Chapter 7

Question 1

genome

Answer 1

• is all the genetic information that defines an organism.

- consist of one or more DNA chromosomes

Question 2

Two types of gene transfer are known

Answer 2

1. Vertical transmission
   - from parent to child, or a cell to its progeny
2. Horizontal transmission
   - transfer of pieces of DNA from one cell to another

Question 3

structural gene

Answer 3

• produces a functional RNA (“coding” DNA)
• mRNA, which encodes a protein
• rRNA, tRNA, small ncRNA, and a few others

Question 4

DNA control sequence

Answer 4

regulates the expression of a structural gene

Question 5

noncoding DNA

Answer 5

• DNA that does not code for any genes

- bacterial DNA does not have a lot noncoding DNA

Question 6

A gene

Answer 6

can operate independently of other genes

Question 7

an operon

Answer 7

• in prokaryotes, it may exist in tandem with other genes in a unit
• often contain genes with related functions that need to be expressed together

Question 8

Regulons

Answer 8

• different genes or operons controlled by the same transcription factor (control protein)
• can be on different parts of the chromosome

Question 9

DNA Structure

Answer 9

• Hydrogen bonding
• polymer of nucleotides

nucleotide consists of three parts

1. Nitrogenous base
   - Purine: adenine (A) and guanine (G)
   - Pyrimidine: cytosine (C) and thymine (T)
2. Deoxyribose sugar
3. Phosphate

• connected to each other by covalent 5′-3′ phosphodiester bonds
• phosphodiester backbone strands to come together in an antiparallel fashion

Question 10

Histone-like proteins

Answer 10

help compact DNA in the

Question 11

DNA-binding proteins

Answer 11

bind DNA

Question 12

Transcription factors

Answer 12

can recognize specific DNA sequences and control gene expression

Question 13

RNA Structure

Answer 13

• Usually single-stranded
• dsRNA viruses
• Contains ribose sugar
• Uracil replaces thymine

Question 14

nucleoid

Answer 14

• Bacteria pack their DNA into a series of loops or domains with proteins
• Loops are anchored by histone-like proteins

Question 15

DNA Supercoiling

Answer 15

-compacts DNA and helps open strands for gene expression

Question 16

topoisomerases

Answer 16

-Enzymes that change DNA supercoiling

• Example: DNA gyrase
• Targeted by quinolone antibiotics
• ciprofloxacin, used for anthrax and others

Question 17

Replication

Answer 17

• cellular DNA is semiconservative
• Each daughter cell receives a double helix with one parental and one newly synthesized strand
• begins at a single origin
• replication bubble (ssDNA) forms
• ends at defined termination (ter) sites located opposite to the origin
• often multiple round of replication occurring at once

Question 18

Bidirectional replication

Answer 18

-contains two replication forks that move in opposite directions around the chromosome

Question 19

major proteins involved in DNA replication

Answer 19

• DnaA: initiator protein
• DnaB: helicase
• DNA primase: synthesis of RNA primer
• DNA Pol III: major replication enzyme, has proofreading activity
• DNA Pol I: replaces RNA primer with DNA
• DNA gyrase: relieves DNA supercoiling

Question 20

Initiation of Replication

Answer 20

-start of DNA replication is precisely timed and linked to the ratio of DNA to new cell mass

In E. coli

• DnaA accumulates during growth, and then triggers the initiation of replication.
• DnaA-ATP complexes bind to short DNA repeats upstream of the origin.
• Then, dsDNA is melted open by the helicase (DnaB)

Question 21

leading strand

Answer 21

is replicated continuously in the 5′-to-3′ direction

Question 22

lagging strand

Answer 22

-is replicated discontinuously in stages, each producing an Okazaki fragment

Question 23

Plasmids can replicate in two different ways

Answer 23

1. Bidirectional replication
   - Starts at a single origin and occurs in two directions simultaneously
2. Rolling-circle replication
   - Starts at a single origin and moves in only one direction

Question 24

Plasmids mechanisms to ensure their inheritance

Answer 24

• Low-copy-number plasmids (often only one per chromosome) segregate equally to daughter cells using special proteins.
• High-copy-number plasmids (often a dozen or more per cell) segregate randomly to daughter cells

Question 25

Genome libraries

Answer 25

- also called clone libraries or clone pools | - contain a mix of all the genes in an organism as random cloned fragments

Question 26

Shuttle vectors

Answer 26

-plasmids that can replicate in at least two different organisms

Question 27

Basic cloning steps

Answer 27

1. Cleavage with restriction enzyme 2. DNA isolation 3. Mixing and annealing vector and insert 4. Ligation with DNA ligase and ATP 5. Transformation into host strain

Question 28

polymerase chain reaction (PCR)

Answer 28

- produce over a million-fold amplification of target DNA within a few hours. - Target specificity provided by synthetic DNA primers that base pair with target and prime DNA synthesis

Question 29

Whole-genome shotgun (WGS)

Answer 29

- Genome is broken into thousands of pieces, which are all sequenced - Computers determines sequence overlaps to recreate entire genome sequence

Question 30

Metagenomics

Answer 30

- is used to study microbial communities in organisms or different environments - Provides information for all organisms, even those that cannot be grown in the laboratory - Total DNA from a sample is shotgun sequenced - Bioinformatics is used to understand the genes that are present in the sample