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BioChem > Chapters 1-3 > Flashcards

Chapters 1-3 Flashcards

1
Q

What are the ways in which biochemical reactions differ from chemical reactions?

A 
Aqueous
Faster
Require energy (ATP)
Localized in the cell
Part of multi-step pathway
Regulated
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2
Q

What are the four types of biomolecules?

A

Lipids
Proteins
Carbohydrates
Nucleic Acids

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3
Q

What is the monomer for lipids?

A

Fatty acids

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4
Q

What is the monomer for proteins? What is the bond called?

A

Amino acids

Peptide bond

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5
Q

What is the bond for carbohydrates?

A

Glycosidic bonds

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6
Q

What is the difference between a nucleoside and a nucleotide?

A

Nucleotide contains a Phosphate

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7
Q

What is the bond for nucleic acids?

A

Phosphodiester bonds

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8
Q

What are the reactions called when monomers are made into polymers and vice versa?

A

Condensation- monomers are made into polymers and release a small molecule (water if dehydration reaction)
Hydrolysis- water ruptures the chemical bond

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9
Q

What are the two categories of DNA bases and which bases are in which category?

A

Purines
Adenine & Guanine

Pyrimidines
Thymine & Cytosine

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10
Q

What are the complementary base pairs in DNA and how many hydrogen bonds can each make?

A

Guanine and Cytosine → 3 hydrogen bonds

Adenine and Thymine → 2 hydrogen bonds

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11
Q

What are the three differences between RNA and DNA?

A

Single-stranded
Ribose (vs deoxyribose)
Uracil (replace CH3 with H)

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12
Q

Describe the three main molecular models

A

Space-filling - Realistic
Ball-and-stick - Bonding arrangements
Skeletal - Simple, good for large molecules

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13
Q

What are the four types of noncovalent bonds?

A

Electrostatic Interactions
Van der Waals
Hydrophobic Interactions
Hydrogen bonding

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14
Q

Describe the effects of hydrophobic interactions in an aqueous environment?

A

Water sequesters anions and cations

Nonpolar molecules are driven together

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15
Q

Define hydrogen bond

A

Hydrogen atom shared by 2 atoms, usually an O or N

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16
Q

Differentiate between hypertonic and hypotonic solutions

A

Hypertonic - water moves out of the cell and it shrinks

Hypotonic - water enters the cell and it swells and bursts

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17
Q

What are the two basic equations needed to begin the derivation of the HH equation?

How do you derive the HH equation?

A 
pH = -log[H+]
Ka = [H+][A-] / [HA]

1) Ka= [H+][A-]/[HA]
2) Ka [HA]/[A-] = [H+]
3) -logKa -log[HA]/[A-] = -log[H+]
4) pH= pKA +p[A-]/[HA]

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18
Q

What is the HH equation?

A

pH = pKa + log [A-]/[HA]

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19
Q

Where is the buffering capacity of a system greatest?

A

pH = pKa, where [HA] = [A-]

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20
Q

Where is the buffering capacity of a system mostly lost?

A

pH is one less or greater than pKa

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21
Q

In a graph of OH- added by pH, where is pH=pKa?

A

Midpoint

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22
Q

What does amphoteric mean?

A

Can act as either a base or an acid

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23
Q

What are the three forms of an amino acid with a non-ionizable side group?

A

Both groups protonated → Zwitterionic form → Both deprotonated

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24
Q

How many pKas will an amino acid have if it has an ionizable side group?

A

3

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25
Q

What is acidosis? Alkalosis?

A

Blood pH < 7.4 in acidosis, blood pH > 7.4 in alkalosis

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26
Q

What is the meaning of respiratory acid/alkalosis? Example?

A

Respiratory ___osis → a change in acid-base status induced by altered respiration
Hyperventilation lowers blood CO2 (alkalosis)

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27
Q

What is the meaning of metabolic acid/alkalosis? Example?

A

Metabolic ____osis → a change in acid-base status inducted by metabolic problems
Caused by excessive vomiting (alkalosis)

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28
Q

What is a domain of a protein?

A

Domains are two or more compact regions connected by a flexible segment

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29
Q

Define the secondary structure of a protein

A

Secondary structure is the spatial arrangement of amino acids that are close to one another

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30
Q

What amino acid forms disulfide bonds?

A

Cysteine, C

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31
Q

What is a protein cofactor?

A

Functional non-amino acid components

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32
Q

What are the two types of protein cofactors?

A

metals and coenzymes-small organic molecules

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33
Q

What are the two types of coenzymes?

A

Prosthetic Groups - Tightly bound coenzymes covalently bonded to the protein

Cosubstrates - Loosely bound coenzymes that dissociate and re-associate

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34
Q

What are the ten essential amino acids?

A

PVT TIM HALL

Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine, Lysine
***Does not follow single letter symbols for the AAs

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35
Q

Define chirality

A

Chiral → the rotated molecule cannot be superimposed on mirror image

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36
Q

What is the chirality of the amino acids?

A

All except glycine are chiral, all are L, all except cysteine are S

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37
Q

What is the isoelectric point of an amino acid? How is it found?

A

The Ph where the net charge on AA is zero

Average of the pKas when the AA is +/- 1

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38
Q

Which amino acids have aromatic rings?

A

Phenylalanine
Tryptophan
Tyrosine

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39
Q

Which amino acids have non-aromatic rings?

A

Proline

Histidine

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40
Q

Which amino acids contain sulfur?

A

Cysteine

Methionine

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41
Q

Which amino acids are negatively charged?

A

Aspartate

Glutamate

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42
Q

Which amino acids are positively charged?

A

Lysine
Arginine
Histidine

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43
Q

What are peptides?

A

Small condensation products of amino acids

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44
Q

How are peptides named?

A

Naming begins on the N-terminus side and ends at the carboxyl-terminus

Using either the partial amino acid name with (yl) in between, the three letter code abbreviation with dashes in between, or the single letters with nothing in between

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45
Q

Describe the peptide bond. Is it flexible? Cis?

A

The bond between the carbonyl carbon of one amino acid and the nitrogen of the next has partial double-bond character, so it is rigid

Almost all peptide bonds occur in the trans configuration due to steric clashes from R groups

46
Q

On a peptide, what are the phi angles?

A

Phi (𝝓) angles are between the 𝞪 carbon and the nitrogen of the amide

47
Q

On a peptide, what are the psi angles?

A

Psi (𝜳) angles are between the 𝞪 carbon and the carbon of the carbonyl

48
Q

What is a Ramachandran diagram for?

A

it shows favorable conformations of the phi and psi angles

49
Q

What stabilizes an alpha helix? Where are the bonds?

A

Stabilized by H-bonds
CO of aa(n) bonds with NH of aa(n+4)
All amino acids except the ends are hydrogen bonded

50
Q

How many amino acid residues are there for each turn of the alpha helix?

A

3.6 aa residues per turn of helix

51
Q

Are alpha helices mostly left-handed, right-handed, or found equally in both? Why?

A

Right-handed due to steric clash

52
Q

What are some amino acids that favor alpha helices?

A

Amino Acids → Ala, Glu, Leu

53
Q

What stabilizes a beta sheet?

A

h-bonds

54
Q

What differentiates the two forms of beta sheets?

A

Parallel → Each amino acid connects with two others

Antiparallel → Each amino acid connects with one other

55
Q

Which amino acids favor beta sheets?

A

Amino Acids → Val, Ile, Thr

56
Q

What bond promotes the formation of a reverse turn?

A

CO of aa(n) is H-bonded to the NH of aa(n+3)

57
Q

What amino acid is commonly found in reverse turns and why?

A

Often include proline, especially in 𝜷 sheets due to low rotation around 𝞪 carbon

58
Q

What is the structure of a coiled-coil protein?

A

2 right-handed 𝞪 helices wrap around each other to form a left-handed 𝞪-helical coiled coil
Central region of 300 aas with imperfect repeats of 7 aas

59
Q

What bonds are involved in a coiled-coil?

A

Helixes are bonded by van der Waals, ionic, and disulfide cross-links
Number of disulfide cross links defines properties

60
Q

How many residues are there per turn of a coiled-coil?

A

3.5 aa residues per turn

61
Q

What amino acid is commonly found in coiled-coils and why?

A

Include leucine b/c hydrophobic

62
Q

What is the composition of a collagen strand?

A

Regular aa sequence: every third is Gly, proline and hydroxyproline are also abundant
Gly is used due to small size, forms inside of superhelix

63
Q

What is the structure of collagen?

A

3 strands combine to form a superhelical cable with 3 aas per turn

64
Q

What stabilizes collagen?

A

Stabilized by steric repulsion of pyrrolidine rings and hydrogen bonds

65
Q

What is the tertiary structure of a water-soluble protein?

A

Water-soluble proteins fold into compact structures with nonpolar cores

66
Q

What is the tertiary structure of a trans-membrane protein?

A

Trans-membrane proteins have the opposite structures with polar centers

67
Q

How do prion diseases spread?

A

a misfolded protein serves as a template for others

68
Q

What are intrinsically unstructured proteins (IUPs)?

A

without a defined structure when not interacting with other proteins

69
Q

What are metamorphic proteins?

A

exist in many conformations of about equal energy

70
Q

What is amyloidosis?

A

improperly folded proteins result in protein aggregates (amyloid fibrils or plaques) due to the formation of large parallel 𝜷 sheets

71
Q

What protein is involved in the following conditions: Alzheimer’s, Parkinson’s, and ALS?

A

Alzheimer’s → Amyloid 𝜷 protein
Parkinson’s → 𝞪-synuclein
ALS → superoxide dismutase enzyme (SOD)

72
Q

What is specific activity?

A

ratio of enzyme activity to the amount of protein in the mixture
units per mg

73
Q

What is yield?

A

(total) activity retained after each step

%

74
Q

What is purification level?

A

specific activity at that step over initial specific activity

75
Q

What is the first step of the protein purification process?

A

Homogenate is centrifuged in multiple stages producing pellets of cellular materials and a supernatant consisting of the soluble portion of the cytoplasm

76
Q

Describe gel-filtration or molecular exclusion chromatography

A

separates proteins on the basis of size using a glass column with porous beads, smaller beads enter beads so larger elute first

77
Q

Describe ion-exchange chromatography

A

Separates proteins on the basis of charge using charged beads and solutions of salt or acid/base
Named based on charge of proteins eluted first

78
Q

Describe affinity chromatography

A

Separates proteins on the basis of affinity for specific chemical groups
Wash with solution containing high levels of that chemical group

79
Q

Describe high-performance liquid chromatography

A

A subtype of affinity chromatography with fine beads and high pressure

80
Q

What is salting out?

A

Most proteins are less soluble at high salt concentrations, concentration depends on particular protein

81
Q

What is dialysis?

A

Separate proteins from small molecules by semipermeable membranes with small pore sizes

Place a dialysis bag with a concentrated solution inside a buffer filled container. Smaller molecules and ions transverse the pores and emerge outside the bag

82
Q

What is the general principle of gel electrophoresis?

A

Proteins migrate with a velocity that is proportional to the strength of the electric field and the charge on the protein and inversely proportional to the friction coefficient (mass, shape, medium)

83
Q

Describe SDS-PAGE gels

A

Separate proteins by mass with the addition of SDS, which gives all proteins a high negative charge
Mobility is linearly proportional to the log of their mass
Polyacrylamide Gel is formed by combining acrylamide with the crosslinking agent MBAA

84
Q

How can you visualize the results of your protein gel?

A

Coomassie blue or silver stains

Radioactive labels

85
Q

What is isoelectric focusing?

A

Gel with pH gradient, each protein moves until pH = pi

Can be combined with SDS-PAGE

86
Q

What factors influence sedimentation coefficient (s)?

A

Depends on the mass (of the particle), shape (of the particle), and density (both)

87
Q

What is zonal/band/gradient centrifugation?

A

Used to separate proteins with different sedimentation coefficients

88
Q

How does zonal/band/gradient centrifugation work?

A

Formation of sucrose gradient → addition of sample → swinging bucket rotor

89
Q

Sanger’s Method of sequencing polypeptides UPDATES

A

1-fluoro-2,4-dinitrobenzene binds to the N-terminus

Benzene with F, NO2, space, NO2

90
Q

How do you determine amino acid composition (2-part)?

A

Heat at 110*C with 6 M HCl for 24 hours

Ion-exchange chromatography and ninhydrin indicator dye

91
Q

Edmann’s Method for N-terminus

A

Label N-terminus with phenyl isothiocyanate (PIT), treat with weak acidic conditions to remove the N-most acid

Benzene with N=C=S

92
Q

Cleavage by cyanogen bromide (CNBr)

A

-COOH site of Met

93
Q

Cleavage by trypsin

A

-COOH site of Lys, Arg

94
Q

Cleavage by chymotrypsin

A

-COOH site of Phe, Tyr, Trp

95
Q

Cleavage by pepsin

A

-NH site of Phe, Tyr, Trp

96
Q

Removal of disulfide bonds for amino acid sequence determination

A

Reduce with thiols such as dithiothreitol (DTT) and beta-mercaptoethanol

97
Q

Polyclonal antibodies

A

Polyclonal antibodies are derived from multiple antibody-producing cell populations

Heterogeneous mixtures of antibodies that are each specific for one epitope

98
Q

Monoclonal antibodies

A

Monoclonal antibodies are derived from a single population, are identical, and respond to a single epitope

99
Q

Antibody Production

A

Fuse normal antibody-producing cells with those with multiple myeloma

100
Q

What does ELISA stand for?

A

Enzyme-linked immunosorbent assay

101
Q

What is ELISA for?

A

Quantify the amount of protein present from enzyme-linked antibodies

102
Q

Describe indirect ELISA

A

ANTIGEN-coated well → add ANTIBODY (binds to antigen)→ add enzyme-linked antibody (binds to first antibody) → add substrate (converted by enzyme into colored product that is proportional to the amount of SPECIFIC ANTIBODY)

test for HIV antibodies in blood

103
Q

Describe sandwich ELISA

A

MONOCLONAL ANTIBODY-coated well → add ANTIGEN (binds to antibody)→ add enzyme-linked monoclonal antibody → add substrate (converted by enzyme into colored product that is proportional to the amount of ANTIGEN)

test for antigens in blood/urine, test for food allergens

104
Q

Western Blotting

A

Proteins are separated by SDS, stained with an antibody, then with a second antibody connected to a chemiluminescent or fluorescent tag

105
Q

Product and issue with mass spec

A

mass-to-charge ratio, conversion into gas phase

106
Q

Compound that blocks the amino group of the incoming amino acid for peptide synthesis

A

t-Boc or tert-butyloxycarbonyl

107
Q

Compound that facilitates peptide bond formation for peptide synthesis

A

DCC or dicyclohexylcarbodiimide

108
Q

Product and issue with x-ray crystallography

A

3D structure, needs a crystalized molecule

109
Q

Product and issue with NMR

A

3D structure, only some atoms show up

110
Q

Product of cryo-electron microscopy

A

3D structure from many orientations

111
Q

Condition with really stretchy skin

A

Ehlers-Danlos

BioChem (6 decks)

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