UNIT 2

Question 1

Which of the following statements are FALSE about the DNA in bacteria and eukaryotes? [choose all that apply]

• The DNA macromolecule is not different, all organisms use the DNA to store genetic information.
• The DNA in bacteria is in the nucleoid region of the cytoplasm, while the DNA in eukaryotes is in the nucleus.
• The DNA in bacteria, but not eukaryotes, follow Chargaff’s base pairing rules
• The DNA double helix forms a circle in bacteria and a linear structure in eukaryotes.
• Thymine is used instead of uracil in eukaryotic DNA only.

Answer 1

FALSE:

• the DNA in bacteria, but not eukaryotes, follow Chargaff’s base pairing rules
• Thymine is used instead of uracil in eukaryotic DNA only

Question 2

Which feature does NOT contribute to the structure of the DNA double helix?

• The sugar phosphate backbone is negatively charged so it interacts with the aqueous environment.
• The A-T and C-G purine-pyrimidine base pairs have the same geometries.
• The phosphodiester bonds link the 1’ carbon atom of the sugar to the nucleotide.
• The bases group together away from aqueous solution due to the hydrophobic effect.
• The bases project towards the centre, stacked one on top of the other.

Answer 2

DOES NOT:

• the phosphodiester bonds link the 1’ carbon atom of the sugar to the nucleotide

Question 3

T or F: As part of a viral defense system, Cas9 carries a single stranded viral DNA molecule to target viral DNA entering the cell for cleavage.

Answer 3

false (rna)

Question 4

T or F: The complementary base pairing between the guide RNA and viral genomic DNA is the basis for specific targeting of viral DNA for degradation by Cas9.

Answer 4

true

Question 5

T or F: CRISPR arrays in the bacterial genome include viral DNA sequences from previous exposure of the bacteria to those viruses.

Answer 5

true

Question 6

T or F: For genome editing, Cas9 uses viral DNA to target the sequence to be disrupted.

Answer 6

false

Question 7

T or F: In bacteria, a gene commonly includes introns and exons.

Answer 7

false

Question 8

T or F: In bacteria, a gene is a transcription unit, where DNA codes for RNA.

Answer 8

true

Question 9

T or F: In bacteria, the terminator is part of the gene.

Answer 9

true

Question 10

T or F: In bacteria, for each gene, there is a corresponding protein product.

Answer 10

false

Question 11

Which statement is always true about DNA polymerase? Choose the one best answer.

• It catalyzes a reaction at the 2’ deoxyribose sugar.
• It requires a primer to begin nucleic acid synthesis.
• It unwinds the DNA at the replication fork.
• It always moves towards the replication fork on both strands.
• It reads the template in a 5’ to 3’ direction.

Answer 11

it requires a primer to begin nucleic acid synthesis

Question 12

A bacterium has a mutation that deletes the entire operator of the malPQ operon. What will happen if these mutant bacteria are transferred from media with only glucose, to media with only maltose?

Answer 12

The malT gene will be constitutively transcribed, and malPQ operon will be transcribed at low/ basal levels.

Question 13

function of Helicase

Answer 13

An enzyme that untwists the double helix of DNA at the replication forks

Question 14

function of Topoisomerase

Answer 14

Enzyme that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork.

Question 15

How does a transcription factor specifically recognize the promoter sequence in DNA?

Answer 15

It It makes specific non-covalent interactions with the bases in the promoter.

Question 16

In normal double-stranded DNA, purines base pairs with only certain types of pyrimidines. This is because…
- a purine-purine pair would be too small, and a pyrimidine-pyrimidine pair would be too large

• the number of A must equal the number of T and the number of G must equal the number of C
• the strongest stacking interactions are found between purines and pyrimidines, making the DNA more stable
  purine-pyrimidine pairs maximize the number of hydrogen bonds, making the DNA more stable.
• all Watson-Crick purine-pyrimidine base pairs have the same geometries

Answer 16

all Watson-Crick purine-pyrimidine base pairs have the same geometries

Question 17

Outline the steps of PCR:

Answer 17

1.Denaturation- heat to 95 degrees to separate the strands
2. Annealing- cool to 50-60 degrees to allow DNA primers to bind to homologous sequences (one primer per strand)
Two primers are required, one for each strand
They are made by in vitro polynucleotide synthesis, thousands of copies are made and added in excess
Scientists design the primers to target specific section
3. Extend TAQ POL (DNA POL III from thermus aquaticus) is used to replicate DNA between primers at 72 degrees
Each cycle, the number of strands doubles

Question 18

Why do you need to use heat in PCR?

Answer 18

• Heat treatment is used to separate DNA strands in each molecule at the beginning of each cycle
• Heating causes separation because thermal energy increases rotational, vibrational and translational energy of molecules, and at some point this energy exceeds the bond energy

Question 19

What is an advantage that bacteria have due to their circular DNA?

Answer 19

The length of their DNA is not decreasing with each cell division.

Question 20

What catalyzes DNA synthesis?

Answer 20

DNA POL

Question 21

Put the following steps of DNA replication on the lagging strand in chronological order.

A. Single-stranded binding proteins attach to the DNA strands.
B. Hydrogen bonds between base-pairs of the DNA strands are broken.
C. Primase binds to the single strand DNA.
D. DNA polymerase elongates the primer.
E. A short RNA primer is created.

Answer 21

BACED

Question 22

Organize the eukaryotic genome organization terms below starting the lowest level of molecules and ending with the highest level of organization. Repeat for bacteria. Include only the elements that apply.

Nucleosome
Chromosome
Genes
Nucleoid
DNA molecule
Chromatin
Nucleotides

Answer 22

eukaryote: nucleotides-DNA molecule - genes- nucleosome-chromatin-chromosome
bacteria: nucleotides -DNA molecule - genes- chromosome- nucleoid

Question 23

How does the genome of a virus compare to cellular genomes?

Answer 23

Viruses can have DNA or RNA genomes. They can be doubled stranded, single stranded or both. The strands can be circular, linear (one piece) or be segmented.

Question 24

What is the difference between a gene, genome and chromosome? Practice by writing this in your own words

Answer 24

Gene- a sequence of nucleotides in a region of the DNA that have some function/code for proteins/RNA
Chromosomes - consist of all the DNA associated with proteins and are organized in some manner.
Genome - all the genetic material that is transferred from parent to offspring

Question 25

In CRISPR DNA editing, what are the functions of the CRISPR-associated protein Cas9

Answer 25

Bind guide RNA
Bind target DNA
Cleave target DNA

Question 26

If a researcher wants to edit a DNA sequence in a cell using the CRISPR-Cas9 technique, what does she need to insert into the cell?

Answer 26

DNA coding for the Cas9 protein

Question 27

During CRISPR-Cas9 DNA editing, how does Cas9 identify the target DNA?

Answer 27

Cas9 binds to a customized RNA sequence, and the RNA recognizes the complementary sequence in the target DNA.