Exam II

The nucleic acids DNA and RNA are _______.

polynucleotides

What do nucleotides consist of?

• pentose sugar

• nitrogenous base

• phosphate

DNA has a _____ sugar.

deoxyribose

RNA has a _____ sugar.

ribose

Which is more stable, DNA or RNA?

DNA

What do nucleosides consist of?

• pentose sugar

• nitrogenous base

What is the backbone connected by between the 5’ and 3’ hydroxyl groups on the ribose sugar?

phosphodiester bonds

What are the four bases in DNA?

• adenine

• cytosine

• guanine

• thymine

What are the four bases in RNA?

• uracil

• cytosine

• guanine

• thymine

Base pairing is by hydrogen binding between _____ and ______.

NH group and an O or N

Cytosine base pairs with…

guanine

How many hydrogen bonds between cytosine and guanine?

3

How many hydrogen bonds between adenine and thymine?

2

How many rings do purine bases have?

2

How many rings do pyrimidine bases have?

1

What are the purine bases?

A and G

What are the pyrimidine bases?

C, U, T

One helical turn = __ base pairs

10

What is at the 3’ end?

hydroxyl group

What is at the 5’ end?

phosphate group

Where do proteins often interact with DNA?

in the major groove

1 bp =

1 base pair

1 kb =

1,000 base pairs

1 mb =

1,000,000 base pairs

How is long is E. coli DNA?

~ 5 mb

How many turns in E. coli DNA molecule?

500,000 turns

What is the difference between K-12, B, and W?

K-12 → wimpy

B → industrial

W → environmental

How big is E. coli?

1-2 µm long by 0.25-1.0 µm wide

How is E. coli so small when its chromosome is so long?

DNA inside the cell is packaged by proteins and supertwisting to make it fit in a smaller space

What directions can DNA be supertwisted in?

positive or negative

DNA in bacteria is ______ supercoiled.

negatively

What is negative supercoiling?

when the DNA is twisted about its axis in the opposite sense from the right-handed double helix

Some hyperthermophylic archaea _____ supercoil their DNA.

positively

Why do some hyperthermophylic archaea positively supercoil their DNA?

keeps their DNA from unwinding at high temperatures

What are the steps of DNA supertwisting?

1. one part of circle is laid over the other

2. helix makes contact in two places

3. DNA gyrase makes double-strand break

4. unbroken helix is passed through the break

5. double-strand break resealed behind unbroken helix

6. two negative supercoils following DNA gyrase

DNA gyrase introduces _______ in the DNA.

2 negative supertwists

What does gyrase require to introduce two negative supertwists?

energy (ATP)

What do hyperthermophilic archaea have to introduce positive supercoils?

reverse gyrase enzyme

How is supercoiling relaxed?

topoisomerase enzymes nick the DNA and “relax” the supercoils

• cut one strand

• release energy

• ligate back together

• result is +1

gene

functional unit of genetic information

What are the two genetic elements/DNA pieces in the microbial cell?

1. chromosome

2. plasmid

chromosome

the main genetic element in prokaryotic cells containing all the genes necessary for life

plasmid

circular or linear double stranded DNA molecules that replicate separately from the chromosome and provide “extra” characteristics for the cell

genome

total complement of genetic elements in the cell

operon

a group of genes transcribed together to form a single RNA or single mRNA

What percentage of E. coli is protein encoding genes?

88%

What percentage of E. coli is tRNA and rRNA genes?

1%

What percentage of E. coli is regulatory sequences, spacer regions, etc?

11%

Can different plasmids exist in the same cell?

yes

How are plasmids diverse?

in size and copy numbers

Plasmids often encode genes that allow…

survival under specialized conditions

What is an example of plasmids encoding genes that allow survival under specialized conditions?

R plasmids encoding resistance to antibiotics

Plasmids often contain ______ that can move from one location to another.

transposable elements

Which antibiotics does R100 encode resistance to?

mercury, sulfonamide, streptomycin, chloramphenicol, tetracycline

What do R plasmids do?

encode resistance to antibiotics

DNA replication is (conservative/semiconservative/dispersive).

semiconservative

DNA replication requires a…

template

What does the new daughter DNA of semiconservative replication consist of?

one original parent strand and one newly synthesized strand in the double helix

How many different DNA polymerases are in E. coli?

5

What enzyme replicates the majority of DNA?

DNA polymerase III

What enzyme fills in gaps in the new DNA?

DNA polymerase I

What do DNA polymerases require?

• primer (DNA or RNA)

• nucleotide triphosphates as the building blocks; dNTPs

In what direction do DNA polymerases synthesize DNA in?

5’ to 3’

What enzyme catalyzes the nucleophilic attack of the 3’ hydroxyl to the 5’ phosphate and releases pyrophosphate?

DNA polymerase

pyrophosphate

2 phosphates joined together

What enzyme proofreads and has 3’ to 5’ exonuclease activity to remove an erroneously added mismatched base?

DNA polymerase

What enzyme unwinds the DNA at the replication fork?

helicase

What does helicase require to unwind DNA at the replication fork?

ATP

What proteins keep the two single strands from winding up again?

single strand binding (SSB) proteins

The leading strand is synthesized (continuously/discontinuously) in the 5’ to 3’ direction.

continuously

The lagging strand is synthesized (continuously/discontinuously) in the 5’ to 3’ direction.

discontinuously

The (lagging/leading) strand synthesizes toward the replication fork.

leading

The (lagging/leading) strand synthesizes away from the replication fork.

lagging

Can DNA polymerase III remove the RNA primer?

no

What enzyme removes the RNA primer one base at a time using 5’ to 3’ exonuclease activity?

DNA polymerase I

What does DNA ligase require?

3’ hydroxyl and 5’ phosphate

What enzyme supertwists the DNA in a negative direction?

gyrase

What does SSB do?

protects the single strand DNA and keeps it from winding up again

What does primase make?

RNA primer

What enzyme makes RNA primers?

primase

What does DNA polymerase I do?

fills in gaps between the Okazaki fragments and replaces the RNA primer with DNA

What does DNA ligase do?

seals the discontinuous fragments together

What enzyme seals the discontinuous fragments together?

DNA ligase

E. coli chromosome replication is __directional.

bi

E. coli chromosome replication is initiated by…

DNA A protein at oriC

oriC

origin chromosome

What does it mean when replication is bidirectional?

there are two replication forks going in opposite directions

In E. coli chromosome replication, a ____ structure is formed.

theta

SEQ E. coli chromosome replication

1. replication is initiated by DNA A protein at oriC

2. 2 replication forks go in opposite directions

3. a theta structure is formed

4. 2 forks hit a terminus of replication and meet each other

5. 2 circular DNAs are separated

mRNA

• linear

• short-lived

• template for translation to make proteins

tRNA

• folded up to prevent degradation; stable and long-lived

• delivers amino acids to the ribosome during translation

rRNA

• folded up to prevent degradation; stable and long-lived

• plays a structural and functional role in ribosomes

  • helps the ribosome bind to mRNA

  • helps catalyze addition of a new amino acid to the growing polypeptide

gene

basic unit of genetic information;

nucleic acid sequence that codes for a polypeptide, tRNA, or rRNA

A gene is a linear sequence of nucleotides with a fixed…

start point and end point

Where are codons found and what do they do?

in mRNA;

code for single amino acids

Does bacterial RNA polymerase require a primer?

no

holoenzyme

contains multiple subunits: β, β’, α, ω, σ

core enzyme

responsible for RNA synthesis

Do core enzymes have σ?

no

What is sigma (σ) subunit used for?

promoter recognition