Lecture 2 - Exam 2

Question 1

Clamps remain associated with DNA polymerase allowing uninterrupted synthesis of many thousands of DNA nucleotides. But, how does DNA unwind in front of the polymerase?

Answer 1

Helicases.

Question 2

What do helicases do?

Answer 2

Helicases unwind (in counterclockwise rotation) the two strands of parental DNA ahead of the replication fork.

Question 3

After helicase unwinds the two strands of parental DNA ahead of the replication fork, what happens?

Answer 3

The unwound DNA strands are then stabilized by single-stranded DNA-binding proteins so that they can serve as templates for new DNA synthesis.

Question 4

As the two strands of template DNA unwind, the DNA ahead of the replication fork is forced to…?

Answer 4

Rotate in the opposite direction, causing circular molecules to become twisted around themselves.

Question 5

As the two strands of template DNA unwind, the DNA ahead of the replication fork is forced to rotate in the opposite direction, causing circular molecules to become twisted around themselves. How did cells evolve to handle this?

Answer 5

Topoisomerases.

Question 6

What do topoisomerases do?

Answer 6

Topoisomerases catalyze the reversible breakage and rejoining of DNA strands.

Question 7

The transient breaks introduced by topoisomerases serve as…?

Answer 7

Swivels that allow the two strands of DNA to rotate freely around each other.

Question 8

We should have 1/100 errors in base pair matching but we only have __________. Why?

Answer 8

1/1,000,000,000
This number is so small because DNA polymerase helps select the correct base for insertion into the new DNA molecule. Binding of dNTPs actually causes conformational change in the polymerase that is necessary for incorporation .

Question 9

___ out of ____ eukaryotic DNA polymerases (epsilon and zeta) have ____’ to _____’ __________ activity.

Answer 9

2 out of 3 ;
3’ to 5’ ;
exonuclease

Question 10

Replication origins in eukaryotic chromosomes: Replication initiates at …?

Answer 10

Replication initiates at multiple origins (ori), each of which produces two replication forks.

Question 11

Origins (ori) are typically ____ rich and serve as…?

Answer 11

A/T rich.
Serve as binding sites for proteins that start replication.

Question 12

An S. cerevisiae ______ element in the DNA contains an ____________ and three additional elements that contribute to origin function:

Answer 12

ARS ;
11-base-pair ARS consensus sequences (ACS) ;
B1, B2, and B3

Question 13

What binds to the ACS and B1?

Answer 13

The origin recognition complex (ORC) binds to the ACS and B1.

Question 14

What additional proteins does ORC recruit to the origin, after it binds to he ACS and B1?

Answer 14

MCM DNA helicase.

Question 15

DNA polymerase extends only in the 5’ to 3’ direction, so it can’t copy…?

Answer 15

The extreme ends with an overhanging 3’ end.

Question 16

What is telomeric DNA?

Answer 16

A simple repeat sequence with an overhanging 3’ end.

Question 17

Describe telomerase.

Answer 17

Telomerase carries its own RNA molecule (it’s a reverse transcriptase) which is complementary to telomeric DNA, as part of the enzyme complex.

Question 18

The overhanging end of telomeric DNA binds to the …? Which then serves as…?

Answer 18

The overhanging end of telomeric DNA binds to the telomerase RNA, which then serves as a template for extension of the template strand by one repeat unit.

Question 19

After the overhanging end of telomeric DNA binds to the telomerase RNA, which then serves as a template for extension of the template strand by one repeat unit, then what happens?

Answer 19

The lagging strand of the telomeric DNA can then be elongated by conventional RNA priming and DNA polymerase activity. Of course, then the RNA primer is removed and then telomeric DNA is extended by one unit repeat.

Question 20

What prevents RNA nucleotides (NTPs) from becoming incorporated into a growing DNA strand?

Answer 20

DNA polymerase discriminates against nucleotides containing the ribose sugar.

Question 21

What is the central dogma of molecular biology?

Answer 21

An explanation of the flow of genetic information within a biological system.
It deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.

Question 22

What are the 6 steps in the central dogma of biology?

Answer 22

1. Transcription
2. Processing
3. Transport out of nucleus
4. Translation
5. Protein folding and modification
6. Carry out function

Question 23

What is transcriptional control and what is its major role?

Answer 23

Regulation of gene expression in response to:
- Environmental changes
- Intracellular signals
- Cell-to-cell interactions within the organism
Basically, what makes us, us. It is about what genes are turned on and off in cells.

Question 24

The human genome encodes approx. ________ genes, about the same number as that for _____ and nearly twice as many as that for the common ______.

Answer 24

25,000 ;
Corn ;
Fruit fly

Question 25

The 25,000 genes that are encoded, are encoded in about ______% of the genome.

Answer 25

1.5

Question 26

Do almost all cell have the same DNA?

Answer 26

Yes, genomic equivalence.

Question 27

Functions of cells are not determined by…?
What is it determined by?

Answer 27

Differences in the genome.
It is determined by the expression of genes, which ones are turned on and off.

Question 28

What is the best evidence for genomic equivalence?

Answer 28

Dolly, the first organism to be cloned.
The hypothesis was that if each cell’s nucleus is identical to the zygote nucleus (fertilized egg), then each cell’s nucleus should be able to direct development of the entire embryo if transplanted to an enucleated cell.
The experiment was ultimate proof that nuclei of vertebrate adult somatic cells contains all the genes needed to generate an adult organism.
The cloned goat was genetically identical to the nuclear donor with the Finn-Dorset strain.

Question 29

Is gene expression controlled at the same levels?

Answer 29

NO! Different levels.

Question 30

Transcription is controlled by?
What can regulate the translation of mRNA into proteins?
What modifications can also regulate gene expression?

Answer 30

Limiting the amount of mRNA that is produced from a particular gene.
Post transcriptional events that regulate the translation of mRNA into proteins.
Post translational modifications can also regulate gene expression.

Question 31

What are the six control points that can affect the activity of a gene?

Answer 31

Starts with DNA:
1) Transcriptional control
RNA transcript produced
2) RNA processing control
mRNA is produced
Moved from nucleus to cytosol
3) RNA transport and localization control
mRNA either (4 and 6, or 5)
4) translation control, making mRNA a protein.
6) protein activity control
either to an inactive protein or an active protein
or mRNA can
5) mRNA degradation control, making inactive mRNA

Question 32

Gene expression can be regulated at several levels so that different cell types synthesize:

Answer 32

Different sets of proteins (and proteins are activated differently in different cells)