Quiz
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Please expand to alternate seats
5 points
10 minutes (starting on the hour)
#2 pencils
1.
DNA was iden tified as the genetic material in experiments done by
A.
Mendel.
B.
Beadle and Tatum.
C.
Avery, MacLeod, and McCarty.
D.
Watson and Crick.
2.
During formation of haploid egg s and sper m, one member of each chromosome pair is separated to
each cell in a type of cell division call ed
A.
mitosis.
B.
meiosis.
C.
cytokinesis.
D.
gametogenesis.
3.
When thymidine and adenosine interact within the DNA molecule they form
A.
two hydrogen bond s.
B.
three hydrogen bonds.
C.
nucleotide triphosphates.
D.
sphodiester bonds.
4.
An experiment in which cell s were grown in 15N after growth in 14N and their DNA then separated
by density gradient centrifugation demonstrated that
A.
DNA is replicated by DNA polymerase.
B.
DNA replication is conservative.
C.
DNA replication is semiconservative.
D.
A forms doub le helices by hydrogen bonding between base pairs.
5.
In the base pairing within a DNA double helix,
A.
purines pair with puri nes.
B.
A pairs w ith U and G pairs with C.
C.
A pairs with G and C pairs with T.
D.
A pairs with T and G pairs with C.
6.
DNA contains the base uracil whereas RNA contains the base thymine.
A.
True
B.
False
7.
RNA molecules that serve as templates for prot ein synthesis are called
A.
transfer RNAs.
B.
messenger RNAs.
C.
ribosomal RNAs.
D.
cytoplasmic RNAs.
8.
Which of the foll owing dele tions will not chan ge the reading frame of a gene?
A.
One nucleotide
B.
Two nucleotides
C.
Three nucleotides
D.
Four nucleotides
9.
RNA is copied from DNA by a process called __________.
A.
transformation
B.
translation
C.
replication
D.
transcription
E.
transfection
10.
A codon is a
A.
region of DNA coding for one protein.
B.
sequence of three nucl eotides on a tRNA that binds to an mRNA.
C.
sequence of three nucl eotides on an mRNA that binds to specific tRNAs.
D.
sequence of three nucl eotides on the codi ng strand of DNA.
11.
Restriction nucleases are enzymes that
A.
act only in a single species of bacteria.
B.
act only on the ends of DNA str ands.
C.
cleave DNA only at specific seq uences.
D.
cleave only nuclear DNA.
Energy Metabolism
• Metabolism (meta=after; Bol=to throw)
– Greek : Metabole = change)
• Catabolism (kata=down; Bol=to throw)
• Anabolism (ana=upward; Bol=to throw)
Thermodynamics
• First Law: Energy cannot be created or destroyed.
• Second Law:
– Heat will flow only from hot to cold
– Entropy of a closed system always increases
– The second law, in its most general form, states that the world acts
spontaneously to minimize potentials
– All reactions proceed in an “energetically favorable” direction until
they reach equilibrium
• Intrinsic properties of reactants and products
• Relative concentrations of reactants and products
• Temperature
Gibbs Free Energy
A+B
•
•
•
•
C+D
G (Gibbs free energy)  H(heat)+S(entropy)
∆G=∆H-T∆S (releasing heat or increasing entropy makes ∆G negative)
Change(∆) in (Gibbs)free energy= ∆G = ∆Gº +RTlnK
Convention
– If ∆G is negative A and B continues to get made into C and D
– If ∆G is positive C and D continues to get made into A and B
– Therefore if nothing is happening any more (ie equilibrium is reached), then ∆G is
ZERO
– When ∆G =0 then ∆Gº=-RTlnK
• The standard free energy ∆Gº is different that the free energy ∆G
• The standard free energy at 37ºC in water is ∆Gº’
Reaction Equilibrium
Thought Experiment:Mix 100 As with 100 Bs
No reaction
A+B
C+D
K =0.0001
Complete Reaction
A+B
C+D
K =10000
Partial Reaction
A+B
C+D
K =1
99
1
50
99
1
50
1
99
50
[C][D]
K =
[A][B]
1
99
50
Relationship of Equilibrium Position and Standard Free Energy
at 37ºC
15
²Gº= -RTlnK
²Gº (in kcal/mol)
10
²Gº'= -0.62kcal/mol lnK
K=1/10000
²Gº =+ 6
5
K=1/1
²Gº =0
0
K=10000/1
-5
²Gº = - 6
-10
-15
10-9
10-7
10-5
10-3
10-1
101
103
105
107
K = Ratio products to reactants ([C][D]/[A][B])
109
Which way do reactions go?
Two paradoxes
• Reactions that break bonds are generally
thermodynamically favorable (catabolism)
– They release heat
– They increase entropy
• Reactions that make bonds are generally
thermodynamically unfavorable(anabolism)
– they create more order, therefore lower entropy
Why doesn’t everything break down?
Resolution to the catabolism paradox
• Thermodynamics vs. Kinetics
• Activation Energy
Why does anything build up?
Resolution to anabolism paradox
• Coupling of reactions
∆Gº’=-7.3kcal/mol
A-P-P-P
A-P-P
Glucose
Glucose-6-P
∆Gº’=+3.3kcal/mol
Oxidation /Reduction
A. Passing H- around
H
S1 C
O H
H
Reduced
NAD+
Oxidized
Reduced
H
S2
C
H
O H
C
S1
O
H
Oxidized
2e-
Reduced
Oxidized
S2
C
H
O
NAD-H
H+
Carbon Oxidation
Oxidation /Reduction
B. Reducing Oxygen
O
S1
C
O
O H
Reduced
NAD+
Oxidized
C
O
Oxidized
2e-
Reduced
Reduced
Oxidized
H
O
O H
+3ATP
O
NAD-H
H+
Metabolism
• Catabolism
– Breaks bonds to yield energy in ATP currency
– Results in smaller carbon skeletons
-Cells prefer to use glucose for energy generation
(catabolite repression)
• Anabolism
– Uses ATP to make bonds and increase the size of
carbon skeletons
Where does the glucose come from?
• Sun emits photons of light
• Photons excite chlorophyll
• Excited chlorophyll converts water to
oxygen, protons, and electrons
• Electrons are coupled to ATP generation
and NADP+ reduction
• ATP and NADPH are used to generate
glucose (Calvin cycle Fig. 2.39)
• Glucose is eaten by animals
Light
reactions
Dark
reactions
Where did the glucose come from?
• Sun emits photons of light
• Reducing atmosphere and sparks created
amino acids
• Amino acids were assembled into
glucose?
Biosynthesis
Carbohydrates, Lipids
• Gluconeogenesis
– lactate, amino acids, glycerol to pyruvate
– pyruvate to glucose
• Polysacharide synthesis (Fig.2.40)
– glucose to UDP-Glucose to chain
• Lipid synthesis
– Pyruvate to Acetyl-CoA to chain
Biosynthesis
Amino acids
Biosynthesis
Nucleotides
Catalytic Mechanisms
Active Sites
Feedback Regulation
• Thermostat
• Toilet
Allosteric Control
• Allo (other ,different); Stere (solid, three dimensional)
• Non-covalent: O2 in hemoglobin, metabolites in feedback control
• Covalent: Phosphorylation, methylation,acetylation, etc..
Genetics
• Mendelian
– independent segregation of traits; 1865
– Traits determined by pairs of inherited factors (alleles)
• Chromosomes
– Exist as pairs
• Linkage
– dependent segregation of traits; early 1900s
• Incomplete Linkage
– Recombination during Meiosis
• One gene-one enzyme
– multiple mutations in one gene
– George Beadle; Edward Tatum; 1941
Discovery of the Genetic Substance
• Chromosomes have both DNA and Protein
• Activation of Inactive Pneumococcus
– Oswald Avery; ColinMcleod; Maclyn McCarty; 1944
• Ratios of A:T and G:C are 1
– Erwin Chargaff
• DNA is helical
– Maurice Wilkins; Rosalind Franklin; 1952
• Model Building
– James Watson; Francis Crick; 1953
• Semiconservative Replication
– Mathew Meselson; Frank Stahl; 1958
Readout of DNA
• Colinearity of genes and proteins
– Charles Yanovsky
– tryptophan synthetase
• Discovery of mRNA
– Sidney Brenner, Francois Jacob; Mathew Meselson
– E. Coli; T4 phage
• Genetic Code; triplet code
– In vitro translation
– tRNA adapters
– Mathew Meselson; Frank Stahl; 1958
Recombinant DNA Technology
• Restriction Enzymes
– Restriction Maps
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•
•
•
•
•
•
•
•
Gel Electrophoresis
Vectors
Libraries
cDNA vs Genomic
Sequencing
PCR
Southern; Northern
Antibodies
Western Blots
Immunoprecipitations
Recombinant DNA Technology
• Reverse Genetics
– Use yeast to illustrate
• Gene Transfer
– Selectable markers
• Controlled mutagenesis
Molecular Biology Methods