Textbook 1.3

Question 1

Dispersed chromatin

Answer 1

associated with interphase activity of cell (replication and transcription)

Question 2

When is chromatin in its most condensed state

Answer 2

In a mitotic cell—facilitates delivery of DNA to daughter cell.

Question 3

Telomere sequence

Answer 3

TTAGGG (complementary strand is AATCCC) repeated about 500 to 5000 times

Question 4

Which strand overhangs after DNA replication and what is done with it

Answer 4

3’ end overhangs because primer is removed leaving empty space on 5’ end of DNA. Overhanging strand is tucked back into double stranded portion of telomere.

Question 5

Telomerase

Answer 5

A reverse transcriptase that uses an RNA template to synthesize DNA. Adds repeat units to 3’ end which serves as a template for a conventional DNA polymerase to add to 5’ end. Actually contains RNA.

Question 6

Function of telomeres

Answer 6

• protect chromosomes from nucleases

- prevent ends of chromosomes from fusing with each other

Question 7

Why do telomeres shrink?

Answer 7

Because most cells lack telomerase. When telomere shortening reaches a critical point, cell stops dividing.

Question 8

Which cells contain telomerase?

Answer 8

germ cells of gonads, stem cells, and 90% of human tumours.

Question 9

Topoisomerases

Answer 9

Relax supercoiled DNA strands. One cuts through a single strand and the other cuts through the whole duplex.

Question 10

Human genome

Answer 10

Equivalent to all the genetic information that is present in a single (haploid) set of human chromosomes (22 autosomes and sex chromosomes).

Question 11

Denatured DNA strands absorb…

Answer 11

more UV radiation

Question 12

Melting temp corresponds to

Answer 12

half the shift towards increased UV radiation. More G and C means higher melting temp.

Question 13

Difference between NER and BER

Answer 13

Nucleotide excision repair removes a whole sequence of nucleotides which is then filled in by DNA polymerase and sealed by ligase while Base ER removes single altered nucleotides.

Question 14

Which bond does DNA glycosylase cleave?

Answer 14

The glycosidic bond between the sugar and the base

Question 15

Difference between MMR in eukaryotes and E. coli

Answer 15

Mismatch repair in eukaryotes recognizes the nicks in the newly synthesized strand while in E. coli a protein looks for methylated adenines

Question 16

RNA polymerases in eukaryotes vs prokaryotes

Answer 16

Even the simplest euk. have three types of RNAPs while prok.s have one.

Question 17

Difference in transcription between euk. and prok.

Answer 17

Euk. require many accessory proteins called transcription factors

Question 18

RNA polymerase in E. coli

Answer 18

E. coli contains a single type of RNAp composed of 5 subunits which associate to form a core enzyme

Question 19

Function of sigma factor

Answer 19

Increases RNAps affinity for promoter sites while decreasing affinity for DNA in general (allows whole complex to slide along DNA until promoter region is reached).

Question 20

The nucleotide at which transcription is initiated is denoted as…and the one right before is…

Answer 20

• +1

- -1 (upstream)

Question 21

Promoters

Answer 21

sites of DNA that bind RNAp

Question 22

What happens to the sigma factor after the RNAp enzyme has been transformed into a transcriptional elongation complex?

Answer 22

After ten ish nucleotides have been successfully transcribed, enzyme undergoes conformational change and sigma factor is released.

Question 23

consensus sequence

Answer 23

TTGACA
sequence that is found 35 bp upstream initiation site of many bacterial genes

-10 bp upstream from initiation is also important

Question 24

Protein required for termination of bacterial transcription (half the time)? How is termination achieved otherwise?

Answer 24

• Rho, a ring shaped protein

- RNAp stops transcription when it reaches terminator sequence

Question 25

Primary transcript/Pre-RNA

Answer 25

Initial precursor RNA that leads to all major forms of Euk. RNAs—mRNA, rRNA, and tRNA. Equivalent in length to full length of DNA transcribed. Usually transient as they are processed quickly.

Question 26

Gene expression

Answer 26

production of a functional product (ex. an enzyme) from a stretch of DNA

Question 27

mRNA

Answer 27

messenger RNA
coding RNA that creates a complementary strand to section of DNA that can be used to produce polypeptide. Allows huge DNA molecule to stay in nucleus while smaller RNA molecule with genetic info copied can pass into cytoplasm.

Question 28

Where are proteins synthesized

Answer 28

in the cytoplasm

Question 29

Ribosomes contain both…

Answer 29

RNA and protein.

Question 30

Ribosomes

Answer 30

participate in protein translation

Question 31

rRNA

Answer 31

ribosomal RNA
Does not function in an informational capacity, rather provides structural support for ribosome and helps catalyze chemical reaction in which amino acids are covalently linked to one another.

Question 32

tRNA

Answer 32

Transfer RNA

translate info in mRNA nucleotide code into amino acid sequence (polypeptide)

Question 33

What is RNA folding driven by?

Answer 33

Formation of regions of complementary base pairs. Base-paired regions form double stranded stems which connect to single stranded loops.

Question 34

Difference between RNA and DNA base pairing

Answer 34

RNA base pairing is MUCH less discriminatory—contains non standard base pairs which serve as recognition sites for proteins and other RNAs.

Question 35

Do Euk. and Prok. have different RNAp?

Answer 35

No, RNA polymerase is same in both.

Question 36

Function of RNAp

Answer 36

enzymes that incorporates nucleotides into strand of RNA that is complementary to template DNA.

Question 37

Which direction does RNAp move along template strand

Answer 37

3’ to 5’, synthesizing a 5’ to 3’ strand

Question 38

How does RNAp link nucleotides together

Answer 38

Catalyzes highly favourable reaction in which ribonucleoside triphosphates are cleaved into nucleoside monophosphates as they are polymerized into covalent chain.

Question 39

What happens to the pyrophosphate produced in polymer reaction of RNA synthesis?

Answer 39

Because the nucleotide incorporation reaction MUST be essentially irreversible, the pyrophosphate (PP) produced in first rxn is hydrolyzed into inorganic phosphate, releasing a large amount of free energy.

Question 40

All Euk. mRNA precursors are synthesized by…

Answer 40

RNA polymerase II

Question 41

Promoter sequence for Euk. transcription

Answer 41

TATA box

Question 42

First step in assembly of preinitiation complex

Answer 42

TATA-binding protein (TBP) (which is part of TFIID) recognizes TATA box and inserts itself into minor groove

Question 43

CTD of RNAp II

Answer 43

Consists of a sequence of seven amino acids that is repeated over and over (7 times in yeast 52 times in humans)

Question 44

What part of the RNAp II is modified between the pre-initiation complex and the actually transcription enzyme

Answer 44

RNAp is phosphorylated and the chemical activity is localized in the CTD.

Question 45

Kinase

Answer 45

a specific enzyme that catalyses the addition of a phosphate group onto a substrate

Question 46

Function of TFIIH

Answer 46

Phosphorylates serine at position 5 in the CTD repeat peptide

Question 47

What do phosphorylated sites on the CTD provide?

Answer 47

Sites for proteins involved in RNA processing to bind to ex. 5’ cap formation

Question 48

Difference between EUk. and bacterial RNAp II transcription termination?

Answer 48

There is no identified termination sequence in Euk. 3’ end of bacterial sequence is generated simply by termination of transcription while in Euk. transcription goes far beyond where the 3’ end will eventually be suggesting a series of processing steps in Euk. transcription termination.

Question 49

Properties mRNAs share

Answer 49

1. Contain a continuous sequence of nucleotides encoding a specific polypeptide 2. They are found in the cytoplasm
2. They are attached to ribosomes when they are translated
3. Most mRNAs contain a significant noncoding segment (regions at both 5’ and 3’ end)
4. Eukaryotic mRNAs have special modifications—poly A tail on the 3’ end (50 to 250 adenosine residues) and a 5’ methylated guanosine cap.

Question 50

What’s at the junction of exon-intron sites in Euk.?

Answer 50

conserved gene sequence

Question 51

Difference between prok. and euk. transcription?

Answer 51

Euk. have three types of RNA polymerase and Prok. have only one. Transcription and translation can occur at same time.