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Biochemistry Charter > Block 1 > Flashcards

Block 1 Flashcards

1
Q

Hydroxyl group

A

-OH

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2
Q

Amino acids with ring structures

A

phenylalanine, tryptophan, tyrosine

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3
Q

Nonpolar amino acids

A
  • Surface of membrane proteins
  • Hydrophobic, do not form hydrogen bonds
  • glycine, alanine, proline, valine, leucine, isoleucine, methionine, tryptophan, phenylalanine
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4
Q

Polar amino acids

A

Surface of soluble proteins

-serine, threonine, cysteine, asparagine, glutamine, tyrosine

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5
Q

How is the alpha helix stabilized?

A

Hydrogen Bonds

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6
Q

What remains intact during protein denaturation?

A

Peptide Bonds

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7
Q

Branched Amino Acids

A

Valine, leucine, isoleucine

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8
Q

Imino Group

A

Hydrophobic

-Proline

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9
Q

Which amino acids can form hydrogen bonds?

A

Serine, Threonine, Tyrosine, Asn, Gln

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10
Q

Hydrogen Bonds

A

Non-covalent

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11
Q

Disulfide Bonds

A

Covalent

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12
Q

Acidic Amino Acids

A

Aspartate and Glutamate (w/o H)

Aspartic acid and Glutamic acid (w/H)

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13
Q

Basic Amino Acids

A

Histidine, lysine, arginine

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14
Q

Arginine

A

R or Arg

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15
Q

Asparagine

A

N or Asn

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16
Q

Aspartate

A

D or Asp

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17
Q

Glutamate

A

E or Glu

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18
Q

Glutamine

A

Q or Gln

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19
Q

Phenylalanine

A

F or Phe

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20
Q

Tyrosine

A

Y or Tyr

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21
Q

Tryptophan

A

W or Trp

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22
Q

Lysine

A

K or Lys

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23
Q

Strong Acids

A

Completely Dissociates in Water
Very large Ka
-HCl, HBr, HI, HNO3, HClO4, H2SO4

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24
Q

Strong Bases

A

Completely Dissociates in Water
Very large Kb
-LiOH, NaOH, KOH, Ba(OH)2, Mg(OH)2

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25
Q

Equivalence point

A

Acid is mixed with equal amounts of Base

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26
Q

Buffer

A

Weak acid and a similar amount of its conjugate base, buffers resist pH change

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27
Q

pI

A

Isoelectric point= no net charge

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28
Q

How is acid released from the body?

A

Exhaled CO2 or excreted in urine

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29
Q

Uncharged drugs in the intestinal lumen how?

A

More readily than charged drugs

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30
Q

Primary Protein Structure

A

Bead on a string, sequence of AA

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31
Q

Peptide Bonds

A
  • Formed by a condensation rxn (dehydration)
  • Connects 2 AA
  • Uncharged and Polar
  • Rigid and planar
  • no rotation around a peptide bond (double bond)
  • prefers trans configuration
  • cleaved by Acid hydrolysis
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32
Q

Acid Hydrolysis

A

Cleaves peptide bonds (hydrolyzed by a strong acid at 110C)

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33
Q

Chromatography

A

AA separated by ionic strength and pH

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34
Q

Quantified analysis

A

Ninhydrin, intensity of color measured on spectrophotometer

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35
Q

Edman’s reagent (phenylisothiocyanate)

A

Makes N-terminal residue peptide bond weak (cleaves it), only can be used for polypeptides of 100 AA or less

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36
Q

Secondary Protein Structure

A

Alpha Helix, Beta Structure, Beta Bend

-repetitive hydrogen bonding

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37
Q

Alpha Helix

Secondary Structure

A

R groups extend outwards

  1. 6 residues per turn
    - Disrupted by: proline, many charged AA, many AA with bulky side groups, maybe glycine
    - helical wheel
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38
Q

Beta Sheets

Secondary Structure

A

Hydroben bonding, SILK

  • parallel: line up in order
  • antiparallel: don’t line up in order
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39
Q

Beta Bend

Secondary Structure

A

Usually composed of just a few AA, can link helices and beta sheets to others

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40
Q

Supersecondary Structure

A

Result from folding of secondary structures into small and discrete elements

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41
Q

3 Examples of fibrous proteins

A
  1. Silk
  2. Keratin
  3. Collagen
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42
Q

Collagen

A

Has a triple helix, very tight, most abundant protein in mammals, secondary structure, NOT an alpha helix, fibrous protein, every 3rd AA is glycine

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43
Q

Tertiary Structure

A

When secondary structures fold on themselves, domains

44
Q 
Globular Proteins
(tertiary structure)
A

Good water solubility

45
Q

Disulfide Bonds

A
  • SH group of 2 cysteines

- important for insulin

46
Q

Quaternary Structure

A

More than 1 polypeptide, disulfide bond is not involved

  • hemoglobin
  • held together by NON-covalent bonds
47
Q

Homomultimer

A

all same polypeptides

48
Q

Heteromultimer

A

some polypeptides are different

49
Q

Denaturation

A

Usually irreversible, loss of biological activity

50
Q

Chaperones

A
  • Keep unfolded proteins separate
  • Enhance folding rate
  • Synthesis increases with heat
  • Reusable
51
Q

Diseases that are resistant to degradation protein?

A

Alzheimer disease and Prion disease

52
Q

Alzheimer Disease

A

amyloid-B protein gets degraded causing a possible neurotoxin to be formed and leads to the disease

53
Q

Prion Disease

A

Scrapie: Sheep
Creutzfeldt-Jakob disease: humans
Mad Cow disease

PrPSc protein

54
Q

Globular proteins

A

Water soluble, spherical, hydrophobic core

55
Q

Porphyrin Ring

A

Heme (prosthetic group) after it accepts ferrous ion, can form 6 coordinate covalent bonds

56
Q

Myoglobin

A

Stores O2 in the cell and delivers to mitochondria when needed, hyperbolic shape

57
Q

Hemoglobin A

A

4 O2 molecules can be carried, alpha beta peptides, many hydrophobic

58
Q

AA with aromatic side chains

A

Phenylalanine, Tyrosine, Tryptophan

59
Q

Cooperative ligand binding

A

Binding of O2 molecule promotes binding of another O2 molecule

60
Q

Positive Allosteric Regulator

A

Binding of O2 at one site, increases affinity for O2 at another site

61
Q

Enzyme

A

Biological Catalyst: increase chemical rxn without itself undergoing any permanent chemical change, specific, change the activation energy NOT free energy, use weak non-covalent interactions

62
Q

Substrate

A

the reactants that are activated by the enzyme

63
Q

Apoenzyme

A

enzyme without it’s nonprotein component

64
Q

Holoenzyme

A

an active enzyme with its nonprotein component

65
Q

Cofactor

A

a metallic nonprotein component (Zinc)

66
Q

Coenzyme

A

non-metallic small organic molecule, typically vitamins

  • Co-substrate: transient association (reversible) with the enzyme and dissociates into an altered from (NAD+)
  • Prosthetic group: permanent association with an enzyme and the form is not changed at the end of the reaction
67
Q

Turnover number

A

number of substrate molecules converted to product per enzyme molecule per second

68
Q

Oxidoreductases

A

Use coenzymes NAD/NADH or FAD/FADH2

-add an H to the product

69
Q

Transferases

A

Catalyze transfer of C-, N-, or P-

-2 substrates, 2 products

70
Q

Hydrolases

A

Use H2O

71
Q

Lyases

A

Catalyze cleavage of C-C, C-S, C-N

72
Q

Isomerases

A

intramolecular rearrangements

73
Q

Ligases

A

Use ATP to ADP

74
Q

Kinases

A

adds a phosphate

75
Q

Phosphatase

A

takes away a phosphate

76
Q

Catalytic Site

A

where the rxn occurs

77
Q

Binding Site

A

area that holds the substrate in proper place

78
Q

What is the effect of temp on enzyme activity?

A

Reduces enzyme rxn rates (usually 25-40C)

79
Q

What is an enzyme inactive form?

A

Zymogen, can be activated by the removal of truncation

80
Q

Allosteric

A

“other site” both positive and negative effectors

81
Q

Enzyme induction or upregulation

A

increase gene expression, synthesis of more enzyme molecules

82
Q

Repression-downregulation

A

decrease gene expression, decrease synthesis of enzyme molecules

83
Q

Degradation

A

can be achieved by specific changes in the protein structure that is recognized from degradation by the ubiquitin-proteasome

84
Q

What factors affect enzyme activity?

A

Substrate concentration, temp changes, pH changes

85
Q

Ionic Bond

A

A bond between an anion and cation

86
Q

Which AA can be phosphorylated?

A

Serine and Threonine and (tyrosine)

87
Q

Which AA can have N-linked glycosyation?

A

Asn

88
Q

Which AA can have O-linked glycosyaltion?

A

Ser and Thr

89
Q

N-terminus

A

On the left, free amino acid end

90
Q

C-terminus

A

On the right

91
Q

Prosthetic group

A

Coenzyme that is permanently bound to an enzyme and remains unchanged after a reaction

92
Q

Induction

A

increasing the amount of enzymes

93
Q

The affinity of two different enzymes for their substrates can be compared by

A

Km

94
Q

the inhibitor can bind to either the E or ES complex at a site that is not the enzymes catalytic site

A

noncompetitive

95
Q

What are statin drugs?

A

Competitive inhibitor

96
Q

Where does a noncompetitive inhibitor bind?

A

Different than the catalytic site

97
Q

What is Km?

A

substrate concentration required to attain ½ maximal velocity

98
Q

Do competitive inhibitors bind to the ES site?

A

NO

99
Q

Myoglobin

A

Consist of many alpha helices

100
Q

What stabilizes hemoglobin?

A

High pH

101
Q

How many covalent bonds can a ferrus ring have?

A

6

102
Q

What does Histidine allow Hb to do?

A

Regulate O2 in the blood and buffer and manage pH

103
Q

What does the Histidine pKa do with Hb?

A

Changes the pKa to go closer to physiological so it gets better

104
Q

Carbonic anhydrase

A

is an enzyme that speeds up CO2 dissolving in H2O

105
Q

What does 2,3-BPG do?

A
  1. Higher levels promote O2 release to the tissues
  2. Decreases the affinity of Hb for O2
  3. Negative allosteric effector

Biochemistry Charter (3 decks)

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