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BIOL2030 > FINAL EXAM > Flashcards

FINAL EXAM Flashcards

1
Q

4 MAJOR CLASSES OF BIOMOLECULES

A

nucleic acids
proteins
carbohydrates
lipids

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2
Q

Lipids are different from proteins, polysaccharides and nucleic acids in that:

A

They aren’t polymers of monomers. They are an association of similar units.

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3
Q

Biochem connects genotype and phenotype through various ‘omes’
genome -> transcriptome -> proteome -> metabolome

What are each of these?

A 
Genome = protein coding human genes
Transcriptome = collection of mRNA
Proteome = collection of proteins
Metabolome = breakdown and synthesis of biomolecules.
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4
Q

Anabolism

A

biosynthesis of larger biomolecules

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5
Q

Catabolism

A

degradation (oxidation) of molecules

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6
Q

Reactions move toward order/disorder

A

disorder

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7
Q

For a reaction to be spontaneous, deltaG should be +/-ve
deltaH should be +/-ve
detlaS should be +/-ve

A

-ve
-ve
+ve

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8
Q

The major chemical elements in living system

A

C, N, O, P, H, S

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9
Q

Chemical conformation is defined by

A

rotation around covalent bonds

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10
Q

Chemical configuration changes require

A

making and breaking bonds.

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11
Q

What is D?

A 
D = dialectic constant = force between two ions
D = 0 in a vacuum and D = 80 in water
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12
Q

Vander waals interactions

A

Very weak attractive forces doe to dipole or induced dipole interactions of closely spaced atoms.
Atoms can’t get closer than their radii without covalent bonding.

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13
Q

Hydrogen bonds are strongest when

A

3 atoms are in a line

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14
Q

Hydrogen bonds are

A

when one hydrogen atom is shared between two electronegative atoms. Partial covalent character

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15
Q

Hydrogen bonding between two peptide groups would be strongest….

A

at protein surface exposed to water (D=80)

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16
Q

Hydrophobic Effect

A

Since water is polar it repels the non polar substance, losing entropy.

So, when a non polar substance is placed in water it will congregate to decrease the amount of SA exposed to water.

Leads to clusters, beading, micelles/vesicles/bilayers

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17
Q

If an acetate buffer (pH -4.76) solution is at pH 5.76, what is the ration of [CH2COO-] to [CH3COOH]?

A

10 : 1 because one cahnge in pH up means that there is 10 times as much base as acid int here.

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18
Q

What thing affects the usefulness of the buffer?

A

pK value and total concentration

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19
Q

Why does DNA have a polar exterior?

A

Negative phosphate groups

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20
Q

Most common form of DNA

A

B form

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21
Q

Things that stabilize the DNA double helix?

A

hydrogen bonds
Mg2+ binding to phosphate backbone
hydrophobic effect

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22
Q

Oligonucletotides…

A

are short stretches of nulceotide polymer that will hybridize with matching ssDNA.
PROBES!

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23
Q

Exons make up how much of our total DNA?

A

ABout 2%

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24
Q

miRNA

A

regulates gene expression by blocking mRNA translation or stability

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25
Q

siRNA

A

work similarly to miRNAs. Have therapeutic potential.

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26
Q

Dominant level of regulation of gene expression in prokaryotes and eukaryotes

A

initiation of transcription

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27
Q

IF a genome, proteome and metabolome are defines by the number of genes, proteins and metabolites, what’s the order?

A

Proteome > genome > metabolome

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28
Q

isoelectric point

A

Every amino acid has an isoelectric point - the pH value at which, the net charge of the molecule is 0
Low number for acid AAs and high number for basic AAs (intuitively)

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29
Q

Proline

A

The only imino acid. The side chain connects to the NH group and forces a kink into the polypeptide.

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30
Q

Trypotophan

A

is the largest AA

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31
Q

Glycine

A

Is the only achiral AA

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32
Q

Cysteine

A

Has a sulhydryl group that can be oxidized to forma disulfide bond with another cysteine. Inside the cell it’s usually in SH form and outside the cell it is usually in S-S form. It can be kept in SH form invitro by adding reducing agents (mercaptoethanol or diotheitol)

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33
Q

Acidic AAs

A

Aspartate and Glutamate

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34
Q

Basic AAs

A

Lysine and Arginine

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35
Q

How should be write proteins in conventional form

A

N->C direction

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36
Q

Protein conformational diseases

A

ALzheimers, Prions (CJD, Mad Cow)

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37
Q

Alzheimers

A

Transition between a-helix and B-sheet problem

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38
Q

Prions diseases

A

CJD and Mad Cow

Protien undergoes conformational change that changes its function. Change to B-sheet allows stacking of it into a fibre

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39
Q

Protein Motifs

A

Small regions with a defined stequence or structure, often serving a common function in different proteins

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40
Q

Protein Domain

A

Sub regions of single poly-peptide chains that can fold and function independently

Proteins can evolve by swapping one domain for another (eg antibodies)

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41
Q

wireframe model

A

shows every atom

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42
Q

Backbone model

A

shows only the polypeptide backbone shape

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43
Q

Ribbon model

A

shows the secondary structures

44
Q

Spacefill model

A

Shows the vander waals radii

45
Q

Denaturation

A

conformational change that leads to loss of function

46
Q

The native state

A

functional state of a protein

47
Q

The native state is stabilized by

A
  • Burying NP side chains
  • Optimizing H-bonding
  • Maximizing side chain packaging in interior (vander waals)
48
Q

Denatured state is favoured by

A
  • Increased conformational entropy of the unfold R group

- heat, chemicals, pH extremes, mutations

49
Q

Chaperonin assisted folding of proteins

A

While the primary protein structure dictates its 3D structure, many larger proteins require assistance to explore their conformational space before something bad happens to them

50
Q

Anfisen Experiment

A

Native structure of RNAse only recovered is urea is removed before/during removal of the reducing agent, but not after

51
Q

Levinthal Paradox

A

If explored randomly it would take the age of a universe to explore all of the conformations possible for a protein, but they do it in seconds.
Folding is directed by rapid formation of secondary structure that limits further possibilities.

52
Q

Some regions of proteins are intrinsically disordered. What does this mean?

A

They only fold upon interaction with binding partners.

53
Q

Dialysis

A

A semipermeable sac and small molecules (urea, mercaptoethanol) may leave while large molecules (RNAse) stay.

54
Q

Differential Centrifugation

A
  • a type of subcellular fractionation
  • Done in buffer w similar density to water
  • Initially low speed; big things to bottom
  • Centrifuge supernatant at higher speed to get second pellet of organelles
  • Keep spinning at higher and high speeds for ribosomes and large molecules
55
Q

Isopyonic centrifugation

A

Gradient of density where lower density things are at the top. Spin until light things migrate to top and heavy things are at bottom.

56
Q

The most discriminating property of a protein is…

A

its function

57
Q

Affinity chromatography

A

Protein will bind to an immobilized, specific ligand and all other proteins will pass through. Use an affinity tag to the recombinant protein for expression and purification. BInds to the protein and extracts it.

58
Q

Size exclusion chromatography

A

Packed course polymer beads and run protein and solvent through. Large proteins will come out first.

59
Q

Ion exchange chromatography

A

Polymer beads with -vely charged functional groups. Protein mixture added and basic proteins won’t ionize until higher pH
Proteins with -ve charge will move out first with -ve beads.
Adding salt interacts with the -ve beads and displaces the proteins.

60
Q

SDS-PAGE

A

reducing agent usually added to cleave S-S bonds and resolve individual polypeptide chains

61
Q

2D page

A

Separates based on pH and size.

Can be useful for revealing disease related to protein levels.

62
Q

Protein sequence techniques (3)

A

1) Mass Spec
2) X-Ray Crystallography
3) Protein NMR

63
Q

Mass Spectrometry

A

A way to deduce protein sequence.
Distinguish proteins on a basis of mass to charge ratio.
Trypsin used to cleave Lys-Arg
Get Protein Mass Fingerprinting - each pattern has a unique pattern of Lys/Arg Fragments
Tandem MS-MS further breaks up the fragments at peptide bonds and finds masses of fragments on a coupled second mass spectrometer.

64
Q

X-Ray crystallography

A

3D arrangement of atoms in a protein deduced by measuring diffraction of xrays in a protein crystal.
Provides detailed information on conformation, enzyme mechanism and binding.
Protein Data Bank stores deduced structures.

65
Q

Protein NMR

A

Samples the nuclear environment using spin
Electromagnetic resonance requency of nuclei in a stron magnetic field can prvide information on neighbouring atoms
Done in solution so can give info on mobility (see frays on the end where there is more space for movement)

66
Q

Post Translational modifications

A

Phosphorylation
Glycosylation
Proteolysis

67
Q

Phosphorylation of Proteins

A

Transfer a PO4 group from ATP. Catalyzed by protein kinases.
Regulates metabolism and signal transduction

68
Q

Glycosylation of proteins

A

Attachment of carbohydrate group to Asn and Ser on secreted, EC or luminal proteins

69
Q

Proteolysis of protein

A

A way to synthesize peptide hormones.

70
Q

Ubiquitin and proteasomes

A

The final post-translational modification

Ubiquitinate and degrade proteins

71
Q

Invariant residues on hemoglobin and myoglobin

A

The proteins are different but the things they have in similar indicate critical functions.

72
Q

Hemoglobin and myoglobin curves

A

Hemoglobin has a sigmoidal curve meaning it can release much more oxygen at lower pO2
Myogolib oxygen binding is hyperbolic.

73
Q

Myoglobin strcture

A

monomeric. Oxygen binds to the Fe2+ porphyrin heme prosthetic group. When the heme is buried, it can’t be oxidized.

74
Q

Hemoglobin ALlosteric effectors

A

H+ (Bohr Effect) - CO2 production in tissues leads to decreased pH, protonating a side chain and stabilizing T state
CO2 rects with N terminal to form carbamate. Stabilizes T
BPG binds at the +vely charged hole, ONLY in the T state to stabilize it. Increased at high altitudes and in chronic anemia (favours O2 release)

75
Q

Sickle Cell anemia

A

Point mutation in DNA codes for structurally different hemoglobin. It polymerizes into long fragments and distrorts the RBC

76
Q

IgG

A

2 heavy chains and 2 light chains stabilized by intra and inter-chain disulfide bonds
Organized into complement and antigen binding regions of globular B-sheet domains

77
Q

Actin filaments

A
  • Microfilaments (smallest)
  • Fibrous, F actin is a polymer of globular, G actin
  • +ve pointed end and -ve barbed end
  • Organized into cables by actin binding protein
  • Functions: cortical skeleton under p. membrane and motility.
78
Q

F-Acting Assembly and Treadmilling

A

ATP bound to G actin hydrolyzed when it is incorporated into F-actin
Polymerization more rapid at +ve end.
Capping proteins block +ve end polymerization.
Severing Proteins break filaments.
Hydrolysis of ATP allows treadmilling. Net poly at +ve end and loss at -ve end.

79
Q

phalloidin

A

fungal compound that stabilizes F actin - too much assembly

80
Q

cytochalasins

A

fungal compound that destabilizes f actin

81
Q

Immunochemical detection

A
  1. F(AB) has heavy and light chain residues
  2. Specific binding to antigen’s EPITOPE due to complementary surface, H bonds and electrostatic interactions
  3. Antibody specificity can be used to detect selected proteins by ELISA and Western Blot
82
Q

Collagen

A

Fibrous. Most abundant protein in human body.
Twisted braid of 3 extended chains. Uses proline for kinks.
Makes cables and meshes in EC matrix, connective tissue and bone.
GLYCINE at every 3rd residue allows proximity of chains.
Interchain hydrogen bonding strengthened by hydroxyglycine and hydroxyproline residues.

83
Q

Diseases of collagen

A

Scurvy (requires ascorbing acid for hydroxylase rxn)
Ehlers-Danlos (stretchy skin)
Osteogenesis imperfects (brittle bone)

84
Q

Elastin

A

Fibrous protein.
Deformable. Found in elastic tissues.
Chains connected by Lys-cross linking
Cleaved in alveolar wall by ELASTASE, which is inhibited by a-1 antitrypsin, which has decreased activity in EMPHYSEMA

85
Q

Where does collagen processing occur?

A

ER, Golgli and outside of the cell. Further assembly outside of the cell.

86
Q

Microtubules

A

Reversible aggregates of tubulin heterodimer forming hollow tubes.
Polar - polymerize and depolymerize from +ve end. Regulated by GTP.
-ve end anchored to an organizing centre (radiate and retract).
Straight and rigid tracks, form cilia and flagella.
Target of anti-cancer drugs.

87
Q

Which filament is the target of anti-cancer drugs

A

Microtubules

88
Q

Intermediate filaments

A

Insoluble fibrous proteins.
Fundamental unit is a a-helical coiled coil., strengthened by NP residues bt helices.
No polarity
In nuclear lamin, keratin in epithelial cells and neurofilaments.
Must depolymerize during mitsosis (nuclear membrane)

89
Q

Actomyosin

A

ATP hydrolysis generates muscle contraction.
Thick and thin filaments slide past each other because of myosin.
Myosin head bound to an actin subunit of a thin filament. ATP binds to myosin head and it releases actin. Hydrolysis of ATP causes rotation of myosin and rebinding of actin farther along.
Binding actin causes ADP + P to be released from myosin and myosin head returns to normal conformation. (rigor)

90
Q

3 ways to incr rate of rxn

A

increase temp
increase [ ]
add catalyst

91
Q

How do enzymes do what they do?

A

Put substrates in proximity
Put them in correc torientation
Provide functional groups for catalysis

92
Q

Carbonic anhydrase

A

One of the fastest enzymes converts CO2 to H2CO3 in the blood to regulate pH of the blood.

93
Q

3 types of enzyme catalysis

A

acid base
covalent
metal

94
Q

Acid-base catalysis

A

Transfer or removal of H+ lowers free energy of the transition state

95
Q

Covalent catalysis

A

Transient formation of a covalent bond bt enzyme and substrate (enzyme acts as a nucleophile, donating an electron pair)

96
Q

Metal catalysis

A

Metal plays a direct or indirect role.
At the active site, metal ions fan mediate redox reactions, promote reactivity of other functional groups or interact directly with the substrate.
Ex: Alcohol dehydrogenase uses a Zn ion to stabilize the developing O-

97
Q

apo enzymes

A

don’t require cofactor

98
Q

holoenzyme

A

enzyme with a cofactor for the reaction

99
Q

The elctrophile

A

is an electron deficient atom

100
Q

Chymotrypsin

A

A member of the serine protease family with a preference for bulky, NP residues on the carboxyl side of the peptide bond.
Uses covalent and acid-catalyzed catalysis in hydrolysis of a peptide bond.
Catalytic triad of Asp102, His57 and Ser195 at the active site of all serine proteases.
Flexible protein. Adopts diff conformation as it goes through catalytic cycle - induced fit.

101
Q

Catalytic triad

A

Asp102, His57, Ser 195 on all Ser Proteases.
Asp102 anchors His57
His57 acts as a base and later as an acid
Ser195 acts as a nucleophile to attack the peptide bond.
Replacing Asp102 or His57 has a huge -ve effect, but replacing Ser195 isn’t as bad.

102
Q

Serine Proteases

A

Syntehsized as inactive precursors (zymogens) and are activated by cleavage by other proteases (autoactivation)

103
Q

COX isozymes

A

Catalyze the 1st step in the synth of prostaglandins
COX 1 involved in prostaglandin production and COX2 does pain and inflammation.
Both cox isozymes are targets of NSAIDs
COX 2 has a larger active site so there are now COX2 specific drugs.

104
Q

Glucogenic

A

AAs that can be converted into pyruvate, oxaloacetate or other citric acid cycle intermediates

105
Q

Ketogenic

A

AAs that can only be converted into acetyl CoA, ketone bodies or FAs

BIOL2030 (2 decks)

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