Purines
Adenine (A)
Guanine (G)
Double ring structures
Pyrimidines
Thymine (T) - DNA
Cytosine (C)
Uracil (U) - RNA
Single ring structures
Components of a nucleotide
Nitrogenous base (purine/pyrimidine) (C'1) + sugar (deoxyribose in
DNA/ribose in RNA) (C'2) + phosphate (C'5)
How are nucleotides bound together?
Adjacent nucleotides are linked by 5' - 3' phosphodiester bonds/linkages
at one end of the linear DNA chain, the nucleotide will have a
free 5' phosphate and 3'hydroxyl on the other end
Nucleotide
Base + sugar + phosphate
Nucleoside
Base + sugar
What is antiparallel?
3' ---- 5'
5' ---- 3'
Complementary bases
Holds two chains together
How many bonds does A-T have?
Two hydrogen bonds
How many bonds does C-G have?
Three hydrogen bonds
DNA is a ____ -handed double helix
right
Complete turn of helix =
34A or 3.4nm
Bases are separated at
3.4A or 0.34nm
Diameter of DNA double helix=
20A or 2nm
B Form DNA
biologically significant right-handed helix
10 bp per 360 degree turn 10 bases = 3.4nm
Is a nucleoside or nucleotide bigger?
nucleotide
Is adenine or thymine bigger?
adenine because it is a purine with a double ring structure
Z DNA Form
left-handed helix 12 bp per 360 degree turn
18 A diameter zigzag conformation
How do you tell if one DNA molecule is more stable than another?
More C-G content due to the triple hydrogen bonds
Given a molecule with the following content (10%A), what is the
percentage of cytosine?
0.4
If A=U
dsRNA
If A does not equal U
ssRNA
Given that a DNA molecule is 6,800 micrometers, how many nanometers
is that?
6,800,000 nm
Find how many turns in a molecule that is 6,800,000 nm
6,800,000 x 10 / 3.4 = 20,000,000 bp
20,000,000 / 10 = 2,000,000 turns
mode of bacterial replication
theta
bacterial replication
one origin of replication bidirectional
terminus
True or false: In bacteria, there is only one origin of replication?
TRUE
True or false: In bacteria, it is one directional?
false, it is bidirectional
Meselson-Stahl Experiments
Semi-conservative
First generation - 14N/15N one band
Second generation - 14N band
14N/15N band
Meselson-Stahl Experiments
Conservative
First generation - 14N band
15N band
Second generation - 14N thick band
15N thin band
Meselson - Stahl Experiments
Dispersive
First generation - 14N/15N band
Second generation - 14N/15N thick band
(3:1)
How will the bands look for semi conservative?
N14 will appear more with each round of replication. You
will still have a hybrid band
What happens in conservative?
You will not get intermediate bands, only 14 and 15
What happens in dispersive?
A mix with a hybrid band that will get thicker and then higher
You have an alien that has an extra base pair and the codon is
quadruplet. How many total codons are there?
A
C
G
T
B
54=625
If the alien replicates DNA conservatively, how many hybrids are
expected after 4 replicates?
zero
What is the ratio of heavy to light molecules?
After 4 rounds, you expect 16 molecules. How many are expected to be
heavy (black only) to light?
1 to 15
(3:1)
Know roles and order of events
DnaA - opens DNA Helicase (DnaB) - binds to DNA
Primase for RNA primer DNA pol III - replicate DNA
DNA pol I - remove primers and replicate fragments of DNA
Ligase attach to DNA
Match the following:
A. leading
B. lagging
C. both strands
D. neither
1. DNA pol III - both strands (C.)
2. Primase - both strands (C.)
3. RNA pol holoenzyme - neither strands (D.)
4. Okazaki fragments - lagging (B.)
5. Ligase - both strands (C.)
True or false:
Ligase activity on leading strand is higher than lagging?
false - ligase seals phosphodiester bond between adjacent nucleotides
RNA primer
leading strand
Lagging strand
a lot of Okazaki fragments - lots of RNA primers
Primase is more active on ______ strand.
Leading
Telomere function
found at the end of linear chromosomes
Prevents ends from acting in "sticky" fashion
Prevents ends from being degraded Allow chromosome ends
to be properly replicated
Telomerase activity:
Somatic cells
not active
Telomerase activity:
Germ cells
active
Telomerase activity:
Lower eukaryotes
active
Telomerase activity:
cancer cells
active
Hutchinson-Gilford Syndrome
Type of progeria
aging starts 1-2 years after birth
death occurs in teens
Werner Syndrome
Type of progeria
aging begins in teens
death in 40s
Somatic cells of individuals who have progeria have ____ telomeres
and exhibit decreased proliferative capacity when in grown culture
short
Central Dogma
1. DNA ---> DNA
2. DNA ---> RNA
3. RNA ---> DNA
4. RNA ---> Protein
1. Replication
2. Transcription
3. Reverse transcription
4. Translation
RNA holoenzyme
RNA polymerase is termed RNA holoenzyme and composed of:
a2BB'w
catalytic subunit: B'
Sigma factor
a specificity factor that directs RNA polymerase to bind to the promoter
rho-dependent termination
rho protein binds to the rut site and moves toward the 3'
end RNA polymerase reaches terminator Stem loop
causes RNA polymerase to pause
rho - independent termination
RNA polymerase pauses due to interaction w/ stem loop
rho protein catches up to open complex and separates RNA/DNA
hybrid
RNA holoenzyme
only initiates transcription
RNA polymerase
does everything
Eukaryotic polymerase
RNA pol I
rRNA
Eukaryotic polymerase
RNA pol II
mRNA and snRNA
Eukaryotic polymerase
RNA pol III
tRNA and 5srRNA
Eukaryotic polymerase
RNA pol IV
organellar RNA pol
Eukaryotic mRNA undergoes ____ processing
extensive
3' have poly ____ tail
A
Introns
(non-coding sequence) removed
Exons
(coding-sequence) spliced
RNA editing
2 types
Substitution editing - individual nucleotides altered
Insertion/Deletion - nucleotides are added or subtracted
5' cap
7-methylguanosine
Phenyl alanine anticodon
located on the 5' end
AAG
Phenyl alanine codon
located on the 5' end
UUC
Proline anticodon
located on the 3' end
GGC
Proline codon
located on the 3' end
CCG
5' end is ____ in length
shorter
3' end is _____ in length and charged when ______ is attached
longer ; amino acid
Promoter of a gene is not ______ with a gene
transcribed
Coding strand
non-template strand; has the same sequence as mRNA except U replaces T
also called sense strand
Template strand
non-coding strand/antisense; transcribed
Bacterial transcription
mRNA is more stable, polycistronic (carries more than one gene) and short-lived
Eukaryotic transcription
monocistronic (carries one gene), long-lived
Know aspects of genetic code
written in mRNA form triplet code - 61 sense codons; 3
stop codons essentially unambiguous
degenerate biased non-overlapping
nearly universal
Trytophan codon
UGG
AUG
start codon but can be found in the middle of a sequence as well
tRNA clover shaped structure
secondary structure; result of intramolecular hydrogen bonding
enzyme that transfers amino acids
aminoacyl-tRNA synthetases
Does gene mutation have a start codon?
Yes, the 5' end of mRNA amino group
First amino acid
Methionine, brought into EPA or APE? P is in the middle and goes
first to P while others enter through A
EF2 brings initial tRNA to P site, then new tRNA EF-tu in A site,
peptidyl transferase (catalytic RNA) connects them and _____
translocates
Charged RNA in P site transfers amino acid to A site and then to
______ site
E
Stop codon cannot bind to ______
tRNA, hydrolyzes strand from ribosome