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BMSC 200 > Midterm > Flashcards

Midterm Flashcards

1
Q

Define: biochemistry

A

The study of life at the molecular level

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2
Q

Characteristics of living things:

A

Chemical complexity and microscopic organization, systems for using energy, defined functions and regulated interactions between components of the organism, responding to environment, self-replication and -assembly, evolution

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3
Q

Biochem is __ not __ life exists.

A

how, why

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4
Q

Fundamental features of cells:

A

Plasma membrane, cytoplasm, nucleic acid

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5
Q

How big are prokaryotic cells?

A

~1 micrometer in diameter

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6
Q

How big are eukaryotic cells?

A

~100 micrometers in diameter

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7
Q

What percent of macromolecules are which?

A

15% protein
7% nucleic acid
3% polysaccharides
2% lipids

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8
Q

In vivo vs in vitro:

A

In vivo is reductionist and success does not translate to in vitro.
In vitro success in a mouse does not translate to success in a human.

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9
Q

Chemical foundations of life - what %?

A

CHONPS - 97%

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10
Q

Bulk elements (structural):

A

CHONPS Cl Na Ca K

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11
Q

Trace elements (co-factors):

A

Mg, V-Zn, Se, Mo, I

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12
Q

Define: configuration

A

Flexible spatial arrangement of atoms within a molecule - can be changed without breaking bonds

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13
Q

Define: conformation

A

Fixed spatial arrangement of atoms within a molecule - cannot be changed without breaking bonds

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14
Q

Geometric isomer:

A

Same formula but different arrangement of groups with respect to a double bond (can’t rotate)

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15
Q

Define: stereoisomers

A

Non-superimposable molecules that differ in configuration at a chiral centre.
Ex: shaking hands - they look the same but interact with others differently

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16
Q

Enantiomer vs diasteromer

A

Mirror images; not.

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17
Q

How many stereoisomers can be made about n chiral centres?

A

2^n

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18
Q

First law of therm:

A

Energy cannot be created or destroyed or whatever

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19
Q

Gibbs free energy:

A

Enthalpy (number and kinds of bonds), entropy (randomness); G = H - TS

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20
Q

Endergonic vs exergonic:

A

Ender - nonspon, positive delta G

Exer - spon, negative delta G

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21
Q

Energy-coupling:

A

Coupling endergonic reactions with exergonic ones can drive thermodynamically unfavourable reactions, giving overall exergonic reactions

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22
Q

ATP and metabolism:

A

Anabolic: ATP to ADP
Catabolic: ADP to ATP

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23
Q

Cost to fuel body:

A

150 pound person consumes 2800 Calories/day; 50% efficiency so 1400 Calories of ATP; 65 kg of ATP; $10/gram

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24
Q

Perpetuation of biology requires that genetic information be:

A

Stably stored, expressed accurately in gene products, reproduce accurately
DNA is v stable because it’s missing a something group

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25
Q

How DNA encodes proteins:

A

Nucleotide sequence -> mRNA -> AAs sequence -> structure of protein -> biological function of protein

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26
Q

Water’s passive role in biological systems:

A

Structures of biomolecules are formed in response to interaction with water

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27
Q

Water’s active role in biological systems:

A

Participant in many biochemical reactions

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28
Q

Define: hydrogen bond

A

An electrostatic non-covalent interaction between an electronegative atom with a hydrogen linked to it and another electronegative atom with a free electron pair

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29
Q

How does a hydrogen bond compare to a covalent bond?

A

Twice as long, 5% as strong

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30
Q

Strength of hydrogen bonds:

A

Depends on geometry - a straight one is stronger than a bent one

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31
Q

Unusual properties of water:

A

High internal cohesion, heat of vap, specific heat capacity, melting/boiling points; the low density of ice

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32
Q

Biological significance of the high specific heat capacity of water:

A

Most animals are isothermic (need to regulate and maintain temp)
Metabolic processes give off heat

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33
Q

Reasons water rocks at hydrogen bonding:

A

Can be an acceptor or a donor; it’s little for optimal positioning

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34
Q

Hydrophobic effect:

A

Water excludes nonpolar substances, and nonpolar substances group together to interact with each other rather than with water

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35
Q

Micelle structure (and example):

A

Shape: Hydrocarbon tails are in the middle with a shell of heads surrounding them in a sphere.
Soap functions like this, allowing greases to come hang out in these hydrophobic centres.

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36
Q

Amphipathic molecules:

A

Contain both hydrophobic and hydrophilic portions (ex: fatty acids)

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37
Q

Solubility:

A

Depends on ratio of polar to nonpolar groups - the larger the nonpolar portion, the less soluble

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38
Q

Effects of weak interactions:

A

Formation and stabilization of structures, recognition interactions of one biomolecule with another, and binding of reactants to enzymes - PASSIVE

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39
Q

Important non-covalent interactions:

A

Hydrogen bonding; ionic, hydrophobic, van der Waals interactions - ACTIVE

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40
Q

Hydrogen bonding in nucleotides:

A

A and T form two; C and G form three

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41
Q

Hydrogen bonds and formation of biomolecules:

A

Not a force for the formation of structures but determinants of specificity

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42
Q

Ionic interactions vs water:

A

Contribution to biomolecular structures is reduced by shielding from water molecules

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43
Q

Van der Waals interactions:

A

Electron clouds of two uncharged atoms interacting
Abundant in core of proteins due to close packing
When two atoms are separated by the sum of their van der Waals radii, attraction is greatest

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44
Q

Ionization of water:

A 
Keq = [H+][OH-]/[H2O] = 1.8*10^-16M
[H2O] = 55.5 M, constant
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45
Q

Titration curves of weak acids: *

A

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

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46
Q

Buffering region: *

A

When solution is best able to resist changes in pH. Extends one pH unit to either side of the pKa. On a graph, midpoint of the buffer region is pKa.

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47
Q

Protonated vs unprotonated:

A

pH > pKa, unprotonated.

pH

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48
Q

Ideal buffer:

A

pKa matches the pH you want

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49
Q

Henderson-Hasselbalch:

A

Describes the relationship between pH of solution, pKa of weak acid, and the relative concentrations of the weak acid and conjugate base.
pH = pKa + log ( [A-] / [HA] )

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50
Q

Physiological pH:

A

pH = 7.4

Changes of 0.05 pH are dangerous (alkalosis, acidosis)

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51
Q

Triprotics:

A

Life Always Has A Goal plus Cysteine and Tyrosine

Lysine, arginine, histidine, aspartate, glutamate, cysteine, tyrosine

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52
Q

When does a polypeptide become a protein? Why?

A

51 AAs. It was decided that insulin was the shortest protein, and it has 51 AAs.

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53
Q

AAs are “bifunctional” which means hecking what?

A

Have acid and amino groups

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54
Q

Stereoisomers of AAs:

A

All AAs except for glycine have chiral carbons (enantiomers). Typically only L stereoisomers are found in proteins.

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55
Q

All AAs have:

A

Carboxyl group, amino group, alpha carbon, R group

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56
Q

Phosphorylation of AAs:

A

Take an AA that has a hydroxyl group. Add a phosphoryl group by kinase or remove it by phosphatase. Modifies behaviour in a de/activate kind of way.

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57
Q

Zwitterion:

A

The dipolar ion of an AA (ionized in aq)

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58
Q

Lecture 8, 42 minutes – exam question????? Fuck

A

check this out i guess

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59
Q

Peptide bonds:

A

Condensation reactions between carboxyl and amino groups - usually dehydration

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60
Q

Orientation of R groups around peptide bonds:

A

R groups tend to be in trans config

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61
Q

How are peptide chains numbered?

A

From N (amino) to C (carboxyl) termini

62
Q

I literally have no idea what this sentence means

A

Formation of peptide bonds eliminates the ionisable alpha-carboxyl and alpha-amino groups of the free amino acids

63
Q

Host Defence Peptides:

A

Naturally occurring antibiotics that can be used as treatment (adaptive immune system) AND as signalling molecules in the innate immune system – EXPENSIVE

64
Q

Retro-inverse peptides:

A

Isomers of natural peptides in which the sequence is reversed and D-AAs are used; they keep the topology of the regular peptide but are more resistant to proteolytic degradation. They usually work better than just D-isomers.

65
Q

yeah this makes sense i guess

A

Reverse (321 rather than 123) and change chiral conformation so that the peptide residues are in the right place, but the carbonyl and amino groups are in different places and it uses D-AAs, so it’s harder to break down

66
Q

How many unique proteins do bacteria/fruit flies/humans have?

A

5k, 16k, 25k

67
Q

Protein size:

A

Typically 100-1000 AAs - insulin is shortest with 51, titin is longest with 34 350

68
Q

Estimate protein size:

A

Divide molecular weight of the protein by 110 (the average weight of an AA)

69
Q

The three-dimensional (secondary/tertiary) structure of proteins is determined by…?

A

AA sequence

70
Q

The most important forces stabilizing the specific structures of proteins are…?

A

Non-covalent

71
Q

Protein folding:

A

Rapid step-wise process. Some can fold into the native conformation without help; some need chaperone/heatshock proteins. Driven by hydrophobic interactions etc.

72
Q

Chaperone proteins:

A

Help the protein adapt to gradual changes in temperature or other stressors.

73
Q

What does it mean that protein folding is a cooperative process?

A

If it starts to fold, the whole thing folds. If it starts to fall apart, the whole thing falls apart.

74
Q

Primary structure:

A

Main chain has NCCNCC pattern with side groups coming off

75
Q

Rules of secondary structure:

A

Optimize hydrogen bonding potential of main-chain carbonyl and amide groups; represent a favoured conformation

76
Q

Configuration of secondary structure:

A

Rotation around the C-N bond is restricted due to its partial double-bond nature. Side chains are in trans (except for PRO). Oxygen of carbonyl and hydrogen of amine nitrogen are trans to each other

77
Q

Conformation of secondary structure:

A

Each alpha-carbon is held in the chain by single bonds, about which there is complete freedom of rotation.

78
Q

Phi and psi angles: *

A 
Phi = C-alpha-N
Psi = C-alpha C
79
Q

Ramachandran plots:

A

Show every possible combination of phi and psi angles and highlights actually observed combinations.

80
Q

Steric interference (secondary structures):

A

Where the polypeptide is running into itself

81
Q

Alpha-helix:

A

Right-handed helix with 3.6 residues per turn. Each C=O (residue #n) forms a hydrogen bond with the amide hydrogen of residue #n+4. The bonds are almost parallel, which stabilizes the protein.

82
Q

AAs that like helical structures:

A

MALEK (methionine, alanine, leucine, glutamate, lysine)

83
Q

Tell me something about the phi and psi angles of each residue in an alpha-helix.

A

They’re all pretty similar I guess.

84
Q

AA sequence affects helix stability.

A

No proline or glycine.
No stretches of similarly charged AAs to minimize repulsion.
Positives and negatives are often 3-4 away from each other in the primary structure so they can be close in the secondary structure.
Aromatics are often 3-4 away to enable hydrophobic interactions.

85
Q

Tell me some things about the dipoles of alpha helices.

A

Result of C=O groups pointing toward C-terminus; +N, -C. Stabilized by putting an oppositely charged AA at each end (negative at the N terminus, positive at the C).

86
Q

Tell me something about the amphipathic nature of alpha helices.

A

By placing hydrophobic/philic AAs 3-4 residues apart, you can create a helix with one face all philic and the other face all phobic.

87
Q

Beta sheets and strands:

A

Almost fully extended polypeptides arranged side by side. Side groups alternately stick out above/below the plane of the sheet.

88
Q

Pauling was the coolest.

A

Concur.

89
Q

Amphipathic beta sheets:

A

The whole sheet may be amphipathic, with hydrophobic side chains on one face and hydrophilic side chains on the other.

90
Q

Hydrogen bonds stabilize beta strands.

A

Bonding between C=O and -NH on adjacent strands.

91
Q

Parallel vs anti-parallel beta strands:

A

Anti-parallel - strands run in opposite N to C direction. This is more stable due to better hydrogen bonding geometry. A beta sheet can be a mix of parallel and anti-parallel.

92
Q

How are the subunits of quaternary structure held together?

A

Non-covalent interactions. As per usual?

93
Q

Advantages of quaternary structures:

A

Stabilizes subunits and prolongs protein life.
Unique active sites are produced at the interface between subunits.
Helps facilitate unique and dynamic combinations of structure/function through physiological changes in tertiary and quaternary structures.
Conserving functional subunits is more efficient than selecting new proteins with ideal functions.

94
Q

What’s keratin part of?

A

Hair and fingernails.

95
Q

Primary structure of keratin:

A

Pseudo-seven repeat. A and D are hydrophobic.

96
Q

Secondary/tertiary structure of keratin:

A

Right-handed, amphipathic alpha-helices. A and D residues form a hydrophobic strip.
(Secondary and tertiary are the same I guess.)

97
Q

Quaternary structure of keratin:

A

Two hydrophobic strips put together to form a coiled-coil, two right-handed helices wrapping around each other in a left-handed fashion.

98
Q

Disulfide bonding in keratin:

A

Individual units are linked together by cysteine’s disulfide bonds. The more bonds there are, the stronger the substance will be (horn vs hair).

99
Q

What’s collagen part of?

A

Tendons, skin, holding the vascular system together. 25% of proteins in the body.

100
Q

Primary structure of collagen:

A

Gly-X-Y where X is usually proline and Y is usually hydroxyproline, a post-translational modification of proline.

101
Q

Secondary structure of collagen:

A

Left-handed helices of 3 residues per turn.

102
Q

Tertiary structure of collagen:

A

The whole thing is a helix okay just accept it

103
Q

Quaternary structure of collagen:

A

Coiled-coils with three left-handed helices wrapping around each other in a right-handed fashion

104
Q

Strength of collagen comes from…?

A

Successive linking of individual units into higher order structures. Post-translational modifications (hydroxyproline, hydroxylysine) provide covalent linkages.

105
Q

Collagen and age:

A

More cross links occur with age, resulting in brittle skin and tougher meat

106
Q

Collagen and post-translational modifications:

A

The enzymes that perform these reactions require vit C to function. Scurvy happens.

107
Q

Symptoms of scurvy:

A

Bruising, tooth loss, poor wound healing, bone pain, eventual heart failure.
Milder symptoms include fatigue, irritability, susceptibility to respiratory infections

108
Q

Vit C deficiency: (not scurvy though we already talked about that)

A

Vit C deficiency leads to defective triple helix (skin lesions, fragile blood vessels, bleeding gums)

109
Q

Genetic diseases involving collagen:

A

Osteogensis imperfecta, Marfan’s syndrome (Paganini violinist), Stickler syndrome, Ehlers-Danlos syndrome
Associated with brittle and abnormal bone structure, weakened cardiovascular capabilities, abnormal facial features, loose skin/joints, hyperflexibility

110
Q

Primary structure of silk:

A

Six-residue repeat that is rich in small AAs.

GSGAGA)(GSGAGA

111
Q

Secondary structure of silk:

A

Composed primarily of beta-sheets. The extendedness gives strength; the hydrogen bonds between strands and the van der Waals between sheets give flexibility.

112
Q

Uses of genetically engineered silk:

A

Sutures, artificial ligaments, body armour

113
Q

Where do prion diseases hang out?

A

Tend to be localized in brain and spinal cord.

114
Q

TSEs:

A

Transmissible spongiform encephalopathies - proteins misfolding into a pathological, infectious conformation. Progressive and fatal neurodegenerative diseases.
Ex: mad cow, chronic wasting, kuru.

115
Q

PRPCs:

A

Proteins involved in memory formation. Can misfold into PRPSC, which is pathological (kills neurons) and infectious.

116
Q

Prions are super stable.

A

They can survive in dirt for decades.

117
Q

Define: ligand

A

A molecule that is reversibly bound by a protein

118
Q

Ligands and binding sites are complimentary in:

A

Size, shape, charge, hydrophobicity, electronegativity, hydrogen bonding tendency

119
Q

Myoglobin:

A

Monomeric protein that facilitates oxygen storage in peripheral tissue. Consists of a polypeptide of 153 residues arranged in eight alpha-helices, and a heme prosthetic group.

120
Q

Hemoglobin:

A

Tetrameric protein found in erythrocytes that transports oxygen from the lungs to the periphery

121
Q

Heme:

A

A photopophryn ring system bound to a single Fe2+ atom, to use its oxygen affinity in a controlled way (no free radicals pls).

122
Q

Fe2+ vs Fe3+

A

2+ binds reversibly; 3+ does not.

123
Q

Heme’s interaction with Fe2+:

A

The ring provides four coordinating interactions with the iron. N acts as an electron donor to stop Fe2+ from becoming Fe3+.

124
Q

Fe2+ needs six coordinating interactions.

A

Four from heme, one from a histidine imidazole group, and one for oxygen. A distal histidine stabilizes the bound oxygen.

125
Q

How are heme groups bound to Mb or Hb?

A

In a specific and discrete pocket

126
Q

Oxygen-saturation curve of myoglobin:

A

Hyperbolic, indicating a single O2 binding constant.

127
Q

P50:

A

The amount of O2 required to half saturate the protein.

128
Q

P50 of myoglobin:

A

0.26 kPa - pretty low

129
Q

PO2 of lungs vs of periphery:

A

13.5 kPa in lungs and 4.0 kPa in periphery. (Myoglobin has a high affinity for O2 so it can grab it even when the PO2 is low.)

130
Q

The fraction of myoglobin saturated with oxygen at a given partial pressure of oxygen:

A

(theta) = [pO2] / ([pO2] + [P50])

131
Q

Oxygen’s positive cooperativity:

A

The first O2 causes a conformational change that makes it easier to bind subsequent O2. O2 promotes and stabilizes the R state of hemoglobin, which has higher oxygen affinity.

132
Q

A reaction equation concerning R and T states:

A

Deoxy-T + O2 oxy-R

133
Q

Define: allosteric

A

“Other site” - allosteric modulators/effectors bind to allosteric proteins at sites separate from the functional binding site.

134
Q

Homotropic vs heterotropic modulators:

A

Homo: when the modulator and normal ligand are the same.
Hetero: when the modulator is different from the normal ligand.

135
Q

Allosteric activators/inhibitors:

A

Activators stabilize R state; inhibitors stabilize T state.

136
Q

Structural/functional changes when Hb binds O2:

A

Iron atom moves into the plane of the ring, making it R state and causing massive changes in the quaternary structure.

137
Q

Flat vs puckered cells:

A

Deoxygenated is flat; oxygenated is puckered.

138
Q

Oxygen-binding curve of hemoglobin:

A

In the high PO2 of the lungs, Hb will completely saturate. In the periphery, Hb will release about half of its O2. It is most likely to give up O2 where PO2 is low and that body part needs it.

139
Q

P50 of oxygen closely matches … ?

A

Peripheral PO2

140
Q

Oxygen and 2,3-BPG: allosterics

A

O2 is a homotropic allosteric activator. BPG is a heterotropic allosteric inhibitor.

141
Q

BPG’s role in hemoglobin function:

A

Decreases Hb’s affinity for oxygen. Makes basketball stay away for longer.

142
Q

Structure of BPG:

A

Carries five units of negative charge and binds to the positively charged pocket that is formed at the interface between the subunits of deoxyHb

143
Q

How fetuses breathe:

A

Foetal Hb has one less unit of positive charge (AA) than adult Hb because it has to steal O2 from the mother’s blood. By having a less positive charge, it is less likely to bond with BPG, giving it a higher affinity for Hb.

144
Q

BPG and high-altitude adaptation:

A

BPG increases (from 5 to 8 mM), lowering O2 affinity to ensure delivery to periphery.

145
Q

Bohr effect:

A

pH dependence of hemoglobin’s oxygen affinity - at lower pHs, affinity decreases. Active tissues have lower pHs, so Hb releases more oxygen there. During extreme exercise, muscles may produce lactic acid to further drop the pH.

146
Q

Coordination of O2 delivery and CO2 removal - mechanism 1:

A

CO2 is taken up into red blood cells and converted to bicarbonate and a proton by the enzyme carbonic anhydrase.
CO2 + H2O ←→ H+ + HCO3
While CO2 is being taken up, the Bohr effect releases more O2.

147
Q

Coordination of O2 delivery and CO2 removal - mechanism 2:

A

CO2 can form a covalent carbamate linkage to the N terminus of each chain of a hemoglobin chain to form carbaminohemoglobin.
Carbamino hemoglobin has a lower O2 affinity than Hb. Bohr effect releases more O2.

148
Q

Sickle-cell anemia:

A

Results from a single amino acid change (Glu6Val – sixth spot turns from a glutamate to valine). Hydrophilic residue replaced with a hydrophobic. Fibres form at low PO2, blocking blood flow to the extremities.

149
Q

How does SCA affect R/T states?

A

T state hemoglobin is rigid; R state is aight, still flexy

150
Q

Malaria and SCA:

A

Malaria infects red blood cells and decreases their pH. The lower pH will cause the cell to dump its O2 and sickle. The malarial cells will be identified as sickled and will be destroyed by the spleen.

BMSC 200 (2 decks)

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