BIOL 3200 - Exam 3

What is the Central Dogma of molecular biology?

DNA → RNA → Protein

What is an exception to the Central Dogma?

RNA → DNA (reverse transcription in retroviruses)

What is a gene?

A DNA sequence that codes for a functional product (usually protein)

What is a genome?

The complete set of genetic material in a cell

What is an operon?

A group of genes transcribed together under one promoter

What is polycistronic mRNA?

One mRNA that encodes multiple proteins

What is a monocistronic mRNA?

One mRNA that encodes a single protein

What type of genome do bacteria typically have?

Single circular chromosome

What are plasmids?

Extrachromosomal DNA that often carriers benefical genes

Why are plasmids important?

They can carry traits like antibiotic resistance

What is the nucleoid?

Region where bacterial DNA is compacted

Why is DNA supercoiled?

To compact DNA and regulate accessibility

What does semiconservative replication mean?

Each daughter DNA has one old strand and one new strand

What does bidirectional replication mean?

Replication proceeds in two directions from the origin

What is oriC?

The origin of replication in bacteria

Why can DNA only be synthesized in one direction?

DNA polymerase only adds to the 3` OH end

What is the leading strand?

Synthesized continuously

What is the lagging strand?

Synthesized discontinuously in fragments

What are Okazaki fragments?

Short DNA segments on the lagging strand

What does DnaA do?

Initiates replication at oriC

What does helicase (DnaB) do?

Unwinds DNA

What does primase do?

Synthesizes RNA primers

What does DNA Polymerase III do?

Main enzyme that synthesizes DNA

What does DNA Polymerase I do?

Replaces RNA primers with DNA

What does DNA ligase do?

Joins Okazaki fragments

What does DNA gyrase do?

Relieves supercoiling ahead of fork

What does topoisomerase IV do?

Seperates replicated chromosomes

What is PCR used for?

Amplifying DNA

Key differences between PCR and replication?

PCR uses synthetic DNA primers; cells use RNA primers

What enzyme performs transcription?

RNA polymerase

What is a promoter?

DNA sequence where RNA polymerase binds

What does the sigma factor do?

Helps RNA polymerase recognize the promoter

What happens to sigma factor after initiation?

It dissociates

What happens in transcription initation?

RNA polymerase binds promoter and begins RNA synthesis

What happens in transcription elongation?

RNA strand is extended

What happens in transcription termination?

RNA polymerase detaches

What is Rho-dependent termination?

Requires Rho protein to stop transcription

What is Rho-independent termination?

Uses hairpin loop to stop transcription

What happens when a repressor binds the operator?

Transcription is blocked

WHat happens when an activator binds?

Transcription increases

What is translation?

mRNA → protein

What is a codon?

A 3-base sequence coding for an amino acid

How many codons exist?

64 (61 amino acids, 3 stop)

What does “degenerate code” mean?

Multiple codons can code for the same amino acid

What does tRNA do?

Brings amino acids to ribosome

What is an anticodon?

Sequence that pairs with mRNA codon

What are ribosomal subunits in bacteria?

30S + 50S = 70S

Why is the reading frame important?

Incorrect frame produces wrong protein

What is the Shine-Dalgarno sequence?

Ribosome binding site that aligns start codon

What happens in translation initation?

Ribosome assembles and first tRNA binds

What happens in translation elongation?

Amino acids are added

What happens in translation termination?

Stop codons release protein

What is a missense mutation?

Changes amino acids

What is a nonsense mutation?

Creates stop codon

What is a silent mutation?

No amino acid change

What is a frameshift mutation?

Alters reading frame

What is 16S rRNA used for classification?

Highly conserved with variable regions

What does BLAST do?

Compares DNA seuqnces

What are the three types of horizontal gene transfer?

Transformation, conjugation, transduction

What is transformation?

Uptake of free DNA from environment

What is conjugation?

DNA transfer via direct cell contact

What is transduction?

DNA transfer via bacteriophages

What did the Griffith experiment demonstate?

DNA can be transferred between bacteria (transformation_

Why is GC-rich DNA more stable?

It has 3 hydrogen bonds vs 2 with (A-T)

What does Type 1 topoisomerase do?

Cuts one strand to relieve supercoiling

What does Type II topoisomerase do?

Cuts both strands and introduces supercoils

What is a replication fork?

Region where DNA is being unwound and copied.

What are catenanes?

Interlinked daughter chromosomes after replication

What is Tus protein?

Stops replication at terminator sites

What are the three steps of PCR?

Dnaturation, annealing, extension

What enzyme is used in PCR?

Taq polymerase

Why is an inducible operon?

Turned ON by substrate (lac operon)

What is a repressible operon?

Turned OFF by product (trp operon)

If given a DNA template strand, what is the mRNA?

Complementary sequence (just U replaces T)

If given mRNA, how do you find protein?

Translate codons using genetic code

One key difference between prokaryotic and eukaryotic genomes?

Prokaryotes have little noncoding DNA

What is a major feature of archael genomes?

Similar processes to eukaryotes but structure like bacteria

What is the letter “a” pointing to?

Coding Sequence

What is the letter “b” pointing to?

Template Sequence

What is the letter “c” pointing to?

mRNA strand (5` end direction)

Template vs Coding Strand

• Template Strand → used to build RNA

• Coding Strand → matches RNA (T → U)

If it looks like mRNA, its the coding strand

Base Pair Rules in Transcription

A ↔ U

T ↔ A

C ↔ G

G ↔ C

In what direction is RNA polymerase read?

RNA polymerase reads 3` → 5` (template)

In what direction is RNA synthesized?

RNA is synthesized 5` → 3`

Where is the acceptor end of this tRNA?

Acceptor end, which is 3`, is on the same side as the TΨC loop. So “a” on this image.

What is the function of the Shine-Dalgarno sequence?

Ribosome binding site

What does sigma-70 recognize?

Promoter regions (-10 and -35)

What does DnaA do?

Initiates DNA replication

What does SeqA do?

Inhibits DNA replication initation

Which antiboiotic targets the A site of the ribosome?

Tetracycline

Which antibiotic inhibits RNA synthesis?

Rifamycin

What did Selman Waksman discover?

Streptomycin

Which antibiotic inhibits folic acid synthesis?

Sulfonamides

How does zidovudine (HIV drug) work?

Mimics thymine

Why is E. coli resistant to vancomycin-like drugs?

Drug cannot cross outer membrane

What are products of transcription?

mRNA, tRNA, and rRNA

What happens if a cell lacks sigma factors?

No transcription

What is the function of a promoter?

RNA polymerase binding site

If no mRNA is produced after mutation upstream, what was mutated?

Promoter

Can multiple ribosomes translate one mRNA at once?

Yes (polysomes)