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Biochem > Basic Concepts, Amino Acids, Proteins > Flashcards

Basic Concepts, Amino Acids, Proteins Flashcards

1
Q

Milli-

A

10__

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2
Q

Micro-

A

10__

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3
Q

Nano-

A

10__

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4
Q

M

A

mol/L

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5
Q

%

A

weight/volume (usually g/dL)

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6
Q

Equivalent

A

available charges of the particular ion

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7
Q

Units of activity

A

Defined in terms of some effect

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8
Q

Osmolarity

A

moles of solute particles in a solution

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9
Q

Henderson-Hasselbach

A

pH= pKa + log ([A_]/[HA])

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10
Q

α-amino acids

A
  • Carboxylic acid with amine group on the α-carbon
  • R-groups change (most are L-amino acids)
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11
Q

Non Polar Aliphatic Amino Acids

A

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine

(GAP, LIV)

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12
Q

Glycine

A

Gly

Non Polar aliphatic

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13
Q

Alanine

A

Ala

Non polar Aliphatic

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14
Q

Proline

A

Pro

Non Polar Aliphatic

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15
Q

Valine

A

Val

Non Polar Aliphatic

Branched Chain

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16
Q

Leucine

A

Leu

Non polar Aliphatic

Branched Chain

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17
Q

Isoleucine

A

Ile

Non polar Aliphatic

Branched chain

most hydrophobic (charges are very balanced)

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18
Q

Aromatic Amino Acids

A

Phenylalanine, Tyrosine, Tryptophan

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19
Q

Phenylalanine

A

Phe

Aromatic

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20
Q

Tyrosine

A

Tyr

Aromatic

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21
Q

Tryptophan

A

Trp

Aromatic

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22
Q

Polar, Uncharged Amino Acids

A

Asparagine, Glutamine, Serine, Threonine

Typically found on the surface

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23
Q

Asparagine

A

Asn

Polar/Uncharged

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24
Q

Glutamine

A

Gln

Polar, uncharged

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25
Q

Serine

A

Ser

Polar, uncharged

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26
Q

Threonine

A

Thr

Polar, uncharged

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27
Q

Sulfur-containing Amino Acids

A

Methionine, Cysteine

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28
Q

Methionine

A

Met

Sulfur-containing

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29
Q

Cysteine

A

Cys

Sulfur-containing, so can form disulfide bonds

Cystine = 2 cysteines bound by disulfide bond

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30
Q

Negatively charged Amino Acids

A

Aspartate, Glutamate

Acidic Amino Acids

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31
Q

Positively Charged Amino Acids

A

Arginine, lysine, histidine

Basic amino acid

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32
Q

Aspartate

A

Asp

Negatively charged (acidic)

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33
Q

Glutamate

A

Glu

Negatively charged (acidic)

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34
Q

Arginine

A

Arg

Positively charged (basic)

Most hydrophilic (very polar)

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35
Q

Lysine

A

Lys

Positive charge (basic)

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36
Q

Histidine

A

His

Positively charged (basic)

37
Q

Hydropathy

A

How hydrophilic/phobic an anima acid is

38
Q

pI

A

The pH at which the net charge on an amino acid is 0

39
Q

Selenocysteine

A
  • Modification fo a serine bound to a unique tRNA to selenocycteine
  • Found in a few enzymes, where it is essential for activity
40
Q

Types of amino acid modifications

A
  • Carbohydrate addition
  • Lipid addition (can anchor to protein membrane or be involved in regulation)
  • Regulation
41
Q

O-glycosylation

A

Occurs on the OH of ser, thr, tyr

Carbohydrate addition

42
Q

N-glycosylation

A

Occurs on the NH2 of asn

Carbohydrate addition

43
Q

Palmitoylation

A

Occurs on the internal SH of cys

Lipid addition

44
Q

Myristolation

A

Occurs on the NH of the N-terminal of gly

Lipid addition

45
Q

Prenylation

A

Occurs on the Sh of cys

Lipid addition

46
Q

Phosphorylation

A

Occurs on the OH of ser, thr, tyr

is reversible

47
Q

Acetylation

A

Occurs on the NH2 of lys (N-terminus)

Reversible

48
Q

ADP-ribosylation

A

Occurs on the N of arg, gln, cys

Reversible

49
Q

Carboxylation

A

Turns gutamyl residues into Ɣ-carboxylglutamyl residues

50
Q

Oxidation

A

Pro/lys into hydroxylpro/hydroxylys

51
Q

Peptide bond

A
  • Bond b/t the α-carboxyl grp of 1 AA and the α-amino group of another AA
  • Is planar
  • Adjacent R-groups are almost always trans
52
Q

Proteins

A

linear polymers of α-amino acids bound together by peptide bonds

53
Q

Primary structure of proteins

A
  • Amino acyl sequence of proteins
  • N-terminal = amino
  • C-terminal = carboxyl
54
Q

Polymorphism

A
  • genetic variation with a species
  • Can produce a variation in phenotype which could be deleterious
55
Q

Developmental variaion

A
  • Different protein isoforms/isozymes may be expressed at different developmental stages of an organism
  • Ex: HbF, HbA, and other hemoglobins
56
Q

Tissue-specific Isoforms

A
  • Different protein isoforms/isozymes are expressed simulteneously in one organism, but are restricted to different tissues
  • Ex: creatine kinase isozymes and lactate dehydrogenase isozymes
57
Q

Secondary Structures

A

Recurring, localized structures found within regions of a poly peptide chain

58
Q

Alpha – Helix

A
  • Helical structure stabilized by hydrogen bonds (b/t amino and carboxyl O atom of 2nd AA 4 residues down the chain)
  • AA R-group projects outward from the axis of the helix
  • Proline cannot be a part of a α-helix
59
Q

Beta-Pleated Sheet

A
  • somewhat planar surface stabilized by H-bonds b/t amide hydrograns and carboxyl Os
  • AA R-groups are perpendicular to the plane of the sheet
  • surfaces formed by β-sheets are often twisted
60
Q

Parallel β-pleated sheets

A

2 polypeptide chains are oriented in the same direction relative to the N/C termini

61
Q

Anti-Parallel β-pleated Sheets

A

2 polypeptide cains are oriented in opposite directions relative to their N/C termini

62
Q

Domain

A

Part of a secondary structure that can exist on its own

63
Q

Motif

A
  • Type of supersecondary structure that is found in an array of different proteins (can make up a domain)
  • Ex: helix-turn-helix motifs are found in many DNA-binding proteins
64
Q

Teriary Structures

A

The folding pattern of the secondary structural elements into a 3D conformation

65
Q

Forces involved in 3º structures

A

H-bonds, Salt bridges, Hydrophobic interactions, Van der Wall forces, Disulfide bridges

66
Q

Globular protein properties

A
  • Core is usually hydrophobic AA
  • Surface is usually charged/polar AA (so hydrophilic) that interacts w/ a polar/aqueous environment and forms salt bridges to stabilize the structure
67
Q

Transmembrane proteins typically have what types of 2º and 3º structures?

A
  • 2º: usually α-helices that have hydrophobic residues that are embedded in the lipid/hydrophobic layer of the membrane
  • 3º: hydrophilic residues interact extra/intracellularly
68
Q

Quaternary structure

A

The individual subunits form a functional protein

69
Q

What determines the protein type?

A

The number of subunits determines what about the protein?

70
Q

Forces in 4º structure in globular proteins

A

H-bonding, Hydrophobic interactions, salt bridges/ionic bonds, rarely disulfide bonds (no covalent bonds)

71
Q

Forces in 4º structure in fiborus/structural proteins

A

Extensive covalent bonds

72
Q

What are the functional aspects of 4º structure

A
  1. Increased stability (bc increased # of interactions b/t AA)
  2. Cooperativity b/t subunits (Ex: hemoglobin-O2 binding)
  3. Different subunits may have different activities
73
Q

Protein folding

A
  • 1º structure of protein determines folding
  • Some fold spontaneously while others require specific cellular processes to promote proper folding
74
Q

Heat Shock Proteins

A
  • Some prevent improper folding
  • Others requires ATP energy to promote folding
75
Q

Cis-trans isomerases and disulfide isomerases promote what?

A

What non HSP function to promote proper protein folding?

76
Q

Size Exclusion Chromatography

A
  • Uses porous beads
  • Larger proteins elude 1st bc smaller proteins get caught in the pores of the beads
77
Q

Ion Exchange Chromatography (Cation)

A
  • bound chemicals have a negative charge
  • Cations adhere to the negatively charged column
  • charges on proteins are pH dependent
78
Q

Ion Exchange Chromatography (Anion)

A
  • bound chemicals have positive charge
  • Anions adhere to the positively charged column
  • Charges on proteins are pH dependent
79
Q

Hydrophobic Interaction Chromatography

A
  • Medium contains hydrophobic groups
  • Proteins w/ hydrophobic groups adhere to the column
80
Q

Affinity Chromatography

A
  • Medium has a bound, protein specific ligand
  • Proteins that bind to the ligand adhere to the column
81
Q

High-Pressure Liquid Chromatography (HPLC)

A
  • Eluent pumped thru column under high pressure
  • Typically looking for hydrophobic interaction chromatography (aka reversed phase)
  • Separation is faster and at higher resolution
82
Q

Electrophoresis

A

Separation based on mirgration of charged molecules applied in an electrical field

83
Q

Native electrophoresis

A
  • Separates by differences in charges due to the 1º structure
  • Ex: hemoglobin isoforms, some isozymes (LDH, CK)
84
Q

SDS-PAGE

A
  • Protein molecules interact with the detergent (SDS) to produce proteins of about = charge-to-mass ratios
  • SDS disrupts 4º structures (proteins become monomers
  • migration thru the gel is based on size: smaller proteins go faster
85
Q

Iso-Electric Focusing (IEF)

A
  • Buffers generate a pH gradients within a PA gel
  • Proteins migrate to pI=pH of gel
86
Q

2D Electrophoresis

A

Uses both IEF and SDS-PAGE

87
Q

Western blot

A
  • Proteins are separated via electrophoresis and transferred to synthetic membrane (incubated w/ antibodies for specific protein
  • 2nd antibody conjugated w/ reporter molecule to help visualize the specific protein
88
Q

Mass Spect

A
  • Separates molecules based on their mass
  • Can identify proteins thru determination of masses of peptides produced thru tryptic digestion of proteins
  • detects covalent modifications of a protein

Biochem (24 decks)

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