Genetics exam 1 (chapters 1-4)

Four major criteria for classifying viral genomes

dsDNA, ssDNA, dsRNA, ssRNA

nuclease that digests free ends of viral genome

exonucleases

nuclease that digest middle of viral genome

endonucleases

a circular viral genome is sensitive to

endonucleases only

a linear genome is sensitive to

endonucleases and exonucleases

both prokaryotic and eukaryotic chromosomes are composed of

dsDNA

prokaryotes have what kind of chromosomes

single circular

eukaryotes have what kind of chromosomes

multiple linear

prokaryotic chromosomes are found in

nucleoid without nuclear membrane

Eukaryotic chromosomes are found in

nucleus

prokaryotic genomes have __ origins of replication

1

eukaryotic genomes have __ origins of replication

many

eukaryotic chromosomes unique factors

centromeres, telomeres, introns and exons, heterochromatin and euchromatin, 60% repetitive DNA

segment of DNA transcribed and translated to encode a protein product

structural gene

sequences that directly encode amino acids that form a protein product

exons

non-coding sequences

introns

centromere function

spindle attachment during division

telomere function

prevent chromosomes from sticking, protect from shortening, form T-loop to protect from exonucleases

heterochromatin is

condensed, lacks structural genes, appears as dark bands, forms centromere and telomere, often highly repetitive

euchromatin is

loose, contains active structural genes, appears as light bands, houses unique gene sequences

what order does dna of differing repetitiveness reassociate

highly, moderate, unique

moderately repetitive DNA sequences include

RRNA genes, Histone protein genes, VNTRs, telomere repeat sequences

histone protein genes encode

histone proteins for organizing chromatin

RRNA genes encode

rRNA needed to build ribosomes

__ contain a specific number of repeat units on a single chromosomes that varies per person, making them good for forensics

VNTRs

highly repetitive DNA sequences include

centromere region, alu family, most heterochromatin regions

elements with potential to move from one location in genome to another

transposable elements

repetitive DNA sequences found where on chromosome

centromere, heterochromatin, dispersed across arms, telomeres, intergenic sequences, short arms of acrocentric chromosomes

rRNA genes found where

short arms of acrocentric chromosomes

T-loop function

protect chromosome ends from exonucleases

centromere near center of chromosome

metacentric

centromere slightly off center

submetacentric

centromere significantly off center

acrocentric

centromere near very end of chromosome

telocentric

human genome does not contain what type of chromosome

telocentric

dna distinguished via

size, centromere location, banding patterns

3 levels of chromosome compaction in prokaryotic cells

microdomains, macrodomains, supercoiling

microdomains formed from

repetitive DNA sequences binding to NAPs

macrodomains formed from

80-100 bundled base pairs bound to NAPs

process of introducing twists into DNA micro domains for purpose of chromosomal compaction

supercoiling

Overwinding DNA ___ resulting in extra twists is called

clockwise, positive supercoiling

Under-winding DNA __ resulting in less twists is called

counterclockwise, negative supercoiling

Positive supercoiling effects

shortens molecule, inhibits replication/transcription

Negative supercoiling effects

Shortens molecule, promotes DNA strand separation required for DNA replication and gene transcription

___ supercoiling is preferred over __ supercoiling

negative, positive

__ introduces negative supercoils

DNA gyrase

DNA gyrase made up of

2 A subunits, 2 B subunits

A subunits in DNA gyrase do what

bind to DNA and act as endonucleases to cut both strands

B subunits in DNA gyrase do what

pass another section of DNA through double strand break using energy from cleaving ATP

DNA gyrase produces __ and consumes

2 negative supercoils, 2 ATP

__ is responsible for generating positive supercoils

Topoisomerase I

topoisomerase is a __ protein subunit that cuts __ and requires

single, one DNA strand, no ATP

DNA gyrase inhibited by

quinolones

nucleosome made up of

146-147 bp negatively supercoiled around 8 histone proteins

protein components within nucleosome core

H2A, H2B, H3, H4

histone structures in nucleosome encourage binding how

globular domain allows histone proteins to bind and form core, histone tails contain positively charges amino acids that bind with negatively charged DNA backbone

DNA sequence that connects adjacent nucelosomes

linker region

linker region made up of how many BP

50

what proteins bind to linker DNA

histone 1, various nonhistone proteins

2 types of 30-nm fiber models

solenoid, zig-zag

solenoid 30-nm fibers have __ structure

compact, symmetrical cylinder-like structure

zig-zag 30-nm fibers have __ structure

bendy/twisty due to minimal nucleosome interaction

solenoid 30-nm fibers advantages are __ and disadvantages are _

allow for more compaction, difficult to activate structural genes inside

zig-zag 30-nm fibers advantages are __ and disadvantages are _

promotes structural gene transcription, less compaction

loops of 30 nm fiber anchored to nuclear matrix proteins

radial loop domain

specific DNA sequences that bind 30-nm fibers to internal nuclear matrix to organize chromatin into radial loops

matrix attachment regions

radial loop domain made up of

30 nm fiber loops anchored to nuclear matrix proteins

discrete, localized region within the interphase nucleus occupied by a specific chromosome

chromosome territory

euchromatin made up of

loosely compacted radial loops containing actively transcribed structural genes

heterochromatin made up of

tightly compacted radial loops generally lacking active structural genes

two types of heterochromatin

constitutive, facultative

constitutive heterochromain is

permanently compacted and inactive across all cell types

facultative heterochromatin is

dynamic, converting between heterochromatin and euchromatin

4 levels of chromosome compaction in eukaryotes

nucleosomes, 30nm fibers, radial loop domains, metaphase scaffold compaction

what levels of eukaryotic chromosome compaction are observed during interphase

nucleosomes, 30-nm fibers, radial loop domains

during mitosis and meiosis, radial loops

bind to protein scaffold to form highly condensed metaphase chromosomes

SMC family protein activated during mitosis/meiosis

condensin

condensin uses __ to _

atp, link radial loop domains together to form heterochromatin

dosage compensation prevents

females from having double X-linked proteins

inactivation of one of the two X chromosomes in female somatic cells

dosage compensation

who identified barr bodies are present in female cat cells but absent in male call cells

Barr and Bertram

Who explained mosaic patterns of female heterozygous cats as results of random x inactivation in each cell

Lyon

Idea that in early development both X chromosomes are active, but one is randomly chosen for inactivation in each embryonic cell. All daughter cells inherit the same inactivated X, resulting in a mosaic pattern of gene expression.

lyon hypothesis

cells count __ when determining how many barr bodies to create

Xic

three stages of x chromosome inactivation

Initiation, spreading, maintenance

initiation step of XCI involves

choice of which chromosome to inactivate

Spreading step of XCI involves

Xist ncRNA coats spreading and recruiting proteins to compact into barr body

maintenance step of XCI involves

continues chromosome silencing after mitosis

4 major defects in chromosome structure

deletions, duplications, inversions, translocations

defect where part of chromosome is missing

deletions

defect involving repetition of chromosome segment

duplication

defect involving flipping of internal segment within a chromosome

inversion

defect involving attachment of chromosome segment to a nonhomologous chromosome

translocations

three types of translocation

simple, reciprocal, robertsonian

translocation where segment breaks off one chromosome and attaches to a non-homologous chromosome while the receiving chromosome remains intact

simple

translocation where two nonhomologous chromosomes break and exchange pieces with one another

reciprocal

translocation where long arms of two acrocentric chromosomes fuse at centromere and lose their short arms

robertsonian

typs of deletion

terminal, interstitial

deletion involving single DNA break near end of chromosome resulting int one segment with a centromere and one without that is lost

terminal

deletion occuring within interior of the chromosome

interstitial