Exam 1 (Final) Flashcards
1
Q
What can an alcohol be oxidized into?
A
alcohol - aldehyde - carboxylic acid
2
Q
What is kinetics?
A
will the reaction happen, involves activation energy from the reactants to the transition state
3
Q
What is thermodynamics?
A
change in energy between the reactants and the products, spontaneous or nonspontaneous process
4
Q
What is the first law of thermodynamics?
A
energy is conserved, cannot be created or destroyed
5
Q
What is the second law of thermodynamics?
A
entropy is always increasing (spontaneous process -> order to disorder)
6
Q
What is delta H
A
enthalpy
7
Q
What is delta S
A
entropy
8
Q
What does delta H > 0 indicate?
A
endothermic
9
Q
What does delta H< 0 indicate?
A
exothermic
10
Q
What does delta G < 0 indicate?
A
spontaneous process
11
Q
What does delta G > 0 indicate?
A
non-spontaneous
12
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
13
Q
What does delta S > 0 indicate?
A
disorder is increasing
14
Q
What does delta S less than zero indicate?
A
disorder is decreasing
15
Q
What are biochemical reactions initiated by?
A
changes in concentrations of reactants and products
16
Q
What does Keq > 1 indicate?
A
products > reactants
17
Q
What does Keq < 1 indicate?
A
products < reactants
18
Q
What is le chatlier’s principle?
A
deviation from equilibrium stimulates processes to restore equilibrium
19
Q
Describe activation energy at equilibrium.
A
Activation energy is the same in both directions at equilibrium
20
Q
Why is water so important in biology?
A
- controls the structure of biomolecules
- hydrogen bonding and hydrophobic effect
- active participant in biological reactions
21
Q
What is the vanderwaals radius of an H and an O atom?
A
H - 1.2 angstrom
O - 1.4 angstrom
22
Q
What is the bond length between H - O in a water molecule?
A
0.958 angstrom
23
Q
What is the bond angle between the two hydrogens in a water molecule?
A
104.5 degrees
24
Q
What is the bond angle between two Hs in CH4?
A
109.5
25
What is the polarity of a water molecule?
O: -.66e
H: +.33e
26
What is e-?
the charge of an electron
27
What are the two components of a hydrogen bond?
a donor: electron poor (H)
| an acceptor: electron rich (O)
28
What is the length of a typical H-bond?
1.8Å
29
What are the five types of bonds in strength order?
```
Covalent bond - 400kj/mol
Ionic bond - 80kj/mol
H - bond - 20kj/mol
Dipole-dipole - 9kj/mol
London dispersion forces- 0.3kj/mol
```
30
What is a permanent dipole?
between two polar molecules
31
What is an induced dipole?
one polar molecule, one non-polar molecule with an induced dipole
32
What are london dispersion forces?
between two non-polar molecules
33
How many h-bonds can a water molecule form?
4 - Hbonds
Has 2 acceptors (electron pairs on O)
and 2 donors (H atoms)
34
What is ice made up of?
- a tetrahedral array of H-bonds
| - open structure - 6-membered rings
35
What happens molecularly when water freezes?
- water expands when freezing, water molecules are pushed far apart and fixed
- this means ice is less dense than water
36
What is the density of water vs density of ice?
Density of water = 1g/ml
| Density of ice = .92g/ml
37
Describe the bonding/ structure of liquid water.
- irregular, dynamic H-bonding
- break/reform every 2 x 10 -11
- 3-7 member rings
38
Define solubility.
Ability of the solvent to interact with a solute
39
When will a substance dissolve?
a substance will dissolve when solute-solvent interaction is stronger than solute-solute interaction
40
What does hydrophilic mean?
polar/ionic - solvated in H2O
41
What does hydrophobic mean?
non-polar - does not interact w/ H2O (does not necessarily mean no hydrogen bonds)
42
What is the hydrophobic effect driven by?
entropy
43
What is the hydrophobic effect?
- 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
44
How does entropy change when a hydrophobic molecule is dissolved?
- Entropy changes in this reaction: H2O becomes more ordered and forms cages when a hydrophobic/non-polar molecule is dissolved, making this less favorable
45
What are amphiphiles?
contain polar and non-polar groups
46
What structures do amphiphiles form in nature?
micelles and bilayers
47
What is dialysis?
- 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)
48
What is a solvent?
H2O
49
What is a solute?
NaCl, what is being dissolved
50
Describe the ionization of water.
- protons can easily jump from one H2O to another
- H3O and OH have high mobility in water
- acid - base reactions are rapid in H2O
51
What does 1 pH unit indicate?
10 -fold difference in [H+]
52
What is a bronsted lowry acid?
a substance that can donate H+
53
What is a bronsted lowry base?
a substance that can accept H+
54
What does a high or low pka indicate?
- high pKa = less likely to dissociate
| - low pKa = more likely to dissociate
55
When do species have multiple pKas?
- when there are multiple ionization states
56
What is the relationship between pH and pKa?
- pKa is the pH at which 50% of HA has dissociated
| - [HA] = [A-] when pH = pKa
57
What is the buffering capacity?
1 pH unit above/below pKa
58
What is the difference between the sugar of RNA and DNA?
- RNA - ribose
| - DNA - 2'deoxyribose (no OH at the 2' carbon)
59
What are the purines?
Adenine and Guanine
60
What are pyrimidines?
Cytosine, Thymine, Uracil
61
How are bases of DNA linked?
-phosphodiester linkages
62
What is the pKa of O- in a phosphodiester linkage?
pKa = 0 at pH = 7 (prefers deprotonated form)
63
Why are the phosphodiester linkages of RNA polymers weaker?
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
64
Describe the structure of DNA.
- double helix
- 2 polynucleotide strands
- chains are antiparallel
- right-handed helix
- bases are hydrogen bonded to bases on opposite strands
- major and minor groove
65
Describe how the hydrophobic effect is at play in the structure of DNA.
- 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
66
How many hydrogen bonds are there between the bases of DNA?
A - T (two)
| G - C (three)
67
Describe the structure of RNA.
- formation of stem loop structure
- single stranded
- intramolecular -bonding
68
What is the central dogma?
DNA is transcribed into RNA and translated into protein
69
What are the building blocks of DNA replication?
- deoxynucleotide triphosphates are the building blocks (dNTPs)
70
Which direction is DNA replicated in in nature? vs in the lab?
5' - 3' in nature
| 3' - 5' in the lab
71
Describe DNA replication.
- RNA primers - necessary for DNA polymerase to bind to
- generate by primases
- helicase and topoisomerase unwind DNA
- leading strand - continuous
- lagging stranf okazaki fragments
72
Describe the chemical reaction of DNA replication
3' hydroxyl is nucleophile (deprotonated by a base) and phosphate is electrophile
73
What are the two strands of DNA in transcription?
coding strand and template strand (rna identical to codinf strand)
74
Describe the process of transcription.
- DNA template
- catalyzed by RNA polymerase
- synthesis occurs 5'-3'
- building blocks ---> NTPs
- no primer required
75
Which direction are proteins translated in?
N-term to C-term
76
What are the three types of RNA?
messenger RNA - encodes for protein sequence
tRNA - transfer
rRNA - makes up the ribosome
77
Describe tRNA.
- 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
78
What are the steps of classic Sanger Sequencing?
- 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?)
79
What are the steps of one pot sanger sequencing?
- 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)
80
What are two other methods of sequencing (other than sanger)?
- Replace the gel with capillary electrophores - this gives us faster results and better resolution
- Next gen seqeuncing
81
What are ddNTPs?
dideoxynucleotides - deoxyribose lacks -OH at 3' carbon that is required for elongation of a DNA strand
82
What is PCR?
Polymerase chain reaction
83
What is the pKa of the amine group in an amino acid?
9-10
84
What is the pKa of the carboxyl group in an amino acid?
3.1
85
What is the alpha carbon of an amino acid?
central carbon to which the amine and carboxyl group are attached (R group and H also attached)
86
What is the stereochemistry of the alpha carbon?
- 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
87
What is the regular configuration of all natural amino acids?
L - amino acids
88
Describe the pKas given for the amino acids. What would occur if they were place in a hydrphobic pocket?
- 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
89
What direction is s?
counter clockwise
90
How many bonds between each set of base pairs?how does that impact denaturation/ melting temp?
- G-C 3
- A-T 2
- harder to denature, more H- bonds
- higher G-C content = harder to denature and higher melting temp
91
What are the two other amino acids, not naturally occuring?
selenocystein and pyrolysine
92
What character does an amide bond possess?
some double bond character, little rotation
93
What are some possible post-translational modifiactions of proteins?
phosphoserine - add (po4)
| methy - can be added wherever there is an NH
94
What conformation of an amide bond is favored?
trans is always favored to cis 1000:1
| exception: proline trans favored 4:1
95
What is a method for protein quantification?
ELIZA
96
What is an ELIZA?
enzyme- linked immunosorbent assay
97
Describe the steps of an ELIZA?
- 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
98
What are four methods to purify proteins?
- charge
- hydrohpobicity
- size
- affinity chromatography
99
Describe the process to separate proteins by charge.
- 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
100
Describe the process to separate proteins by hydrophobicity.
Hydrophobic interaction chromatography
- hydrophobic proteins stick to the column
- elute with detergents
101
Describe the process to separate proteins by size.
- size exclusion chromatography
- beads with pores
- smaller = longer time to elute
102
What is affinity chromatography?
- specific antibody
- HIS tag - Ni column
- FLAG tags HA tags with specific antibodies
103
What is a strategy for protein sequencing?
Edman degradation
104
Describe Edman degradation.
- 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
105
What is the process of mass spec?
- 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
