Central Dogma

Question 1

Reaction catalyzed by DNA polymerase

Answer 1

(DNA)n + dNTP –> (DNA)n+1 + PPi

Question 2

bases used in DNA replication

Answer 2

doeoxyNTP = deoxyATP, deoxyGTP, deoxyCTP, deoxyTTP

Question 3

hydrogen bonds in base pairs

Answer 3

A-T = 2 hydrogen bonds
G-C = 3 hydrogen bonds

Question 4

key characteristics of DNA synthesis

Answer 4

1. 4 deoxynucleoside triphosphates and Mg2+ are required
2. A template strand is used to direct DNA synthesis
3. A primer from which the new strand grows must be present (DNA polymerase needs a free 3’ hydroxyl)
4. Many DNA polymerases have nuclease activity that allows for the removal of mismatched bases (i.e. editing ability)

Question 5

helicase

Answer 5

separates the 2 strands of DNA so that DNA polymerase can access them for DNA replication

Question 6

topoisomerase/gyrase

Answer 6

a protein needed to straighten out the tangling that can occur as the two helices are being pulled apart

Question 7

leading strand v. lagging strand

Answer 7

leading strand - new bases are added at the 3’ end and the leading strand grows continually in the 5’ to 3’ direction
lagging strand - replication occurs by Okazaki fragments, whereby a new primer is put in and the synthesis occurs in fragments. DNA ligase closes the gaps at the end.

Question 8

transcription

Answer 8

the process of synthesizing RNA from DNA. It is catalyzed by RNA polymerase. Eukaryotic transcription is significantly more complicated and has complicated regulatory mechanisms than prokaryotic b/c prokaryotes have only one circular chromosome.

Question 9

RNA polymerase needs

Answer 9

1. A template (i.e. a strand of DNA to replicate)
2. four ribonucleoside triphosphates
3. divalent metal ions, usually Mg2+ or Mn2+

Question 10

overall equation for transcription

Answer 10

(RNA)n residues + ribonucleoside triphosphate –> (RNA)n+1 residues + PPi

Question 11

coding strand

Answer 11

also known as the sense strand. the strand of DNA that has the same sequence as the RNA being synthesized. (except RNA has U’s where DNA has T’s)

Question 12

template strand

Answer 12

also known as the antisense strand. The strand of DNA that is serving as the template for the new strand of RNA.

Question 13

bacterial RNA polymerase

Answer 13

RNA polymerase I. Has several subunits including a special subunit called sigma. When the sigma factor is associated, the whole thing is called the holoenzyme. Without sigma, it’s called the core enzyme. The sigma factor needs to be bound in order to transcription to begin.

Question 14

types of RNA

Answer 14

1. mRNA - encodes information to generate a protein. It has the code for the order of amino acids in a protein
2. tRNA - plays a key role in translating mRNA to protein. It brings the appropriate amino acid that matches the codon on the mRNA and transfers it onto the growing polypeptide chain.
3. rRNA - part of ribosomal structure that also plays a key role in translating mRNA into protein. There are 4 different rRNA’s, one of which has the enzyme activity that makes the peptide bond (this is the peptidyl transferase rRNA).
4. small nuclear RNA’s (snRNA) - e.g. snurps - do the processing in eukaryotes

Question 15

rRNA

Answer 15

4 strands of rRNA are part of the structure of the ribosome and one provides the peptide transferase activity

Question 16

tRNA

Answer 16

61 species of tRNA are loaded with a specific amino acid and binds to codons in the mRNA using their anticodon loop

Question 17

translation

Answer 17

Ribosome is the major structure doing the translation. It has a large and small subunit with different sizes of rRNA components (these sizes differ for prokaryotes and eukaryotes). There are 3 sites on the ribosome - A site, P site, and E site. The tRNA brings an amino acid into the A site, the polypeptide bond is formed in the P site, and the tRNA exits at the E site to go pick up another amino acid.

Question 18

Prokaryotic transcription v. Eukaryotic transcription

Answer 18

Bacteria: RNA polymerase I is composed of 5 subunits. Sigma factor is needed to find the promotor. When it does, RNA polymerase I elongates the RNA product.

Eukaryotes: More proteins are needed to recognize the promotor. These are called transcription factors. Some transcription factors bind to repressors or activators and others are called basal transcription factors because they are always needed to initiate transcription. Eukaryotes have more than one RNA Polymerase.

Question 19

Eukaryotic RNA polymerases

Answer 19

1. RNAPII - transcribes mRNA
2. RNAPI - transcribes rRNA
3. RNAPIII - transcribes tRNA

Question 20

constitutive RNA

Answer 20

rRNA and tRNA are constitutive, meaning we need them all the time. They do our housekeeping.

Question 21

eukaryotic mRNA

Answer 21

is different in different cell types. We need to regulate this more specifically than the other two types.

Question 22

regulators for eukaryotic RNAPII

Answer 22

transcription factors - basal transcription factors or specific transcription factors

Question 23

Eukaryotic promotors

Answer 23

RNAPII recognizes some specific promotor sequences. The main ones:

1. TATA box
2. CAAT box
3. GC box

Question 24

strong vs. weak promotors

Answer 24

If the promotor is close to the gene being transcribed, it is strong.

Question 25

cis acting elements

Answer 25

DNA sequences that regulate the expression of a gene located on the same molecule of DNA. Promotors are referred to as cis-acting elements.

Question 26

trans acting elements

Answer 26

proteins that recognize cis-acting elements and regulate RNA synthesis. They are commonly called transcription factors.