Biology: Dna And Protein Synthesis

Front 1

What is the Watson-Crick model of DNA?

Back 1

-Double helix - 2 single chains of DNA bonded via H-bonds of base pairs
-Strands are antiparallel to each other

Front 2

1) What is DNA made of?
2) What is the difference b/t a nucleotide & nucleoside

Back 2

1) Purine & pyrimidine bases, sugar, phosphate
2) nucleotide: base+sugar+phosphate (Adenine, Guanine, Thymine, Cytosine)
nucleoside:base+sugar (Adenosine, Guanosine, Thymidine, Cytidine)

Front 3

1) Difference b/t purines & pyrimidines
2) What makes DNA acidic?
3) How many H-bonds does A form with T?
4) How many H-bonds does G form with C?

Back 3

1) A&G are purines (big w/2 rings), C&T are pyrimidines (small w/1 ring)
2) Phosphate group
3) 2
4) 3

Front 4

1) What is the difference b/t a DNA molecule with more GC bonds vs AT bonds?
2)
3)

Back 4

1) GC will be harder to break apart b/c there are more Hbonds holding them together
2)
3)

Front 5

Describe the mechanism of DNA replication

Back 5

1) dsDNA separates/unwinds
-DNA gyrase (class II topoisomerase) uncoils ahead of replication fork
-Helicase unwinds at fork
-Single-strand binding protein (SSB) keeps DNA unwound after helicase and stabilizes ssDNA by binding
2) Make complementary DNA (synthesis occurs 5'-->3')
-Primase lays down a short RNA primer
-DNA pol then 'takes over' and makes compl. DNA
-DNA synthesis occurs on both sides of the strand
3) RNA primers are replaced w/DNA and the Okazaki frags are connected by DNA ligase

Front 6

In what 2 way can DNA be repaired during the replication process?

Back 6

1) DNA polymerase has proof-reading ability, also called 3'-->5' exonuclease activity, If a wrong nucleotide is placed, the pol will "back up" & replace it
2) The special pol that replaces RNA primers w/DNA can clear short stretches of incorrect nucleotides

Front 7

Describe the experiment that proved DNA's semi-conservative nature

Back 7

Heavy (15N) DNA and light (14N) DNA were used. The heavy chain was the initial point and the light chains were used for synthesis of new DNA. After round 1, the DNA strands were of intermediate weight. After round 2, the chains were b/t intermediate & light weight

-If DNA rep were conservative, only heavy & light would be seen
-If DNA rep were dispersive, everything would be of intermediate weight

Front 8

1) Is DNA synthesis bidirectional or unidirectional?
2) In what phase does replication occur?

Back 8

1) Bidirectional, 2 replication forks form and proceed in opposite directions
2) Once every cell generation in S phase

Front 9

1) Mismatch repair?
2) Base-excision repair?
3) Nucleotide-excision repair?
4) Nick translation?
5) SOS response in E. Coli

Back 9

1) Enzymes recognizes incorrectly paired bp & cuts out stretch of DNA w/mismatch, then pol re-adds correct bp's
2) A damaged base gets cut out and a few surrounding bp's
3) Damaged nucleotides are cut out and pol replaces (for dimers & damages that change normal bases to abnormal ones)
4) 5'-->3' exonuclease activity coupled to pol activity
5) DNA pol replicates over DNA as if it were normal, better than not replicating at all

Front 10

How do mismatch strand mutations know which strand to repair?

Back 10

Soon after replication, the new DNA strand is not methylated, so the mismatch repair enzyme cuts the unmethylated strand

Front 11

1) What is a palindromic sequence?
2) What cuts dsDNA at palindromic sequences?
3) When can restriction enzyme products hybridize?

Back 11

1) A strand the is the same read 5'-->3' & 3'-->5'
2) Restriction enzymes (restriction endonucleases) - the resulting fragments are called restriction fragments
3) When they form sticky ends rather than blunt ends

Front 12

1) What is hybridization/annealing?
2) What is Southern Blotting?
3) Describe hybridization in gene cloning

Back 12

1) Where DNA strands base pair w/each other
2) DNA probes are used to hybridize onto DNA fragments containing a target sequence
3) Sticky ends from a restriction fragment base pairs w/the same sticky ends on a plasmid - forming a recombinant plasmid that can be inserted into bacteria for replication to take place

Front 13

What must a plasmid have in order to perform gene cloning? (3 things)

Back 13

The plasmid must have a restriction site to open it to insert the gene,
-It must have an origin of replication so the gene can be cloned,
-It must have an antibiotic resistant gene b/c this allows you to kill bacteria that don't have your gene - after antibiotic is added, only bacteria w/the antibiotic resistant plasmid will live

Front 14

Describe PCR

Back 14

1) Denature: heat (90C) to separate dsDNA
2) Annealing: Cool for primers to anneal to the now ssDNA
-Add excess primer, so they outcompete reannealing to template strands
3) Elongation: use hear stable pol to extend primers
4) Repeat steps for n cycles. Amplification is 2^n

Front 15

1) What is the Central Dogma?
2) Where does transcription take place?
3) After transcription, where do mRNA's go?

Back 15

1) DNA --> RNA --> Protein
2) Nucleus (DNA transcribed to mRNA)
3) mRNA's go to the cytoplasm

Front 16

1) What does it mean for a codon to be degenerate?
2) Missense codon?
3) Nonsense codon?

Back 16

1) An amino acid can code for more than one codon
2) A mutated codon that results in a different amino acid
3) A mutated codon that results in something other than an amino acid, like a stop codon

Front 17

1) What are the start and stop codons?
2) What protein terminates translation?

Back 17

1) start: AUG, stop: UAG, UGA, UAA
2) A protein called "release factor" when a stop codon is reached

Front 18

1) Describe mRNA structure
2) Difference b/t eukaryotic & prokaryotic mRNA

Back 18

1) 5' cap, 3' polyA tail (protect both ends from exonuclease degradation)
2) Eukaryotic: 5'cap - nucleotides - 3'polyA
Prokaryotic: no 5'cap or 3'polyA

Front 19

1) Describe the 3' end of a tRNA
2) Why si rRNA highly structured?

Back 19

1) At the 3' end the amino acid is attached to the 3'OH via an ester linkage
2) It contains the active site for catalysis. The large subunit is responsible for catalyzing peptide bonds

Front 20

Describe the mechanism of transcription

Back 20

1) Initiation - RNA pol binds to promoter (TATA box) of dsDNA (closed complex), the dsDNA opens up
2) Elongation - No primer required. RNA elongates as the RNA pol moves down the DNA template from 5'-->3'
3) Termination - 2 ways:
-Intrinsic termination - specific sequences form a stem loop structure on the RNA that cause RNA to slip off the template
-Rho (ρ) dependent termination - the ρ factor travels along the synthesized RNA and bumps off the polymerase

Front 21

Describe the regulation of transcription in prokaryotes
-Transcription factors
-Operons
-co-repressors/co-inducers
-alpha factors
-transcription attenuation

Back 21

-Transc. factors (proteins) bind to enhancers or silencers (DNA) near the promoter to increase or decrease transcription
-Operons are groups of genes whose transcription can be altered by repressors or inducers
-Co-repressors and co-inducers make repressors/inducers active when they bind to them
-alpha factors - how phages control transcription in bacterial hosts - by making diff. a factors at specific times. Ex. the late a gene isn't made until last
-Transc. attenuation - works in trp (tryptophan) operon, when tryptophan is scarce - transcription occurs, when present - transcription ends

Front 22

How is transcription regulation in eukaryotes different from prokaryotes?

Back 22

-Eukaryotes also have transcription factors (protein) that bind to enhancers or silencers (DNA) to affect transcription, but the enhancers/silencers can be far from the promoter in eukaryotes and the DNA must loop back on itself so the factor can make contact w/the promoter
-Eukaryotes lack regulation mechanism like the operon and attentuation

Front 23

Describe rRNA

Back 23

-Ribosome is the enzyme that catalyzes protein synthesis
-Has 2 subunits - large & small
-Large subunit does the peptidyl transfer rxn - attachment of the new amino acid to the existing chain in the P site.
-Small subunit recognizes mRNA and binds to Shine-Dalgarno sequence on mRNA (Kozak sequence for eukaryotes)
-Both subunits are needed for translation

Front 24

Describe the mechanism of translation

Back 24

1) Initiation: Assembly of everything needed for translation, mRNA, tRNA, and ribosomes. The complex forms around the start codon, AUG, which is downstream from the Shine-Dalgarno sequence (Kozak sequence in eukaryotes) - equivalent to promoter in prokaryotes
2) Elongation - Protein made from N to C terminus, mRNA codons are read 5'-->3'. new aminoacyl tRNA enters A site (GTP & elongation factor required), peptidyl transfer occurs (chain in P-site attaches to new tRNA in A-site), then tRNA in P site is kicked off to E site and the aminoacyl-tRNA moves to P site
3) Termination - When stop factor is encountered, release factors (proteins), bound to GTP, come in and block A site, peptide chain is cleaved and the complex falls apart

Front 25

1) What enzymes attaches the correct amino acid to the corresponding tRNA?
2) What is needed to hold the translation initiation complex together before the large subunit is added?

Back 25

1) aminoacyl-tRNA synthases
2) Initiation factors (IFs)