Genetics Unit 10

What are endosymbiont bacteria

living with host cells

Bacteria genomes compared to eukaryote genome

typically bacteria genome is smaller

Why do endosymbiont bacteria have tiny genome

lots of nutrients and energy from host

Why do soil bacterial have large genome

complex environment/stressful

What is the majority of DNA in bacteria

protein coding genes (non repetitive)

Why do bacteria have a linear positive relationship

more genes = larger genome size

What is the nucleoid in bacteria

region of cytosol that contains bacterial chromosome

Genome shape in bacteria

chromosome have a central core surrounded by microdomain and further out is super coiling

What occurs in microdomain

genes are actively expressed

What does DNA supercoiling do

less expression due to further compaction

Relaxed coils equal

more active transcription

Why is bacterial genomes streamlined

bacteria with fewer genes reproduce faster

What does bacteria do to genes that are not necessary

they purge them

How are genomes in eukaryotes

big and bloated

Why are eukaryote genes big and bloated

DNA replication is no longer rate limiting for reproduction/cell division

What percent of human genome is protein making

2%

What is the majority of human genome

repetitive DNA

What are the majority of repetitive DNA in eukaryotic genomes

transposable elements (TEs)/transposons

What are transposons (TEs)

DNA sequences that can change position in genome

What are TEs also called

jumping genes and selfish elements (replicate independent of the host genome)

What are TEs similar to

virus/plasmid

What is DNA transposon

direct cut and paste (excision and reinsertion)

What is retrotransposons

copy and paste (create a new copy, leaves original) RNa to DNA

What enzyme is for DNA transposons

transposase

What enzyme is for retrotransposons

reverse transcriptase

What are the two enzymes for retrotransposons

reverse transcriptase and integrase

What does reverse transcriptase do

use RNA as a template to make double stranded DNA

What does integrase do

Insertions TEs into new location in host genome

What do DNA transposons do

encode a transposase gene and transposase enzyme cut the DNA transposon out of host DNA and move it to another location within genome

What do DNA transposons lead to

bigger genomes

When does transposition occur

around time of replication

What happens to a TE that has been replicated

can transpose and move ahead of fork to be copied again

What is genome size correlated with in eukaryotes

repetitive transposable

What is 1 meter DNA equal to

5um

How is chromosome in eukaryotes compact

DNA and proteins

What is required to compact chromosome in eukaryotes

histone, nucleosome, chromatin

What does DNA wrap around for compaction eukaryotes

histone proteins

What is a nucleosome

a single DNA histone unit

What is a chromatin

DNA protein complex made of multiple nucleosomes

How many histones does a nucleosome contain

8 histone subunits

What do the 8 histone subunits contain

2 copies each of four different histone (H2a, H2B, H3, and H4

How much DNA wraps around each histone octamer

146 to 157 bp

Why do histone protein contain many positive charged amino acids (lysine and arginine)

attracts negative charge of DNA phosphate group

How does one further compact chromatin

segments of nucleosome are folded into topologically associated domains (TADs) or loop domains

Genes near each other on the same TAD are

Genes that work together for a certain function

Euchromatin means

less condensed regions of chromosome and where gene expression occurs

Heterochromatin means

more condensed regions for chromosome and too tightly packed

What is a facultative heterochromatin

a tightly packed form of chromatin that can switch between condensed and relaxed state

What is a constitutive heterochromatin

A condensed region of DNA that is consistently condensed

What is a telomere

repetitive DNA sequence and protein to protect them

What is the nuclear lamina

protein and filaments that hold chromosome in certain spots

What is chromosome territories

a distinct non overlapping regions within cell nucleus that are occupied by individual chromosomes during interphas

Intergenic proteins

Nontranscribed regions of DNA located between adjacent genes

Origin of replication

a nucleotide sequence that functions as an initation site for the assembly of several proteins required for DNA replication

Nucleoid

where highly compacted chromosome is found in a bacterial cell

Microdomainds

loop that emanate from core

Macrodomains

bundle of adjacent microdomains

How do bacteria form microdomains and macrodomains

Nucleoid- associated proteins (NAPs)

What do NAPs or nucleoid associated proteins do

Bend or bind DNA

What is negatively supercoiled in DNA

Underwinding of DNA double helix that creates left handed torsional starint

What does negative supercoiling do

Makes it easier for two strands to seperate and creates tension that may be relased by their seperation

What is positive supercoiling in DNA

tight, right hand overwinding that increases torsional strain and compresses molecular structure

DNA gyrase/topoisomerase II

introduces negative supercoils or relaxes positive supercoils using ATP energy

What does topoisomerase I dp

relax supercoil, and breaks into one of DNA strands and rotates strant to relieve supercoiling

Centromere

region that play a role in the proper segregation of chromosomes during mitosis and meiosis

How many centromeres in each chromosome (eukaryote)

1

Point centromere

Defined DNa sequence

Regional centromere

repeated DNA sequences

Kinetochore

composed of a group of proteins that linke the centromere to the spindle apparatus during mitosis and meiosis, ensuring proper segregation of chromosomes to each daughter cell

telomeres

orevent chromosomal rearrangement such as translocation and preven chromosome shortening

How do telomeres prevent shortening

protect from exonuclease and specialized form of DNA replication occurs at teomere to ensure eukaryotic chromosomes do not become shortened with each round of DNA replication

tandem array (tandem repeat)

a short nucleotide sequence that is repeated many times in a row

transposition

process which a DNA segment is inserted into a new location in a genome

Simple transposon/cut and paste

removes TE from site and transfers to a new target site

retrotransposon occurs only in

eukkaryotes

retrotransposition

element transcribed into RNA and reverse transcriptase enzyme uses RNA to synthesize DNA

Direct repeats/target site duplications

identical nucleotide sequences in same direction and repeated

How does transposase catalyze the excision and insertion of transposons

1. transposase monamers first bind to the inverted repeat sequence at the end of TE

2. monomers dimerize, which brivers inverted repeats close together

3. DNA is cleaved between inverted and direct repeats, which excises the TE from its original state within the chromosome\

4. Transposase carries the TE to a new site and cleaves the target DNA sequence at staggered recognition sites. THe TE is then nserted into the target DNA and lgiated to it

When does transpotition usually occur

DNA replication

Nucleosome

repeating structural unit within eukaryotic chromatin. It is composed of double stranded DNA wrapped around an octamer of histone proteins

What is the diameter of a nucleosome

11 nm at widest point

loop extrusion model

a model for loop formation in eukaryotic chromation in which cchromatin is forced through an SMC protein as the loop grows

Role of CTCF (CCCTC binding factor)

bind to each other to prevent further loop growhth and stabilize the bottom of loop

SMC protein is responsible for

forming the loop

What are the two ways loops are formed in TAD

One is loop domain via SMC protein and CTCF. In loop domain,m additional loops can for by protein protein itneractions (regulatory and general transcription factors)

Insulator

a structure that limits genetic interactions to a specific region of DNA (TAD boundaries)

Where is heterochromatic abundant

more in centromere region and to a lesser extent in telomeric regions

Level 1 of Cell Nucleus Hierarchy

Scale of entire nucleus, chromosome occupy distinct territories. This arrangement driving by multiple stuff but especially interchromosomal interaction and chromosomal intxn with nuclear structures.

Cell Nucleus Level 2

Within each territory, Chromosomes are organized on a megabase scale into compartments. Active genes associate with other active and repressed cluster together.

Where do heterochromatic regions tend to be

nuclear lamina

Where do euchromatic regions tend to be

closer to interior of nucleus

Cell Nucleus Level 3

At scale of 100kb to 1 Mb, usually 1-5 genes chromosome organized into TADs. Thought to be driven by loop extrusion

Cell Nucleus Level 4

Organization with chromosome occurs at a sclae of 1 to 10 nucleosome. Determined by affinity of nucleosome to each other.

chromosome territory

in a nucleus where single chromosome is located