Chapter 11 Vocab

Question 1

Strands run in opposite directions because they are __________

Answer 1

antiparallel.

Question 2

Because of the pairing rules, the two strands of DNA are ______________
5’ TGCTCTGAACGCTTA 3’
3’ ACGAGACTTGCGAAT 5’

Answer 2

complementary

Question 3

Where is DNA found in prokaryotes?

Answer 3

cytoplasm

Question 4

Where is DNA found in Eukaryotes?

Answer 4

segregated into nucleus

Question 5

What are the challenges of DNA packaging?

Answer 5

• Configure DNA so that this very large
molecule will fit into a very small space
• Storage structure must be stable yet able to be manipulated
• Allow certain parts of the molecule to be accessed frequently
• Allow all parts of the molecule to be accessed at least occasionally

Question 6

Positive supercoiling is related to ______

Answer 6

overcooled DNA

Question 7

Negative supercoiling is related to ________

Answer 7

undercoiled DNA

Question 8

___________ supercoiling is favored because it also functions in strand separation during replication or transcription

Answer 8

negative

Question 9

What is supercoiling mediated by?

Answer 9

topoisomerase I or II

Question 10

Twisted loops held together at the ends by accessory proteins (undescribed)

Answer 10

Nucleoid

Question 11

Telomeres are:

Answer 11

the stable ends of chromosomes

Question 12

Centromere is a:

Answer 12

constructed region of the chromosome where the kinetochore forms and the spindle microtubules attach.

Question 13

majority of DNA, constitutes most of the transcriptionally active DNA

Answer 13

Euchromatin

Question 14

telomeres, centromeres, transcriptionally inactive regions of the chromosome, inactive female X chromosome

Answer 14

Heterochromatin

Question 15

What are characteristics of Nucleosomes?

Answer 15

• A core made from 4 different histone proteins, 2
each (8 total, an octamer)
• H2A, H2B, H3, H4
• DNA double helix wrapped ~ twice around this core
• exposed “+” charged aa tails of core histone proteins bind DNA to the core
• Histone protein H1 binds DNA where it joins and leaves the protein “spool” to form a “chromatosome”

Question 16

What are characteristics of Linker DNA?

Answer 16

• Chromatosomes separated by “linker DNA”
• Distance between chromatosomes different between cell types, but not random
• Chromatosomes separated by lengths of linker DNA appear as “beads on a string”

Question 17

What are characteristics of Chromatin Fibers?

Answer 17

• Chromatosomes fold onto each other
• Tails of core histone proteins hold structure together
• Resulting fiber ~ 30 nm

Question 18

What are the changes that can happen to chromatin structure?

Answer 18

• Degree of condensation changes from region to region on the chromosome and throughout the cell cycle
• Highly condensed = less accessible
• Less condensed = more accessible
• Need for accessibility related to replication and transcription

Question 19

What are the modifications to Histone Tails?

Answer 19

• Modify N-terminals of histone subunits
• Alter extent to which DNA is bound to the nucleosome
• Alter extent to which nucleosomes are bound to each other
• Allows access to particular regions of DNA (temporary)
• Change position of nucleosomes (permanent)

Question 20

Acetylation of lysine is:

Answer 20

decondensation

Question 21

Methylation of lysine is:

Answer 21

condensation

Question 22

Phosphorylation of serine happens during:

Answer 22

mitosis and meiosis

Question 23

What are Polytene Chromosomes?

Answer 23

• Naturally occurring, unusual form of chromosome found in certain cell-types (i.e. Drosophila salivary gland cells)
• Allows visualization of less condensed regions of chromatin (“puffs”)
• Cells treated with radioactive component of RNA reveals that transcription is occurring in these less condensed regions

Question 24

What is DNase I?

Answer 24

• Enzyme capable of digesting DNA
• Must have access to phosphodiester bonds in order to digest DNA
• Experiments show that rate of digestion is greater where transcription is occurring
– (i.e. embryonic globin genes)
• Therefore, regions undergoing transcription are less condensed, more accessible to the DNase

Question 25

What are characteristics of centromeres?

Answer 25

• Specialized regions of chromosomes made up of highly condensed “heterochromatin” • Considerable variation in size and base pair composition between organisms • Primarily function as attachment point for kinetochore complex during mitosis • May also serve as a checkpoint in the cell cycle (prevents premature entry into anaphase) • Functionality defined by local chromatin structure rather than nucleotide sequence

Question 26

What are characteristics of Telomeres?

Answer 26

* Ends of the chromosomes (and hence the ends of the DNA molecule) * Comprised of specific, usually repetitive, blocks of nucleotide sequences which vary from organism to organism * Primary function is to allow replication of the ends of the DNA molecule to prevent shortening during replication

Question 27

What are the three types of Eukaryotic DNA?

Answer 27

* Unique-Sequence * Moderately Repetitive * Highly Repetitive

Question 28

* Sequences that exist as one or only a few copies in the genome * Majority of these are single genes * Some are gene families—closely related genes that result from repeated duplications of an “ancestor” gene * Products of some gene families come together to form functional protein complexes * In some gene families the majority of the members are non-functional

Answer 28

Unique-Sequence DNA

Question 29

• 150 – 300 bp each, up to several 1000 bp • 1K – 100K copies • Some are multiple copies of genes that must be produced in large quantity • Others have no known function • May be tandem or interspersed • Long or short interspersed sequences (elements) • LINE’s (1K repeats) or SINE’s (100 repeats)

Answer 29

Moderately Repetitive DNA

Question 30

* Usually short, 10 bp +/- * 100K – 1M copies * Tandem repeats * Often (but not always) associated with centromeres and telomeres * Function, if any, unclear

Answer 30

Highly Repetitive DNA

Question 31

What are two cellular organelles in eukaryotes that contain DNA.

Answer 31

-- mitochondria | – chloroplasts

Question 32

Their genome is a single circular double-stranded DNA molecule similar to a bacterial chromosome that may be present in multiple copies in each organelle.

Answer 32

Organelles DNA

Question 33

How do Mitochondria and Chloroplasts divide?

Answer 33

Binary Fission

Question 34

Homoplasmic is:

Answer 34

a cell with clonal mitochondria

Question 35

Heteroplastic is:

Answer 35

a cell that contains genetically different populations of mitochondria.

Question 36

Is replicative segregation random in heteroplasty?

Answer 36

yes

Question 37

What is the endosymbiotic hypothesis?

Answer 37

* The similarity of organellar DNA to that of bacteria has led to the hypothesis that these organelles were once * free-living prokaryotes that were engulfed by anaerobic eukaryotic cells and * retained because of their ability to carry out aerobic respiration (mitochondria) and photosynthesis (chloroplasts).

Question 38

* The similarity of organellar DNA to that of bacteria has led to the hypothesis that these organelles were once * free-living prokaryotes that were engulfed by anaerobic eukaryotic cells and * retained because of their ability to carry out aerobic respiration (mitochondria) and photosynthesis (chloroplasts).

Answer 38

The endosymbiotic hypothesis

Question 39

What are characteristics of Mitochondrial DNA (mtDNA)

Answer 39

• Size varies from about 16.5 kb (humans) to >1000 kb. • Number of copies per organelle varies from about 5-40 in different organisms. • A single cell may contain 1000 mitochondria and thus >5000 mtDNA molecules. • mtDNA is not associated with histones, has no introns or repetitive sequences. • Their mRNAs have no UTRs, no 5’ cap, no Shine-Dalgarno sequence, rare poly(A) tails. • The human mitochondrial genome encodes 2 rRNAs, 22 tRNAs and 13 proteins.

Question 40

What are characteristics of Chloroplast DNA (cpDNA)

Answer 40

* Like mtDNA, it is circular, highly-coiled double- stranded and not associated with proteins; * It differs from mtDNA in being much longer, having long noncoding sequences and duplicated sequences and some introns. * The number of copies per organelle is usually greater. * A typical chloroplast genome encodes 4 RNA genes, 30-35 tRNA genes, ribosomal proteins and proteins, many of which are not involved in photosynthesis. * A key protein encoded by cpDNA is RuBisCO (1,5- bisphosphate carboxylase-oxygenase), an enzyme considered the most abundant protein on earth since it makes up 50% of the protein of green plants.