Gn311H Final

Front 1

Rho factor

Back 1

Acts in transcription termination in prokaryotes
- Dependent: helps to detach RNA from polymerase
- Independent: RNA forms hairpin that facilitates the release of RNA

Front 2

TFIID

Back 2

Binds to the promoter sequence in eukaryotes, and has TTBP which is the first thing that binds

Front 3

Transcription factors

Back 3

Build the initiation complex for eukaryotic transcription that attracts RNA polymerase

Front 4

Sigma factor

Back 4

Acts in transcription initiation in prokaryotes (needed for specificity in core RNA polymerase in holoenzyme)

Front 5

AAUAAA

Back 5

- Acts in RNA processing in eukaryotes
- Signal for processing the 3' end
- Attracts binding complex

Front 6

Promoter

Back 6

Lies upstream of RNA-coding region in the transcription apparatus
- Euks: TATA or CCAAT box
- Proks: -10 and -35 boxes

Front 7

Eukaryotic Replication

Back 7

Multiple origins --> Approval --> Helicases --> Nucleases (remove RNA primers) --> Telomerase --> Ligase

- Nucleosome assembly immediately follows
- DNA polymerase III is most important (adds nucleotides to growing 3' end)

Front 8

Prokaryotic Replication

Back 8

Single origin --> Helicase unwinds --> Primase lays down primer --> Gyrase relieves strain --> SSBs straighten DNA --> DNA poly III attaches to primer --> DNA poly I removes primer --> Ligase connects nicks --> Termination protein can block further replication

- Topoisomerases remove supercoils

Front 9

Eukaryotic Transcription

Back 9

- Monocistronic and introns present
- Promoter: CCAATT and TATA boxes (cis elements)
- Transcription factors (trans elements)
- 5' --> 3'
- DNA threaded through RNA polymerase
- Unstable RNA/DNA complex formed with poly II
- Variability at termination point
- AAUAAA

Front 10

Prokaryotic Transcription

Back 10

- Promoters: -10 and -35 boxes
- Transcription bubble formed
- RNA poly separates DNA strands
- RNA poly begins elongation after ~30bps are synthesized
- Rho factors

Front 11

Telomeres

Back 11

- prevent DNases from degrading the ends of linear DNA molecules
- help with replication of ends of linear DNA without loss of material
- gradually shorten with age

Front 12

Telomerase

Back 12

Adds to the 3'-end of the template with a built in RNA template. Without it we lose the telomere length every time we go through replication.

Front 13

Replicative Transposable Elements

Back 13

"copy and paste," moves a copy

Front 14

Nonreplicative Transposable Elements

Back 14

"cut and paste," move original and doesn't repair DNA

Front 15

Conservative Transposable Elements

Back 15

"cut and paste," move original and repairs DNA

Front 16

Retrotransposons

Back 16

Use reverse transcriptase to create DNA molecules from elements RNA

Front 17

Meselson and Stahl

Back 17

- Used heavy and light nitrogen (15N and 14N) to determine old vs new DNA
- Centrifugation determines DNA weight and amount
- E.coli first grown in 15N and then 14N
- Discovered semi-conservative replication

Front 18

Eukaryotic RNA polymerase II transcribes:

Back 18

mRNA, snoRNA, miRNA, and snRNA

Front 19

Position of transcription start site is determined by:

Back 19

the location of the consensus sequences.

Front 20

tRNA

Back 20

- the intermediary between amino acids and mRNA
- the acceptor stem contains 5'-CCA-3'. The ends can be trimmed to allow base modification and it accepts amino acids.
- The anticodon is at the "bottom" of the cloverleaf structure and binds to the codon of the mRNA strand
- tRNA modifying enzymes allow for the 5' and 3' ends of tRNA to be trimmed off, creating modifying bases
- Aminoacyl-tRNA synthatase attaches amino acids to the tRNA

Front 21

mRNA processing

Back 21

1) 5' guanine cap is added as soon as the 5'-end of pre-mRNA is free from RNA polymerase
2) Polyadenylation of 3' end and cleavage
3) Intron excised from pre-mRNA by spliceosome (5' end attaches to branch point "A" to form a lariat)
4) Transport out of nucleus

Front 22

Fire and Mello

Back 22

- discovered RNA Interference
- injected dsRNA into C.elegans and found that it turned down gene expression with matching nucleotide sequences to injected RNA (silenced targeted gene by inhibited translation)
- RNAi limits invasion of foreign genes and censors expression of their own genes

Front 23

siRNA

Back 23

- originates from mRNA, transposons, or viruses
- RNA duplex/ssRNA that forms a long hairpin is cleaved
- triggers mRNA degradation
- targets genes from which they were transcribed

Front 24

miRNA

Back 24

- originates from RNA transcribed from a distinct gene
- Dicer recognizes dsRNA and cleaves ssRNA that forms short hairpins
- some trigger mRNA degradation, others inhibit translation
- targets genes other than those from which they were transcribed

Front 25

Beadle and Tatum

Back 25

"One Gene, One Enzyme"
- irradiated Neurospora spores and looked for auxotrophs
- took auxotroph mutants and tested them for ability to grow with subsets of supplements until they found the biologically significant molecule needed for growth

Front 26

Transition Mutation

Back 26

purine --> purine
OR
pyrimidine --> pyrimidine

Front 27

Transversion Mutation

Back 27

purine <--> pyrimidine

Front 28

Missense Mutation

Back 28

different amino acid in a protein (neutral if doesn't alter function)

Front 29

Nonsense Mutation

Back 29

changes a codon to a stop codon

Front 30

Silent Mutation

Back 30

different DNA sequence without changing specified amino acid

Front 31

Readthrough Mutation

Back 31

stop codon changed to amino acid

Front 32

Cryptic Mutation

Back 32

change in intron splice site

Front 33

Forward Mutation

Back 33

W/T --> Mutant phenotype
(Reverse is opposite)

Front 34

Base Analogs

Back 34

Have structures similar to normal bases but are more likely to undergo tautomeric shifts
(5-Bromouracil is commonly incorporated as thymine)

Front 35

Intercalating Agents

Back 35

Intercalate between base pairs and cause small deletions and insertions during replication (proflavin, acridine orange)

Front 36

Alkylating Agents

Back 36

Donate an ethyl/methyl group to other molecules. It can be used in replicating or non-replicating cells

Front 37

Hydroxylamine

Back 37

A very specific mutagen that acts only on cytosine bases and thus only causes C-G --> T-A transitions

Front 38

Deaminating agents

Back 38

Affect base pairing and can cause transitions (C-->U, A-->G, C-->T)

Front 39

UV radiation

Back 39

Causes thymine dimers by inducing covalent cross linkages between adjacent thymine dimers

Front 40

Photolyase

Back 40

Recognizes and binds to thymine dimers in DNA, and requires blue light to cleave the bonds joining thymine dimers--thus directly repairing them without nucleotide removal.

Front 41

Glycosylase

Back 41

A protein involved in base excision repair (removal of abnormal/modified bases and replacement with entire nucleotide)

Front 42

Nucleotide excision

Back 42

Repairs larger mutations than base excision. An enzyme complex recognizes a DNA bulge, separates the DNA strands, and clips out the damaged section.

Front 43

What are the spliceosome signals for mRNA processing?

Back 43