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Cellular Biochemistry > Exam 1: Ch. 1, 2, and 4 > Flashcards

Exam 1: Ch. 1, 2, and 4 Flashcards

1
Q

Name the 4 biological molecules

A

Amino acids (proteins)
Carbohydrates (polysaccharides)
Nucleotides (nucleic acids/polynucleotides)
Lipids

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2
Q

Amino Acids: What are the names of the two groups

A 
amino group (-NH2) 
carboxylic acid group (-COOH)
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3
Q

Carbohydrate groups

A

Hydroxyl groups
Carbonyl group

(CH2O)n, where n > or equal to 3.

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4
Q

3 components of nucleotides

A
  1. 5-carbon sugar
  2. nitrogen-containing ring
  3. 1+ phosphate groups
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5
Q

Lipid qualities

A

poorly soluble in water due to bulk of structure and hydrocarbon-like chains

Ex: palmitate

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6
Q

monomers linked _____

What are monomers called once they’ve been incorporated into a polymer?

A

covalently

residues

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7
Q

Proteins are linked together by…

A

Peptide bonds

O=C —N

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8
Q

Nucleic acids linked by…

A

phosphodiester bonds

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9
Q

Polysaccharides linked by

A

glycosidic bonds

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10
Q

Starch vs. Cellulose

A

Starch- loose helical conformation

Cellulose- extended and stiff conformation

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11
Q

Proteins

A

Main: Carry out metabolic reactions, support cellular structures. (M S)

Minor: Store Energy (E)

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12
Q

Nucleic acids

A

Main: Encode information (I)

Minor: Carry out metabolic reactions, support cellular structures (M S)

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13
Q

Polysaccharides

A

Main: Store Energy, Support Cellular structures (E S)

minor: Encode information (I)

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14
Q

Gibbs Free Energy

A

A measure of the free energy of a system based on H and S

Units = J • mol-1

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15
Q

Enthalpy, H

A

The heat content of a system

Units = J • mol-1

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16
Q

Entropy, S

A

A measure of the system’s disorder or randomness

Units = J • K-1 mol-1

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17
Q

Exothermic reactions

A

Release heat into surroundings

Hfinal - Hinitial = delta H < 0

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18
Q

Endothermic reactions

A

Absorb heat from the surroundings

delta H > 0

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19
Q

In order for a process to occur overall change in free energy must be

A

negative

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20
Q

Spontaneous reaction

A

Exergonic

Delta G is less than zero

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21
Q

Nonspontaneous reaction

A

Endergonic

Delta G is more than zero

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22
Q

Decrease in enthalpy, increase in entropy is ___ at all temperatures

A

spontaneous, delta G less than zero

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23
Q

Enthalpy increase, entropy decreases

A

does not occur

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24
Q

Enthalpy and entropy increase or decrease

A

delta G depends on temp

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25
Q

What do cells do to ensure that net change in free energy is negative?

A

Couple unfavorable metabolic processes with favorable ones so that the net change in free energy is negative

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26
Q

When thermodynamically favorable reactions are coupled to unfavorable synthesis of monosaccharides from atmospheric CO2,

A

Carbon reduced

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27
Q

Reduction

A

gain electrons

Addition of H or removal of O

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28
Q

When animal eats plant

A

oxygen oxidized

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29
Q

Oxidization

A

Loses electrons

Addition of O, remove H

Carbon becomes CO2

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30
Q

Oxidation of carbon is

A

thermodynamically favorable

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31
Q

If a living organism has low entropy relative to surroundings, how does it maintain thermodynamically unfavorable state?

A

Obtains free energy from food

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32
Q

What is a dielectric constant? and is water’s high or low?

A

measure of solvent’s ability to diminish electrostatic attractions between dissolved ions.

High

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33
Q

The higher the dielectric constant, the less able

A

the ions are to associate with each other.

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34
Q

Hydrophilic

A

Ex: Glucose/ other hydrated substances

polar groups, soluble in water

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35
Q

Hydrophobic

A

insoluble

lacks polar groups

36
Q

Adding nonpolar molecules to water

A

lowers entropy, can’t break/form hydrogen bonds

37
Q

Intracellular

A

K+

38
Q

Extracellular

A

Na+ and Cl-

39
Q

Electronegative rankings

A

H < C < S < N < O < F

Has Charlie Seen Natalie’s Old Frock?

40
Q

Proton Jumping

A

effective mobility of H+ in water is much greater than the mobility of other ions that must physically diffuse among water molecules.

41
Q

Donate proton

A

Acid

42
Q

Accept Proton

A

base

43
Q

Organ which does buffering in humans

A

Kidney

44
Q

Kidney Buffer

A
  1. Ion exchanger moves Na+ into cell and H+ out
  2. H+ combines with HCO3- to make CO2
  3. Kidney cell takes up CO2 and then does the reverse
45
Q

How is HCO3- returned to bloodstream?

A

Cl- ion exchanger,

H+ pumped out

46
Q

Acidosis

A

Blood pH less than 7.35

47
Q

Alkalosis

A

blood pH greater than 7.45

48
Q

Metabolic acidosis

A

accumulation of acidic products of metabolism
CNS depression, rapid deep breaths
Treated by administering sodium bicarbonate

49
Q

Metabolic Alkalosis

A

Loss of HCl in gastric fluid
(overproduction of mineralocorticoids, abnormally high H+ excretion and Na+ retention)
prolonged vomiting
Treated by infusing NaCl

Stop breathing to minimize CO2 loss

50
Q

Respiratory acidosis

A

pulmonary function caused by airway blockage
Kidneys increase synthesis of enzymes that break down glutamine to produce NH3.
Treatment: Excretion of NH4+

51
Q

Respiratory Alkalosis

A

hyperventilation by fear/anxiety

52
Q

N connected to C

A

amino group

53
Q

C=N

A

imino group

54
Q

O=C, then C-N

A

amido group

55
Q

-OH

A

hydroxyl group

56
Q

-SH

A

Sulfhydryl group

57
Q

-O-

A

ether linkage

58
Q

O=C, then C-O

A

Ester linkage

59
Q

C=O

  1. No Side Chains
  2. Side Chain
A
  1. Carbonyl group

2. Acyl Group

60
Q

O=C, then C-OH

A

Carboxyl group

61
Q

O=C-O negative

A

carboxylate

62
Q

Secondary Structure

A

Polypeptide backbone (exclusive of side chains)

63
Q

Tertiary Structure

A

3D confirmation of polypeptide (including backbone atoms and all side chains)

64
Q

Quaternary Structure

A

Spatial arrangement of all chains

65
Q

How do peptide bonds form ?

A

Condensation reaction.
Water is lost, carboxylate and amino groups linked

N –> C

66
Q

In cells, peptide bonds are broken/hydrolyzed by

A

exopeptidases/endopeptidases

67
Q

The electrostatic properties of the polypeptide primary depend on…

A

identities of side chains (R groups) that project out the polypeptide backbone

68
Q

_____ may alter a side chain’s polarity and tendency to lose/accept proton

A

microenvironment

69
Q

Short polypeptides are called

A

oligopeptides

70
Q

Is there rotation around C-N bond?

A

No, due to partial (40%) double bond character.

N-C alpha can rotate, though limited

71
Q

Secondary structure’s goal is to minimize

A

strain

72
Q

amino groups are hydrogen bond ___ whereas carbonyl groups are hydrogen bond ___

A

amino: H donor
carbonyl: H acceptor

73
Q

Secondary: Alpha helix

A

Right-handed. Hydrophobic in the center.

Most 12 residues long

74
Q

Secondary: Beta Sheets (parallel)

A

Jagged O-H bonds, align same direction
N –> C, loop out
longer linker

75
Q

Secondary: Beta Sheets (antiparallel)

A

Ladder O-H bonds, opposite direction.

smaller linker

76
Q

Largest force governing protein structure

A

hydrophobic effect

77
Q

When a protein is misfolded ___ tags it with ______. Which is recognized by ___

A

Proteaosome

Ubiquitin

Ligase

78
Q

Size and Exclusion Chromatography

A

Porous solution.

Larger proteins exclude from bead spaces and will pass faster

79
Q

Ion Exchange Chromatography:

A

If want -, use + (vis versa)

uncharged/+ pass, whereas - binds. then use salt solution to dissociate the bound proteins.

80
Q

Affinity Chromatography

A

Separation based on molecular interactions.

Ex: what proteins will bind to this small immobilized molecule ?

81
Q

HPLC

A

High performance liquid chromatography

Analytical
Closed columns under high pressure

82
Q

SDS

A

Gel electrophoresis
charge and size

SDS is -
All proteins move to + side, smaller proteins move faster.

83
Q

SDS: what if you have dimers of proteins? Or disulfides?

A

Reducing condition: reduce disulfide bonds

Nonreducing: retain associations

84
Q

Mass Spectrometry

A

Protein, ionization, fragmentation, and mass analysis (details?)

Magnet to apply force to charted particles

85
Q

X-ray Crystallography/NMR

A

3D arrangement of atoms
H resonate in NMR
X-ray: diffraction images

86
Q

Only trend that goes down

A

Ionic and atomic radii

87
Q

Denaturation ruins

A

tertiary structure

Cellular Biochemistry (15 decks)

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