Chapter 13

Question 1

13.1

What do chromosomes consist of?

Answer 1

primarily of DNA and associated proteins

Question 2

13.1

Where is the genetic info in chromosomes?

Answer 2

resides in the DNA

Question 3

13.3

What allows us to make comparisons between organisms?

Answer 3

their complete genome sequences

Question 4

13.3

Why is gene number not a good predictor of biological complexity?

Answer 4

as different genomes were sequences and annotated, it came as a surprise to find that humans have about the same number of protein-coding genes as many organisms with much smaller genomes

Question 5

13.3

What does differential gene expression allow?

Answer 5

the same protein-coding genes to be deployed in different combinations to yield a variety of distinct cell types

Question 6

13.3

How can a single genes yield multiple proteins?

Answer 6

either because of alternative splicing or posttranslational modification

Question 7

13.3

What is alternative splicing?

Answer 7

different exons are spliced together to make different proteins

Question 8

13.3

What is posttranslational modification?

Answer 8

proteins undergo biochemical changes after they have been translated

Question 9

13.3

How is genome size measured?

Answer 9

in number of base pairs

Question 10

13.3

What has the complete sequence of small bacterial genomes allowed researchers to do?

Answer 10

to define the smallest genome (therefore, the minimal set of proteins) necessary to sustain life

Question 11

13.3

What is the significance of ~500 genes?

Answer 11

current findings suggest that the minimum number of genes necessary to encode all the functions essential to life is ~500

Question 12

13.3

What does it mean that genomes of bacteria and archaeons are information dense?

Answer 12

most of the genome has a defined function

• 90% or more of their genomes consist of protein-coding genes (protein usually has unknown function)

Question 13

13.3

What do bigger genomes have?

Answer 13

more genes, allowing these bacteria to synthesize small molecules that other bacteria have to scrounge for, or to use chemical energy in the covalent bonds of substances that other bacteria cannot

Question 14

13.3

Describe the relation of genome size and organismal complexity in eukaryotes.

Answer 14

just as the number of genes does not correlate well with organismal complexity, the size of the genome is unrelated to the metabolic, developmental, and behavioural complexity of the organism

Question 15

13.3

What is the C-value paradox?

Answer 15

disconnect between genome size and organismal complexity

• C-value is amount of DNA in a reproductive cell
• paradox is the apparent contradiction between genome size and organismal complexity, leading to the difficulty of predicting one based on the other

Question 16

13.3

Why are some eukaryotic genomes so large?

Answer 16

polyploidy: having more than two sets of chromosomes in the genome, especially prominent in many groups of plants

Question 17

13.3

How has polyploidy played an important role in plant evolution?

Answer 17

• many agricultural crops are polyploid
• 30-80% flowering plants have polyploidy in evolutionary histories, either because of duplication of the complete set of chromosomes in a single species or because of hybridization between related species followed by duplication of the chromosome sets in the hybrid

Question 18

13.3

What is the principal reason for large genomes among some eukaryotes?

Answer 18

their genomes contain large amounts of DNA that do not code for proteins, such as introns and DNA sequences that are present in many copies

Question 19

13.4

What is a nucleoid?

Answer 19

structure with multiple loops formed by supercoils of DNA in bacteria
- supercoil loops are bound together by proteins

Question 20

13.4

Describe the bacterial genomes.

Answer 20

they are circular and the DNA double helix is underwound, which means that it makes fewer turns in going around the circle than would allow every base in one strand to pair with its partner base in the other strand

Question 21

13.4

What is topoisomerase II?

Answer 21

an enzyme that causes underwinding, which breaks the double helix, rotates the ends to unwind the helix, and then seals the break

Question 22

13.4

What does underwinding create?

Answer 22

creates strain on the DNA molecule, which is relieved by the formation of supercoils in which the DNA molecule coils on itself

Question 23

13.4

What does supercoiling allow?

Answer 23

all the base pairs to form, even though the molecule is underwound

Question 24

13.4

What are negative supercoils?

Answer 24

supercoils that result from underwinding

Question 25

13.4 What are positive supercoils?

Answer 25

supercoils that result from overwinding

Question 26

13.4 What kind of supercoils are there in most organisms?

Answer 26

most DNA is negatively supercoiled

Question 27

13.4 What happens when DNA in a loop is nicked?

Answer 27

supercoils in that loop unwind and DNA duplex forms a relaxed double helix

Question 28

13.4 How do bacterial cells package their DNA?

Answer 28

as a nucleoid composed of many loops

Question 29

13.4 How do eukaryotic cells package their DNA?

Answer 29

as one molecule per chromosome

Question 30

13.4 Describe the similarity between bacterial and eukaryotic cell packaging.

Answer 30

- have topoisomerase II | - DNA is usually negatively supercoiled

Question 31

13.4 Describe eukaryotic DNA.

Answer 31

- linear | - each DNA molecule forms a single chromosome

Question 32

13.4 How is DNA packaged in a chromosome?

Answer 32

with proteins to form a DNA-protein complex called chromatin

Question 33

13.4 Describe histone proteins.

Answer 33

- found in all eukaryotes - interact with any double-stranded DNA - are evolutionarily conserved, which means that they are very similar in sequence from one organism to the next - histone proteins from one eukaryote can associate with DNA from another - form the core of a nucleosome (8 proteins) - each nucleosome also includes a stretch of DNA wrapped twice around the histone core - rich in positively charged amino acids lysine and arginine, which are attracted to the negatively charged phosphate groups in each DNA strand

Question 34

13.4 What is the first level of chromatin packaging also called?

Answer 34

- beads on a string (nucleosomes are the beads and the DNA is the string_ - 10-nm fiber (reference to its diameter, which is about five times the diameter of the DNA double helix

Question 35

13.4 Describe the second level and onwards of chromatin packaging.

Answer 35

- occurs when chromatin is more tightly coiled, forming a 30-nm fiber - as chromosomes in nucleus condense in preparation for cell division, each chromosome becomes progressively shorter and thicker as the 30-nm fiber coils onto itself to form a 300-nm coil, a 700-nm coiled coil, and finally a 1400-nm condensed chromosome in a manner that is still not fully understood

Question 36

13.4 What is chromosome condensation?

Answer 36

progressive packaging an active, energy-consuming process requiring the participation of several types of proteins

Question 37

13.4 When is greater detail of the structure of a fully condensed chromosome revealed?

Answer 37

when the histones are chemically removed

Question 38

13.4 What happens to DNA without histones?

Answer 38

DNA spreads out in loops around a supporting protein structure called the chromosome scaffold

Question 39

13.4 What is the size difference between the volume of a fully condensed human chromosome and a bacterial cell?

Answer 39

volume of a fully condensed human chromosome is five times larger than the volume of a bacterial cell

Question 40

13.4 What are the 6 levels of chromosome condensation?

Answer 40

1. DNA duplex (2 nm in diameter) 2. nucleosome fiber (210 nm in diameter) 3. chromatin fiber (30 nm) 4. coiled chromatin fiber (300 nm) 5. coiled coil (700 nm) 6. condensed chromatid (1400 nm)

Question 41

13.4 Describe the first level of chromatin packaging.

Answer 41

eukaryotic DNA winds around histone proteins