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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
What do cells do to ensure that net change in free energy is negative?
Couple unfavorable metabolic processes with favorable ones so that the net change in free energy is negative
26
When thermodynamically favorable reactions are coupled to unfavorable synthesis of monosaccharides from atmospheric CO2,
Carbon reduced
27
Reduction
gain electrons Addition of H or removal of O
28
When animal eats plant
oxygen oxidized
29
Oxidization
Loses electrons Addition of O, remove H Carbon becomes CO2
30
Oxidation of carbon is
thermodynamically favorable
31
If a living organism has low entropy relative to surroundings, how does it maintain thermodynamically unfavorable state?
Obtains free energy from food
32
What is a dielectric constant? and is water's high or low?
measure of solvent's ability to diminish electrostatic attractions between dissolved ions. High
33
The higher the dielectric constant, the less able
the ions are to associate with each other.
34
Hydrophilic
Ex: Glucose/ other hydrated substances polar groups, soluble in water
35
Hydrophobic
insoluble | lacks polar groups
36
Adding nonpolar molecules to water
lowers entropy, can't break/form hydrogen bonds
37
Intracellular
K+
38
Extracellular
Na+ and Cl-
39
Electronegative rankings
H < C < S < N < O < F Has Charlie Seen Natalie's Old Frock?
40
Proton Jumping
effective mobility of H+ in water is much greater than the mobility of other ions that must physically diffuse among water molecules.
41
Donate proton
Acid
42
Accept Proton
base
43
Organ which does buffering in humans
Kidney
44
Kidney Buffer
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
How is HCO3- returned to bloodstream?
Cl- ion exchanger, H+ pumped out
46
Acidosis
Blood pH less than 7.35
47
Alkalosis
blood pH greater than 7.45
48
Metabolic acidosis
accumulation of acidic products of metabolism CNS depression, rapid deep breaths Treated by administering sodium bicarbonate
49
Metabolic Alkalosis
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
Respiratory acidosis
pulmonary function caused by airway blockage Kidneys increase synthesis of enzymes that break down glutamine to produce NH3. Treatment: Excretion of NH4+
51
Respiratory Alkalosis
hyperventilation by fear/anxiety
52
N connected to C
amino group
53
C=N
imino group
54
O=C, then C-N
amido group
55
-OH
hydroxyl group
56
-SH
Sulfhydryl group
57
-O-
ether linkage
58
O=C, then C-O
Ester linkage
59
C=O 1. No Side Chains 2. Side Chain
1. Carbonyl group | 2. Acyl Group
60
O=C, then C-OH
Carboxyl group
61
O=C-O negative
carboxylate
62
Secondary Structure
Polypeptide backbone (exclusive of side chains)
63
Tertiary Structure
3D confirmation of polypeptide (including backbone atoms and all side chains)
64
Quaternary Structure
Spatial arrangement of all chains
65
How do peptide bonds form ?
Condensation reaction. Water is lost, carboxylate and amino groups linked N --> C
66
In cells, peptide bonds are broken/hydrolyzed by
exopeptidases/endopeptidases
67
The electrostatic properties of the polypeptide primary depend on...
identities of side chains (R groups) that project out the polypeptide backbone
68
_____ may alter a side chain's polarity and tendency to lose/accept proton
microenvironment
69
Short polypeptides are called
oligopeptides
70
Is there rotation around C-N bond?
No, due to partial (40%) double bond character. | N-C alpha can rotate, though limited
71
Secondary structure's goal is to minimize
strain
72
amino groups are hydrogen bond ___ whereas carbonyl groups are hydrogen bond ___
amino: H donor carbonyl: H acceptor
73
Secondary: Alpha helix
Right-handed. Hydrophobic in the center. | Most 12 residues long
74
Secondary: Beta Sheets (parallel)
Jagged O-H bonds, align same direction N --> C, loop out longer linker
75
Secondary: Beta Sheets (antiparallel)
Ladder O-H bonds, opposite direction. | smaller linker
76
Largest force governing protein structure
hydrophobic effect
77
When a protein is misfolded ___ tags it with ______. Which is recognized by ___
Proteaosome Ubiquitin Ligase
78
Size and Exclusion Chromatography
Porous solution. | Larger proteins exclude from bead spaces and will pass faster
79
Ion Exchange Chromatography:
If want -, use + (vis versa) | uncharged/+ pass, whereas - binds. then use salt solution to dissociate the bound proteins.
80
Affinity Chromatography
Separation based on molecular interactions. Ex: what proteins will bind to this small immobilized molecule ?
81
HPLC
High performance liquid chromatography Analytical Closed columns under high pressure
82
SDS
Gel electrophoresis charge and size SDS is - All proteins move to + side, smaller proteins move faster.
83
SDS: what if you have dimers of proteins? Or disulfides?
Reducing condition: reduce disulfide bonds Nonreducing: retain associations
84
Mass Spectrometry
Protein, ionization, fragmentation, and mass analysis (details?) Magnet to apply force to charted particles
85
X-ray Crystallography/NMR
3D arrangement of atoms H resonate in NMR X-ray: diffraction images
86
Only trend that goes down
Ionic and atomic radii
87
Denaturation ruins
tertiary structure

Cellular Biochemistry (15 decks)

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