Module 6

Question 1

What are the 5 essential characteristics of hereditary material?

Answer 1

1. Localized to the nucleus
2. stable
3. sufficiently complex
4. accurately replicates
5. mutable

Question 2

Who was DNA isolated by & when?

Answer 2

Friedrich Miescher, 1860s

Question 3

What did Miescher isolate DNA from?

Answer 3

nuclei of white blood cells,
salmon sperm

Question 4

What are the DNA base pairs?

Answer 4

T&A
C&G

Question 5

Directionality of a single strand of DNA is
based on what?

Answer 5

the carbons of (deoxy)ribose

Question 6

5’ end terminates
with _________ group?

3’ end terminates with a ____________
(-OH) group?

Answer 6

1. phosphate group
2. hydroxyl group

Question 7

1. when a new strand of nucleic acid (DNA
   or RNA) is built, the direction is
   always?
2. new nucleotides are added to which end?

Answer 7

5ʹ to 3ʹ

3ʹ end

Question 8

How many bp makes a complete turn in a DNA double helix?

Answer 8

10bp
▪ 3.4 nm distance

Question 9

two strands are antiparallel or parallel?

Answer 9

antiparallel

Question 10

What 2 things hold DNA together?

Answer 10

▪ hydrogen bonding between
nitrogenous bases

▪ base-stacking/pi-stacking between
nucleotides

Question 11

Short segments of what may help control gene expression?

Answer 11

H-DNA

Question 12

What are the 4 important processes for the genome?

Answer 12

1. Synthesis of RNA and cellular proteins
2. Replication
3. Segregation of chromosomes (cell division)
4. Compaction: have to fit in a cell or nucleus of cell

Question 13

1. Which genome is usually 5 to 200 kilo base pairs (Kbp), packaged in chromosome?
2. Bacterial genome how many bp and its shape?

Answer 13

1. Viral genome
2. few million bp (1–10Mbp, avg. 4Mbp),
   circular, looped and supercoiled

Question 14

1. Eukaryotic genome: __ Mbp – >____Gbp, linear, in several chromosomes, coiled with histones, supercoiled and more
2. Archaeal genome – 500Kbp–6Mbp, what is the shape?

Answer 14

1. 5Mbp – >100Gbp,
2. circular, coiled with histones

Question 15

T or F As a general rule, larger genomes
have more genes

Answer 15

True

Question 16

Viral chromosomes can come in what forms (3)?

Answer 16

1. Double or single stranded RNA (ds or ssRNA)
2. Double or single stranded DNA (ds or ssDNA)
3. Circular or linear with single chromosome or a number of DNA molecules

Question 17

which virus is enclosed in protein shell (capsid) and external membrane?

Answer 17

enveloped virus

Question 18

what is a non-enveloped (naked) virus?

Answer 18

a virus enclosed only in protein shell
(capsid)

Question 19

What is a retrovirus?

Answer 19

RNA viruses that contain a gene for reverse transcriptase in their genomes

Question 20

T or F not all RNA viruses are retroviruses
(but all retroviruses are RNA viruses)

Answer 20

True

Question 21

what is an example of an enveloped retrovirus?

Answer 21

HIV is an enveloped retrovirus

Question 22

Haploid genomes often have smaller, circular pieces of autonomously replicating
DNA also known as?

Answer 22

plasmids

Question 23

what is a Nucleoid

Answer 23

the dense non-membrane region where the chromosome is supercoiled

Question 24

Bacterial chromosome condensation by proteins average loop contains how many kb of DNA

Answer 24

40 kb of DNA

Question 24

What proteins form dimers that hold coils of DNA?

Answer 24

SMC (structural maintenance of chromosomes)

Question 25

STARTT ABOVE HERE Define tandem repeat

Answer 25

pattern of one or more nucleotides in repeated units directly adjacent to one another

Question 26

VNTRs fall into which category of repetitive element? A) tandem repeats B) satellite DNA C) retrotransposons D) SINEs E) telomere

Answer 26

A & B

Question 27

What do euchromatin regions contain and how do they look in interphase?

Answer 27

actively expressed genes and are less condensed during interphase

Question 28

What do heterochromatin regions contain and how do they look in interphase?

Answer 28

fewer gene expressions, remain condensed

Question 29

▪ variable levels of condensation ▪ related to levels of transcription of resident genes Facultative or Constituitive?

Answer 29

facultative heterochromatin

Question 30

Where is constitutive heterochromatin found? Is it condensed? What is it composed of?

Answer 30

centromeres & telomeres permanently condensed repetitive DNA sequences

Question 31

What is the size of nucleosomes? What is the core particle of a nucleosome?

Answer 31

- 10 nm fiber - dsDNA wrapped around an octamer of histone proteins

Question 32

Label each step 300nm fiber and scaffold, aka radial loops tighten those loops! Nucleosomes (10nm fiber) 30nm fiber H1 histone on linker DNA

Answer 32

Step 1A: Nucleosomes (10nm fiber) 1B: 30nm fiber 2:H1 histone on linker DNA 3: 300nm fiber and scaffold, aka radial loops 4: tighten those loops!

Question 33

When does the 30 nm fiber form?

Answer 33

when the 10-nm fiber coils into a solenoid structure

Question 34

Interphase chromosomes have variably sized loops of 30-nm fibers attached to what?

Answer 34

a non-histone protein chromosome scaffold

Question 35

What forms the 300 nm fiber?

Answer 35

loops on the scaffold

Question 36

Histone proteins are directly involved in which levels of chromosome packaging in eukaryotes? (select all that apply) A) nucleosomes B) 30nm fiber C) 300nm fiber (radial loops) D) 700 nm fiber E) loop tightening

Answer 36

A & B

Question 37

How can specific locations on chromosomes be visualized?

Answer 37

fluorescence in situ hybridization (FISH)

Question 38

Different stains and dyes are used to produce __________-______ _______ _________ on chromosomes.

Answer 38

broad-scale banding patterns

Question 39

Which banding patterns are standard for human chromosomes?

Answer 39

G (Giemsa) banding;

Question 40

What do archaeal chromosomes look like? Genome size? What % of archael genome sequences are protein coding? (similar to bacteria, greater than eukaryotes)

Answer 40

single, circular chromosome w extra-chromosomal plasmids varies over more than a tenfold 87%

Question 41

Repetitive sequences and intergenic regions are found where?

Answer 41

archaeal genomes

Question 42

T/F Archaea have histone complexes as in eukaryotes.

Answer 42

TRUE

Question 43

T or F DNA can only be negatively supercoiled

Answer 43

False, DNA can be negatively or positively supercoiled

Question 44

which type of super coiling is more common between negative and positive anf why?

Answer 44

negative is more common because

Question 45

The supercoiling process is controlled by which two main enzymes?

Answer 45

DNA gyrase/ topoisomerase II Topoisomerase I

Question 46

The DNA and associated proteins of a eukaryotic chromosomes are called ?

Answer 46

chromatin

Question 47

Total amount of DNA varies substantially amongst eukaryotes and may or may not be associated with what?

Answer 47

relationships or complexity of organism

Question 48

Amoeba has almost 100 times more DNA than Homo sapiens, this is called?

Answer 48

C-value paradox

Question 49

Number of genes is more closely associated with what than total number of base pairs (bp)?

Answer 49

complexity

Question 50

T or F increase in gene number means increase in organismal complexity

Answer 50

True

Question 51

In the human genome, around _____% of the genome is repetitive, while about _____% is coding. A) 60; 30 B) 50; 50 C) 30; 60 D) 60; 1-2 E) 1-2; 90

Answer 51

D) 60; 1-2

Question 52

1. The majority of repetitive DNA in the human genome is found where? 2. LTR = ?

Answer 52

1. in LTR and non-LTR retrotransposon sequences 2. long terminal repeat

Question 53

what carries coding sequence for reverse transcriptase (pol)?

Answer 53

retrotransposons

Question 53

T or F LTRs (long terminal repeats) are a nonrepetitive sequence specifically flanking LTR retrotransposons

Answer 53

False, they are REPETiTIVE

Question 54

LINEs and SINEs are ____-_____ retroelements that together make up over 30% of the human genome

Answer 54

non-LTR retroelements

Question 55

LINE = ? SINE = ?

Answer 55

LINE = long interspersed nuclear element (several thousand bp long) ▪ SINE = short interspersed nuclear element (several hundred bp long)