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Biochemistry > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

What can an alcohol be oxidized into?

A

alcohol - aldehyde - carboxylic acid

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2
Q

What are three differences between prokaryotic and eukaryotic cells?

A 
Prokaryotic: 
- no membrane bound organelles
- free circular DNA
- 1-10 um
Eukaryotic
- membrane bound organelles
- chromatin bound DNA
- 10 -100um
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3
Q

What is the role of the nucleus?

A

carries genetic information, site of transcription

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4
Q

What is the role of the endoplasmic reticulum?

A

secretory protein and lipid synthesis

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5
Q

What is the role of the golgi?

A

glycosylation, distribution center

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6
Q

What is the role of the mitochondria?

A

respiration (TCA cycle), electron transport, ATP synthesis

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7
Q

What is the role of the lysosome?

A

acidic compartments with proteases that break down proteins

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8
Q

What is the role of the peroxisome?

A

lipid breakdown

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9
Q

What is kinetics?

A

will the reaction happen, involves activation energy from the reactants to the transition state

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10
Q

What is thermodynamics?

A

change in energy between the reactants and the products, spontaneous or nonspontaneous process

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11
Q

What is the first law of thermodynamics?

A

energy is conserved, cannot be created or destroyed

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12
Q

What is the second law of thermodynamics?

A

entropy is always increasing (spontaneous process -> order to disorder)

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13
Q

What is delta H

A

enthalpy

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14
Q

What is delta S

A

entropy

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15
Q

What does delta H > 0 indicate?

A

endothermic

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16
Q

What does delta H< 0 indicate?

A

exothermic

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17
Q

What does delta G < 0 indicate?

A

spontaneous process

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18
Q

What does delta G > 0 indicate?

A

non-spontaneous

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19
Q

What does delta G = 0 indicate?

A

the reaction is at equilibrium - forward and reverse are the same, concentrations of A and B not changing

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20
Q

What does delta S > 0 indicate?

A

disorder is increasing

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21
Q

What does delta S less than zero indicate?

A

disorder is decreasing

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22
Q

What are biochemical reactions initiated by?

A

changes in concentrations of reactants and products

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23
Q

What does Keq > 1 indicate?

A

products > reactants

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24
Q

What does Keq < 1 indicate?

A

products < reactants

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25
Q

What is le chatlier’s principle?

A

deviation from equilibrium stimulates processes to restore equilibrium

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26
Q

Describe activation energy at equilibrium.

A

Activation energy is the same in both directions at equilibrium

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27
Q

Why is water so important in biology?

A
  • controls the structure of biomolecules
  • hydrogen bonding and hydrophobic effect
  • active participant in biological reactions
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28
Q

What is the vanderwaals radius of an H and an O atom?

A

H - 1.2 angstrom

O - 1.4 angstrom

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29
Q

What is the bond length between H - O in a water molecule?

A

0.958 angstrom

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30
Q

What is the bond angle between the two hydrogens in a water molecule?

A

104.5 degrees

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31
Q

What is the bond angle between two Hs in CH4?

A

109.5

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32
Q

What is the polarity of a water molecule?

A

O: -.66e
H: +.33e

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33
Q

What is e-?

A

the charge of an electron

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34
Q

What are the two components of a hydrogen bond?

A

a donor: electron poor (H)

an acceptor: electron rich (O)

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35
Q

What is the length of a typical H-bond?

A

1.8Å

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36
Q

What are the five types of bonds in strength order?

A 
Covalent bond - 400kj/mol
Ionic bond - 80kj/mol
H - bond - 20kj/mol
Dipole-dipole - 9kj/mol
London dispersion forces- 0.3kj/mol
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37
Q

What is a permanent dipole?

A

between two polar molecules

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38
Q

What is an induced dipole?

A

one polar molecule, one non-polar molecule with an induced dipole

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39
Q

What are london dispersion forces?

A

between two non-polar molecules

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40
Q

How many h-bonds can a water molecule form?

A

4 - Hbonds
Has 2 acceptors (electron pairs on O)
and 2 donors (H atoms)

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41
Q

What is ice made up of?

A
  • a tetrahedral array of H-bonds

- open structure - 6-membered rings

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42
Q

What happens molecularly when water freezes?

A
  • water expands when freezing, water molecules are pushed far apart and fixed
  • this means ice is less dense than water
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43
Q

What is the density of water vs density of ice?

A

Density of water = 1g/ml

Density of ice = .92g/ml

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44
Q

Describe the bonding/ structure of liquid water.

A
  • irregular, dynamic H-bonding
  • break/reform every 2 x 10 -11
  • 3-7 member rings
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45
Q

Define solubility.

A

Ability of the solvent to interact with a solute

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46
Q

When will a substance dissolve?

A

a substance will dissolve when solute-solvent interaction is stronger than solute-solute interaction

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47
Q

What does hydrophilic mean?

A

polar/ionic - solvated in H2O

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48
Q

What does hydrophobic mean?

A

non-polar - does not interact w/ H2O (does not necessarily mean no hydrogen bonds)

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49
Q

What is the hydrophobic effect driven by?

A

entropy

50
Q

What is the hydrophobic effect?

A
  • Non-polar solutes aggregate in water to minimize the amount of surface area the solutes are exposed to, therefore decreasing the number of ordered H2O molecules
51
Q

How does entropy change when a hydrophobic molecule is dissolved?

A
  • Entropy changes in this reaction: H2O becomes more ordered and forms cages when a hydrophobic/non-polar molecule is dissolved, making this less favorable
52
Q

What are amphiphiles?

A

contain polar and non-polar groups

53
Q

What structures do amphiphiles form in nature?

A

micelles and bilayers

54
Q

What is osmosis?

A

movement of water across a membrane from high to low concentration

55
Q

What is osmotic pressure?

A

pressure applied to prevent inward flow of water

56
Q

Describe osmotic pressure in cells.

A
  • in cells the osmotic pressure is equal inside and outside

- need balanced salt concentrations

57
Q

What is dialysis?

A
  • a membrane removes salt from proteins to purify
  • kidney dialysis removes salt from the blood
  • solutes diffuse through the membrane until equilibrium is reached (not osmosis because water is not crossing a membrane)
58
Q

What is a solvent?

A

H2O

59
Q

What is a solute?

A

NaCl, what is being dissolved

60
Q

Describe the ionization of water.

A
  • protons can easily jump from one H2O to another
  • H3O and OH have high mobility in water
  • acid - base reactions are rapid in H2O
61
Q

What does 1 pH unit indicate?

A

10 -fold difference in [H+]

62
Q

What is a bronsted lowry acid?

A

a substance that can donate H+

63
Q

What is a bronsted lowry base?

A

a substance that can accept H+

64
Q

What does a high or low pka indicate?

A
  • high pKa = less likely to dissociate

- low pKa = more likely to dissociate

65
Q

When do species have multiple pKas?

A
  • when there are multiple ionization states
66
Q

What is the relationship between pH and pKa?

A
  • pKa is the pH at which 50% of HA has dissociated

- [HA] = [A-] when pH = pKa

67
Q

What is the buffering capacity?

A

1 pH unit above/below pKa

68
Q

What is the difference between the sugar of RNA and DNA?

A
  • RNA - ribose

- DNA - 2’deoxyribose (no OH at the 2’ carbon)

69
Q

What are the purines?

A

Adenine and Guanine

70
Q

What are pyrimidines?

A

Cytosine, Thymine, Uracil

71
Q

How are bases of DNA linked?

A

-phosphodiester linkages

72
Q

What is the pKa of O- in a phosphodiester linkage?

A

pKa = 0 at pH = 7 (prefers deprotonated form)

73
Q

Why are the phosphodiester linkages of RNA polymers weaker?

A

RNA is less stable because of an additional 2’ hydroxyl, if a base deprotonates it the oxygen can attack the phosphodiester linkage - this makes RNA more prone to cleavage

74
Q

Describe the structure of DNA.

A
  • double helix
  • 2 polynucleotide strands
  • chains are antiparallel
  • right-handed helix
  • bases are hydrogen bonded to bases on opposite strands
  • major and minor groove
75
Q

Describe how the hydrophobic effect is at play in the structure of DNA.

A
  • bases are at the core of the helix and phosphates are exposed to water
  • this is because the bases are non polar and phosphates are negatively charged
76
Q

How many hydrogen bonds are there between the bases of DNA?

A

A - T (two)

G - C (three)

77
Q

Describe the structure of RNA.

A
  • formation of stem loop structure
  • single stranded
  • intramolecular -bonding
78
Q

What is the central dogma?

A

DNA is transcribed into RNA and translated into protein

79
Q

What are the building blocks of DNA replication?

A
  • deoxynucleotide triphosphates are the building blocks (dNTPs)
80
Q

Which direction is DNA replicated in in nature? vs in the lab?

A

5’ - 3’ in nature

3’ - 5’ in the lab

81
Q

Describe DNA replication.

A
  • RNA primers - necessary for DNA polymerase to bind to
  • generate by primases
  • helicase and topoisomerase unwind DNA
  • leading strand - continuous
  • lagging stranf okazaki fragments
82
Q

Describe the chemical reaction of DNA replication

A

3’ hydroxyl is nucleophile (deprotonated by a base) and phosphate is electrophile

83
Q

What are the two strands of DNA in transcription?

A

coding strand and template strand (rna identical to codinf strand)

84
Q

Describe the process of transcription.

A
  • DNA template
  • catalyzed by RNA polymerase
  • synthesis occurs 5’-3’
  • building blocks —> NTPs
  • no primer required
85
Q

Which direction are proteins translated in?

A

N-term to C-term

86
Q

What are the three types of RNA?

A

messenger RNA - encodes for protein sequence
tRNA - transfer
rRNA - makes up the ribosome

87
Q

Describe tRNA.

A
  • 3’ hydroxyl of tRNA binds to O- of an amino acid
  • when it has an amino acid tRNA is called “amino acylated”
  • contains an anticodon loop that carries 3 nucleotides that read the codon of RNA
  • enzymes called tRNA synthetases add the amino acids to tRNA
88
Q

What are the steps of classic Sanger Sequencing?

A
  • Attach a primer that contains a radiolabel or fluorescence (Why?)
  • Run 4 PCR reactions, with DNA polymerase, and ddNTPs
  • Run the 4 reactions on a gel - (remember a primer was added, so first few nucleotides are known)
  • Read from bottom to top of the gel (5’ - 3’)
  • Reverse complement is the actual template strand
  • Cant get info on the first base (of actual template) using this method (Why?)
89
Q

What are the steps of one pot sanger sequencing?

A
  • No radiolabel/fluorescence on the primer
  • dNTPs and ddNTPs with fluorescent dyes are all added to the same reaction with DNA polymerase
  • Reaction is run on a gel (one lane), colors indicate the places where specific bases were added
  • Read from bottom to top of the gel (5’ - 3’)
  • Reverse complement is the actual template strand
  • (info can be gotten on the first nucleotide)
90
Q

What are two other methods of sequencing (other than sanger)?

A
  • Replace the gel with capillary electrophores - this gives us faster results and better resolution
  • Next gen seqeuncing
91
Q

What are ddNTPs?

A

dideoxynucleotides - deoxyribose lacks -OH at 3’ carbon that is required for elongation of a DNA strand

92
Q

What is PCR?

A

Polymerase chain reaction

93
Q

What does PCR do?

A

amplify (create many copies of) a specific DNA sequence

94
Q

What are the components of a PCR reaction?

A
  • primers - forward and reverse, bind specifically to the region you want amplified
  • DNA polymerase - must be heat stable (Taq which was isolated from a thermophile)
  • dNTPs
  • template strand
95
Q

What is the process of a PCR reaction?

A
  • design primers
  • heat - denature
  • cool - anneal to primers
  • extension
  • 20 cycles will create 2^20 amplification
96
Q

What is the process of cloning?

A
  • Restriction digest
  • Ligation
  • Transformation
  • select for cells with plasmid
97
Q

What are two components of a vector/plasmid in cloning?

A
  • MCS - multiple cloning site - short segment of DNA that contains many restriction sites
  • Amp^R - antibiotic (ampicillin) resistance gene
98
Q

What is site directed mutagenesis?

A
  • uses a primer that carried desired mutation to introduce a specific mutation into the DNA strand
99
Q

What is the pKa of the amine group in an amino acid?

A

9-10

100
Q

What is the pKa of the carboxyl group in an amino acid?

A

3.1

101
Q

What is the alpha carbon of an amino acid?

A

central carbon to which the amine and carboxyl group are attached (R group and H also attached)

102
Q

What is the stereochemistry of the alpha carbon?

A
  • s - stereochemistry (chiral center)
  • counter clockwise when the hydrogen is facing into the page
  • priority goes: amino (N-bonded directly), carboxyl (C=O), then R-group
103
Q

What is the regular configuration of all natural amino acids?

A

L - amino acids

104
Q

Describe the pKas given for the amino acids. What would occur if they were place in a hydrphobic pocket?

A
  • the pKa values are the pKas when directly facing water

- if in a hydrophobic pocket, the amino acids would be LESS likely to ionize and pKa would increase

105
Q

What direction is s?

A

counter clockwise

106
Q

How many bonds between each set of base pairs?how does that impact denaturation/ melting temp?

A
  • G-C 3
  • A-T 2
  • harder to denature, more H- bonds
  • higher G-C content = harder to denature and higher melting temp
107
Q

What are the two other amino acids, not naturally occuring?

A

selenocystein and pyrolysine

108
Q

What character does an amide bond possess?

A

some double bond character, little rotation

109
Q

What are some possible post-translational modifiactions of proteins?

A

phosphoserine - add (po4)

methy - can be added wherever there is an NH

110
Q

What conformation of an amide bond is favored?

A

trans is always favored to cis 1000:1

exception: proline trans favored 4:1

111
Q

What is a method for protein quantification?

A

ELIZA

112
Q

What is an ELIZA?

A

enzyme- linked immunosorbent assay

113
Q

Describe the steps of an ELIZA?

A
  • have a plate with an immobilized antibody that recognizes your protein of interest
  • lyse cell and add mixture of proteins to plate
  • wash away unbound proteins
  • use a secondary antibody (HRP) with an enzyme attached
  • can be amplified to produce a fluorescent product
114
Q

What are four methods to purify proteins?

A
  • charge
  • hydrohpobicity
  • size
  • affinity chromatography
115
Q

Describe the process to separate proteins by size.

A
  • Ion exchange chromatography
  • resins / beads the opposite charge of protein of interest
  • anion (-) cation (+)
  • charged proteins bind to the column, strength of charge determines how tightly
  • elute with changing pH
116
Q

Describe the process to separate proteins by hydrophobicity.

A

Hydrophobic interaction chromatography

  • hydrophobic proteins stick to the column
  • elute with detergents
117
Q

Describe the process to separate proteins by size.

A
  • size exclusion chromatography
  • beads with pores
  • smaller = longer time to elute
118
Q

What is affinity chromatography?

A
  • specific antibody
  • HIS tag - Ni column
  • FLAG tags HA tags with specific antibodies
119
Q

What is a strategy for protein sequencing?

A

Edman degradation

120
Q

Describe Edman degradation.

A
  • requires a pure peptide
  • plucks off single amino acid at a time from end terminus
  • PITC (N=C=S)
  • Creates PTH amino acid
  • Repeat cycles to figure out the sequence
121
Q

What is the process of mass spec?

A
  • protease degradation of peptide mixture with Trypsin
  • (cleaves at K - lysine and R - arginine)
  • run mass spec and isolate a peptide
  • fragmentation of peptide binds at low enough energy that only a certain percentage of the bonds fall apart
  • b fragments left
  • y fragments right

Biochemistry (12 decks)

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