11| CHROMOSOME STRUCTURE AND DNA SEQUENCE ORGANIZATION

Question 1

Eukaryotic cells, in contrast to viruses and bacteria, contain relatively large amounts of DNA organized into nucleaosomes and present during most of the cell cycle as….

Answer 1

chromatin fibers

Question 2

A stretch of DNA that repeats many times in a Genome. More than 50% of the genome consists of this….

Answer 2

repetitive DNA

Question 3

Can be used as genetic markers (such as in finger-printing)

Answer 3

repetitive DNA

Question 4

term for highly repetitive DNA

Answer 4

Satalite DNA

-5% of the genome, viable and short

Question 5

in situ molecular hybridization defines what type of repetitive DNA

Answer 5

Satalite DNA

-5% of the genome, viable and short

Question 6

terms middle repetitive DNA

Answer 6

Tandom repeats and interspersed retrotransposons

Question 7

What are the three tandom repeats?

What are there genetic markers?

Answer 7

middle repetitive DNA = Tandom repeats and interspersed retrotransposons

Tandom repeats:

1. multi - rRNA
2. mini - VNTRs
3. micro- STRs

Question 8

What are the two interspersed retrotransposons?

What are there genetic markers?

Answer 8

middle repetitive DNA = Tandom repeats and interspersed retrotransposons

interspersed retrotransposons:

1. SINEs - Alu
2. LINEs - L1`

Question 9

of the two interspersed retrotransposons which is more abundant in the genome?

Answer 9

LINEs 21%

SINEs are only 13%

Question 10

Multiple copies of genes present in multiple numbers in the genome, termed

Answer 10

multi tandom repeats (rRNAs)

Question 11

in this region, motifs of 10-60bp are repeated 5-50 times, is termed

Answer 11

mini tandom repeats (VNTRs)

Question 12

1-6bp repeating 5-50x

Answer 12

micro tandom repeats (STRs)

Question 13

short interspersed nuclear elements that are non-coding 100-700bp in length

Answer 13

SINEs (interspersed retrotransposons middle repetitive DNA)

Question 14

Long interspersed nuclear elements of 7,000 bp

Answer 14

LINEs (interspersed retrotransposons middle repetitive DNA)

Question 15

What are the uses of the following genetic markers

1. rRNA
2. VNTRs
3. STRs

Answer 15

1. rRNA - taxonomy
2. VNTRs - Finger-printing
3. STRs - comparing loci

Question 16

VNTRs a middle tandem repeat under micro repetative sequences stands for ….

Answer 16

Viable No Tandem Repeats

Question 17

What are the uses of the following genetic markers

1. Alu
2. L1

Answer 17

1. Alu - movement/ ancestry in human populations

2. L1 - identifies L1 insertion in any DNA samples

Question 18

How are STRs used to identify individuals?

Answer 18

to compare specific loci on DNA from multiple samples, it is stable and predictable

Question 19

micro satellite which can be amplified by PCR without mixing other genes in ordegrading it?

Answer 19

Short tandem repeats, STRs

Question 20

Where is Satellite DNA found

Answer 20

Heterochromatin, in the centromeres/ telomeric regions.

• large amounts of non-coding tandomly repeating sequences
• 5%

Question 21

“Jumping genes”, found throughout the genome in single copies making up 45%, termed

Answer 21

intertransposons

Question 22

the three various categories of repetative DNA are

Answer 22

1. satellite DNA
2. Tandem Repeats
3. Interspersed retrotransposons
   - they differ in position, sequence, location and presence or absence of coding regions

Question 23

What is the difference between heterochromatin and euchromatin? give examples of where you would find each?

Answer 23

Heterochromatin - genetically less active, tightly packed, only in eukaryotes. maintains structural integrity.

ie: bar bodies, X-chromosome of females and centromeric/ telomeric regions in the Y-chromosome of males

euchromatin- most active portion of the genome accounting 92%. allows genes to be transcribed and for genetic variation to occur

Question 24

describe the exact composition and arrangement of the nucleosome

Answer 24

Its core parasiticals contain two copies of each histone protein (H2: A B 3 and 4) and it is 146 bp of super helical DNA wrapped around a histone octomer

Question 25

a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones.

Answer 25

nucleosome

Question 26

What genetic processing is occuring in a puff of a polytene chromosome?

Answer 26

RNA transcription

Question 27

The bands of _______ chromosomes become enlarged at certain times to form swellings called a ______

Answer 27

The bands of Polytene chromosomes become enlarged at certain times to form swellings called puffs. Polytene chromosomes- found in various tissues; salivary, rectal. Individual bands are sometimes called chromeres.

Question 28

What important information did lampbrush and polytene chromosomes show?

Answer 28

during interphase polyetenes have a distinct think/thin banding patterns which were at first used in mapping chromosomes to identify small mutation/ taxonomic identification now they are used to study the function of genes in transcription

Question 29

these chromosomes are a special form of chromosome found in the growing oocytes of most animals, except mammals.

Answer 29

Lampbrush chromosomes

Question 30

ellipsoidal symmetrical shape accross 3 axis and large, this defines a chloroplast DNA or a mitochondrial DNA

Answer 30

chloroplast DNA - both contain a double membrane, their own DNA, synthesis machinery and are involved in energy metabolism and photosynthesis

Question 31

Oblong in shape but over time can rapidly change its shape and is small, this defines a chloroplast DNA or a mitochondrial DNA

Answer 31

mitochondrial DNA - both contain a double membrane, their own DNA, synthesis machinery and are involved in energy metabolism and photosynthesis

Question 32

bacterial chromosomes are relativly simple in form. they generally consist of a double stranded DNA molecule, compacted into a structure sometimes referred to as the...

Answer 32

Nucleoid

Question 33

in contrast to eukaryotes, bacteriophage and bacterial chromosomes are largely devoid of associated proteins, are much smaller in size, and most often circular

Answer 33

largely devoid of associated proteins, are much smaller in size, and most often circular

Question 34

Defined as a nucleoprotein organized into repeating units called nucleosomes, an octomer of four types of histones

Answer 34

Eukaryotic chromatin -part of chromatin that remains relatively uncoiled in and replicates much earlier in division

Question 35

Bead-like structure in eukaryotic chromatin, composed of a short length of DNA wrapped around a core of histone proteins

Answer 35

nucleosomes

Question 36

protein molecules around which DNA is tightly coiled in chromatin

Answer 36

histones

Question 37

modification of histone tails via acetylation, methylation, ubiquitination, and phosphorylation, all examples of gene regulation is defined as

Answer 37

Chromatin Remodeling

Question 38

Tandemly repeating, non-coding DNA, found in heterochromatin

Answer 38

satellite DNA

Question 39

viruses with double stranded closed loops of DNA on the protein coat

Answer 39

phi X174 bacteriophage & polyoma virus

Question 40

compact DNA structure in bacteria can be termed a

Answer 40

neucleoid

Question 41

1. Sizes vary greatly by organism | 2. Uniform in size among different organisms

Answer 41

mitochondrial DNA - Sizes vary greatly by organism 2.chloroplast DNA - Uniform in size among different organisms

Question 42

basic positively charged proteins in eukaryotic chromatin are called

Answer 42

histones

Question 43

When chromatin is induced to change it's structure in order to facilitate protein-DNA interactions, this process will happen

Answer 43

chromosome remodeling - is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression.

Question 44

acetylation, methylation, ubiquitination and phosphorylation all modify what

Answer 44

chemical processes that that modify histones and are important to genetic function

Question 45

hybridizes special radioactive DNA with DNA in chromosomes is termed

Answer 45

in situ molecular hybridization -satalite DNA, 5%, highly repetitive

Question 46

____________ are the most common sites of post-translational modifications.

Answer 46

Histone tails

Question 47

What are the three post-transcriptional modifications

Answer 47

1. cap and tail (stabilize and protect from degradation) 2. splicing introns 3. Modification of RNA to be used as a template in translation

Question 48

What are the six post- translational modifications

Answer 48

1. removal of N and C termis; amino acid methonine 2. phosphorylation; modifification of proteins shape/ chemical nature 3. Glycoproteins; "the golgi-bodies"; adding carbon side chains, glycosylation 4. cleaving of the polypeptide chains 5. Signal sequences a re removed (written in the genome) 6. PP chains interact with metals. ie: hemoglobin and 4 iron atoms

Question 49

adding carbon side chains can be termed as

Answer 49

glycosylation - a post- translational modifications adding carbon side chains

Question 50

What is the enzyme that acetylates the histones?

Answer 50

histone acetyltransferase (HAT)

Question 51

it is the addition of a methyl group to arginine or lysine residues in histones - that causes DNA to be wrapped more tightly along histones - thus silencing expression of the gene

Answer 51

methylation

Question 52

What enzyme phosphorylates the histones?

Answer 52

histone kinases

Question 53

T or F: The vast majority of Euk genome does NOT encode functional genes

Answer 53

True | -only a small portion of Euk genome (2-10%) constitutes protein-encoding genes

Question 54

What are psudogenes?

Answer 54

they are large number of single-copy noncoding regions where 1) DNA sequences that represent evolutionary vestiges 2) have undergone significant mutational alterations (insertions and deletions) 3) are NOT transcribed