycine (Gly; G)

alanine (Ala; A)

leucine (Leu; L)

isoleucine (Ile; I)

proline (Pro; P)

tryptophan (Trp; W)

valine (Val; V)

phenylalanine (Phe; F)

methionine (Met; M)

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32
Q

Polar amino acids (6): - hydrophilic

A

serine (Ser; S)

threonine (Thr; T)

cysteine (Cys; C)

tyrosine (Tyr; Y)

asparagine (Asn; N)

glutamine (Gln; Q)

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33
Q

Basic amino acids (3): - positively charged, hydrophilic amino acids

A

lysine (Lys; K)

arginine (Arg; R)

histidine (His; H)

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33
Q

Acidic amino acids (2): - negatively charged, hydrophilic amino acids

A

aspartic acid (Asp; D)

glutamic acid (Glu; E)

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34
Q

Amino acids that the body can synthesize

A

nonessential amino acids (11)

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35
Q

amino that the body cannot synthesize either at all or in sufficient amounts, must also be obtained from the diet.

A

essential amino acids (9)

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36
Q

T/F - The nutritional value of a protein is dependent on what amino acids it contains and in what quantities.

A

T

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37
Q

nonessential amino acids (11)

A

alanine
arginine
asparagine
aspartic acid
cysteine
glutamic acid
glutamine
glycine
proline
serine
tyrosine

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38
Q

essential amino acids (9)

A

histidine
isoleucine
leucine
lysine
methionine
phenylalanine
threonine
tryptophan
valine

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39
Q

T/F - With the exception of Glycine, all protein-derived amino acids have at least one stereocenter (the α-carbon) and are chiral

A

T

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40
Q

uncommon amino acids (2)

A

Hydroxylysine

hydroxyproline

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41
Q

aromatic amino acids (3)

A

phenylalanine

tryptophan

tyrosine

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42
Q

T/F - Amino acids are AMPHOTERIC

A

T - they can either
accept or donate a proton.

43
Q

T/F - Amino acids may act as weak acids and bases within an
aqueous environment

A

how they react depends on the pH of
their environment

44
Q

T/F - at low pH, ionizable groups tend to be protonated; at high pH, they tend to be deprotonated

A

T

45
Q

a number that shows how weak or strong an acid is

A

pKa (The lower the value of pKa, the stronger the acid and the greater its ability to donate its protons)

46
Q

T/F - Under the physiological pH range (6.8-7.4), amino acids are
zwitterions, or dipolar ions.

A

T

47
Q

hybrid, neutral molecule with positive and
negative charges

A

zwitter

48
Q

Net charge of the molecule

A

zero [attained when they reach the ISOELECTRIC
pH (pI)]

49
Q

pH at which zwitterion form predominates

A

Isoelectric point

50
Q

Acidity and Basicity of Amino Acids

Ex. Alanine

A

Acid solution less than 2 = net charge: +1

Neutral solution pH approximately 6 = net charge: 0/isoelectric form

Basic solution pH greater than 10 = net charge: -1

51
Q

Dissociation of the hydrogen:

A

at low pH, both of the amino and carboxyl
groups are fully protonated. As the pH of the solution is raised, the –COOHgroup of Form I can ionize and donate H+
to the medium. The release of the
proton results to carboxylate group, -COO-. The Form II then has a net charge of zero.

52
Q

The workhorses of
biological systems

A

peptide bonds (amide bonds that
join amino acids together)

53
Q

Peptide bond formation is
accompanies by the loss of

A

H2O

54
Q

formed between the carboxyl group of an amino acid
and the amino group of another

A

Peptide bonds

55
Q

planar, rigid and
have partial double bond character.

A

Peptide bonds

56
Q

By convention, peptides
are written from what direction

A

left to right (N to C)

57
Q

beginning of the protein where the free –NH3 + group is located

A

N-terminal end

58
Q

end of the protein where the –COO group is located

A

C-terminal end

59
Q

Levels of structural organization of proteins (4)

A

Primary
Secondary
Tertiary
Quaternary

60
Q

T/F - Most natural polypeptide chains
contain between 50 and 2000 amino
acid residues and are commonly
referred to as proteins.

A

T

61
Q

the amino acid sequence of a protein
from N to C-terminal that determine the 3-D structures

A

Primary Structure

62
Q

primary structure can be obtained through a lab
technique called

A

Sequencing

63
Q

changes to an amino acid with similar properties

A

Conservative replacement

64
Q

ex. of diseases with alterations of the primary structure leading to abnormal protein function

A

Sickle Cell Disease (abnormal form of hemoglobin)

65
Q

The local structure of neighboring
amino acids

A

Secondary Structure (ordered arrangements
in localized regions)

66
Q

the result of intramolecular
hydrogen bonding

A

Secondary Structure

67
Q

Refers only to interactions of the
peptide backbone.

A

Secondary Structure

68
Q

Most common secondary structures

A

a-helix and b-pleated sheet

69
Q

Formed and stabilized by _____
bond between the amide proton and
carbonyl oxygen

A

hydrogen
bond

70
Q

CHARACTERISTICS OF ALPHA-HELIX

A

Spiral structure
Structural features: C=O of each peptide bond is
hydrogen bonded to the N-H of the fourth amino acid
away; there are 3.6 aa/turn
Pitch: 0.54nm
All R groups point outward from helix
Example: Keratin
Bulkiness (steric strain) between adjacent R-groups
Coil is clockwise

71
Q

introduces kinks/bends to the structure, restricted movement, no H bonding

A

Helix Destabilizers - Proline and Glycine

72
Q

strong helix formers

A

small hydrophobic residues (e.g. Ala, Leu)

73
Q

CHARACTERISTICS OF BETA-PLEATED SHEETS

A
  • form when two or more polypeptides line up side-by-side
    stabilized by hydrogen bonds of adjacent polypeptide
    chains (interchain or intrachain)
  • β-strands are extended into a zigzag
  • All R groups extend above or below the sheet in an
    alternating up and down direction
74
Q

TYPES OF BTA-PLEATED SHEETS (2)

A

PARALLEL β-Pleated Sheets
- Run in same directions
- Forms bent H-Bonds (weaker)

ANTI-PARALLEL β-Pleated Sheets
- Run in opposite directions
- Forms linear H-Bonds (stronger)

75
Q

3-D arrangement of all atoms

A

Tertiary Structures

76
Q

T/F - Noncovalent interactions stabilize
the higher levels of protein structure.

A

T

77
Q

T/F - Secondary, tertiary, and quaternary
structure of proteins is formed and
stabilized by weak forces

A

T

78
Q

T/F - Hydrophobic residues prefer to be on
the interior of proteins, which reduces their
proximity to water

A

T

79
Q

T/F - globular proteins fold with a hydrophobic core and a hydrophilic exterior.

A

T

80
Q

the interactions of these drive
protein folding

A

Tertiary Structure:

Hydrophilic &
Hydrophobic
Interactions

81
Q

Acid-base interactions
between amino acids with
charged groups can occur,
also known as salt bridges

A

Tertiary Structure

Electrostatic
Interactions

82
Q

Cysteine residues can
undergo oxidation to
form disulfide bridges, or
cystine. They create
loops in protein chains
and dictate how curly
hair is.

A

Tertiary Structure

Covalent
Bonding

83
Q

Tertiary Structure

Contain polypeptide chains
organized approximately parallel
along a single axis

A

Fibrous Proteins

84
Q

Consists of long fibers or large
sheets, tend to be mechanically
strong

A

Fibrous Proteins

85
Q

Insoluble in water and dilute salt
solutions, and play important
structural roles

A

Fibrous Proteins (ex. Keratin is found in hair, wool, and
nails. Collagen is found in cartilage,
bones, and skin)

86
Q

Tertiary Structure

Proteins that are folded into a spherical
shape

A

Globular Proteins

87
Q

Most of its polar side chains are on the
outside; nonpolar side chains buried
inside the structure

A

Globular Proteins

88
Q

Soluble in water; Function: metabolic (catalytic,
transport, etc.)

A

Globular Proteins

89
Q

Nearly have all substantial sections
of α-helix and β-sheet

A

Globular Proteins

90
Q

association of polypeptide chains into
aggregations

A

Quaternary Structure

91
Q

formed by the assembly of individual polypeptides
(subunit/monomer) into a larger functional cluster

A

Quaternary Structure

92
Q

its subunits are stabilized by non-covalent interactions (like
tertiary structure)

A

Quaternary Structure

93
Q

ROLES OF THE FORMATION OF QUARTERNARY STRUCTURES

A
  • more stable (by further reducing the surface area of the protein complex)
  • reduce the amount of DNA needed to encode the protein complex
  • bring catalytic sites close together (allowing intermediates from one reaction to be directly shuttled to a second reaction)
  • can induce cooperativity, or allosteric effects
94
Q

Disrupts the secondary, tertiary, and quaternary structures

A

Denaturating Agents (Physical Agents & Chemical Agents)

95
Q

Physical Agents (4)

A

High temperature
Vigorous shaking or agitation
Hydrostatic pressure
UV radiation

96
Q

Chemical Agents (6)

A

Change in pH
Change in ionic strength
Organic solvents (e.g. urea, alcohol)
Reducing agents (e.g. performic acid and mercaptoethanol)
Detergents
Salts of heavy metals

97
Q

Hydrogen bonds are most important in this type of structure in proteins:

a. primary structure
b. secondary structure
c. tertiary structure
d. quaternary structure
e. all of these

A

b. secondary structure

98
Q

derive part of their function from covalently-attached molecules called prostehtic groups

A

Conjugated Proteins

99
Q

proteins with
lipid prosthetic groups

A

Lipoproteins

100
Q

proteins with
carbohydrate prosthetic
groups

A

Glycoprotein

101
Q

proteins
with nucleic acid prosthetic
groups

A

Nucleoprotein

102
Q

Cell to cell recognition, depending on blood type of prosthetic groups

A

Glycoproteins

103
Q

ability for all quaternary structures to help or work each other/together

A

Cooperativity

104
Q

Helix Destabilizers (3):

A

Presence of helix breakers
(Proline and Glycine)
* However, small hydrophobic
residues (e.g. Ala, Leu) are strong
helix formers

  • Electrostatic repulsion (or
    attraction) between successive
    charged aa residues.
  • Bulkiness (steric strain)
    between adjacent R-groups
105
Q

T/F - Amino acids cannot share one letter codes.

A

T

106
Q

T/F - Amino acids cannot share one letter codes.

A

T

107
Q

T/F - Trypsin is NOT an amino acid, it is a protein with an enzymatic function

A

T

BIOCHEMISTRY S.Y. 2022-2023 (LAB&LEC) FLASHCARDS (9 decks)

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