Genetics Exam 3

Chromatin condensation pattern

DNA → Chromatin → Metaphase chromosome

Chromatin

DNA + Protein (histone)

Euchromatin

lightly packed chromatin

rich in gene concentration and most often under active transcription

Heterochromatin

tightly packed chromatin consisting mainly of genetically inactive sequences

Constitutive heterochromatin

VERY gene poor

wound tightly most of the time

typically make up centromeres and telomeres

Facultative heterochromatin

can go back and forth from hetero and euchromatin

used in gene silencing and barr bodies (inactive X chromosome)

Folded Fiber Model

• No proteins in chromosomes

• concluded each chromatid must be a single fiber

• random folding

• no evidence to support

Nucleosome Model

• most commonly accepted model for DNA packaging

• DNA wrapped around histones (nucleosomes)

Nucleosome

simplest packaging structure of all eukaryotic chromatin

localized areas of transcription

DNA wrapped around histone

8 proteins

Core histones

• H2A, H2B, H3, H4

• 120 amino acids each

• highly conserved during evolution

• form the core particle

• VERY BASIC in charge (25% lysine and arginine) = hold onto acidic DNA

Linker Histone

• H1

• 200 amino acids

• tissue specific expression and not highly conserved during evolution

• loosely associated with core particle

Linker DNA

DNA that connects one nucleosome to the next

Width of DNA

2nm

Width of nucleosome

10nm fiber

how many base pairs per nucleosome

200

How many histones in a nucleosome

9

2 sets of 4 core = 8

1 linker

by what factor do nucleosomes reduce DNA length

7x

arrangement of nucleosomes

linear

“beads on a string”

Solenoid

helical coiling of 10nm fibers consisting of 6 nucleosomes

H1 histone helps pack into circle formation

width of solenoid

30nm

by what factor does supercoiling reduce the length of DNA

7x

How does Histone H1 work

Binds linker DNA and portion of 146 BP core histone

induces compaction of DNA

“alternate model” of DNA super coiling

Zigzag model

DNA backbone is not flexible enough to bend between nucleosomes so straight linker DNA connects opposite nucleosomes

more recent model

Both kinds will exist, just at different parts of the chromatin fiber

Higher order coiling

Built around a scaffold of topoisomerase II

“chromatin loops”

Width of higher order coiling

300nm

what is the compaction level of euchromatin

higher order coiling

300nm

Final condensation

spiral scaffold composed of topoisomerase II and about 15 non histone proteins

right before metaphase chromosome

Width of final condensation

700nm

compaction level of heterochromatin

final condensation

700nm

when is DNA the most accessible

interphase

between G1 and G2

what phase of the cell cycle are 2nm-10nm fibers in

G1

what phase of the cell cycle are 30 and 300nm fibers in

G2 and interphase

what phase of the cell cycle are 700nm chromatin in

End of G2/prophase

what phase of the cell cycle are chromosomes in

metaphase

Biological complexity

the result of the hierarchical organization of nested levels of cells, tissues, and higher order part types interacting together

C-value paraxon

genome size does not correlate with organismal complexity

G-value paradox

the number of genes does not correlate with organismal complexity

not just size of genome but actual coding genes

Classes of nucleotide sequence

1. highly repetitive (HR)

2. moderately repetitive (MR)

3. single copy (unique)

Highly repetitive DNA sequence (HR)

• mostly located in heterochromatic regions around centromere/telomere → no coding DNA

• comprises 10% of human genome

• function is structural and organizational

• occurs at variable lengths

• ex: alpha satellite DNA

Alpha Satellite DNA

highly repetitive DNA sequence

in tandem repeats

structural function (centromeres, telomeres)

Moderately repetitive DNA sequence (MR)

• found mostly in euchromatin or facultative heterochromatin

• comprises about 30% of the human genome

• average 300bp in size

• function: transcription factor binding, spacing between promoter elements, cytosine methylation, alternative splicing, mRNA stability, transcription start and termination sites

• includes ‘redundant’ genes for histones, rRNA, and proteins (gene-products present in cell in large numbers)

• ex: microsatellite DNA

Microsatellite DNA

variable number of tandem repeats typically occurring in non-coding regions of the genome

occurs through a mutation process known as “slippage recognition”

useful genetic markers as they tend to be highly polymorphic

used to sequence genome, markers for certain diseases, testing in forensics

Single copy DNA sequence (unique)

• found throughout euchromatin

• comprises 1-5% of human genome

• single or low copy number

• “coding DNA regions = genes”

• 20,000 protein coding genes

what is the other 45% that is not HR, MR, or unique DNA

noncoding DNA

Gene

basic physical and functional unit of heredity

sequence of unique nucleotides (genotype) that carry the genetic information which is to be expressed (phenotype)

how many copies of each gene do we have?

2

1 from mom

1 from dad

% of DNA that is the same in all people

99.5%

molecular level definition of gene

transcriptional unit

DNA sequence that gives rise to an RNA molecule

Exon

coding sequence

phenotype

intron

intervening sequences

areas of genes that don’t typically code for phenotype

transcription

DNA → RNA

Translation

RNA → Protein

Does DNA have codons?

no, only RNA

Flanking regions

areas on either side of the gene

5’ untranslated region

mRNA that is directly upstream from the initiation codon

regulates translation

recruits ribosomal subunits

3’ untranslated region

mRNA directly following the translation termination codon

post transcriptional influences on gene expression

Promoter

DNA sequence where the transcription machinery binds and initiates transcription

on/off switch

ex: TATA box

TATA box

type of promoter

on off switch for transcription

found in DNA

5’ TATAAA 3’

Enhancer regions

recruit proteins to regulate transcription

dimmer switch

ex: CAAT box and GC box

CAAT box

enhancer region

upstream 60-100 bases to initial transcription site

required for inducible genes

GC box

enhancer region

region of DNA that can be bound with proteins (activators) to activate transcription of a gene

Termination

end of the gene

DNA recruits protein to stop transcription

Terminator

section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription

Solitary genes (unique)

single copy of a gene in haploid and two copies in diploid

makes up most of euchromatin

Duplicated genes

portion of chromosome is duplicated resulting in an additional copy of a gene

copy is called paralog gene

either original or copy may mutate and change function of the gene

usually occurs during an error in meiosis

Multigene families

set of several similar genes, formed by duplication of a single original gene

usually located in similar regions

used or synthesized at different times

Pseudosomes

dysfunctional relatives of genes that have lost their protein-coding ability

result of multiple mutations within a gene

Repeated genes

multiple copies of small genes clustered throughout the genome at specific sites

often back to back

ex: genes for tRNA or rRNA

why do cells divide

outside of the cell is unable to keep up with the inside because the inside grows at a faster rate

DNA replication

process by which genetic information is duplicated

ensure that each cell in an organism has a complete copy of the genome

G0

resting phase

G1

growth phase, cell increases in size and prepares for DNA synthesis

S

synthesis phase

DNA replication

G2

growth phase, cell increases in size and prepares for mitosis and cell division

M

cell growth stops and cell divides into two daughter cells

Semi-conservative model

one parental and one daughter strand

Conservative model

both parental strands stay together after replication and daughter strands go together

Dispersive model

parental and daughter DNA are interspersed in both stands

randomly break apart and come back together

High-fidelity

accurate replication, few errors due to proofreading

• instability of mis-matched base pairs

• proofreading/ exonuclease activity of DNA pol III

Origin of replication

AT rich region (looser and easier to break strands apart)

GATC methylation sites (precise timing of replication)

Initiator protein

DnaA protein

replication bubbles

Bi-directionality of replication

replicate both strands at the same time in opposite directions

Topoisomerase (gyrase)

reduce torsional strain, unwinds double helix

Helicase

breaks hydrogen bonds between complimentary nucleotides

Single-strand binding proteins

stabilize ssDNA until elongation begins

prevents DNA from coming back together

Primase

RNA polymerase that adds a ribonucelotide primer to ssDNA

Primers

10-12 bases in length

binds to CTA region

creates a fake “double stranded DNA” so DNA polymerase can bind

uses RNA because its easier to remove later

removed after elongation and replaced with DNA nucleotides

Steps of DNA replication

1. initiation

2. Unwinding

3. Priming

4. elongation

Initiation of DNA replication

initiator proteins bind

replication bubbles form

replication forks

Unwinding of dsDNA strand

topiosomerase unwinds DNA

helicase separates strands

ss binding proteins stabilizes ss DNA

priming of DNA strand

primase adds ribonucleotide primer to ssDNA which allows polymerase to bind

DNA polymerase III

responsible for most of the replication process

enzyme that catalyzes attachment of nucleotides to make new DNA during replication

prokaryotic DNA polymerases

DNA pol I → remove RNA primer and start synthesis

DNA pol III → most of replication process

DNA pol II, IV, V → repair DNA

Eukaryotic DNA polymerases

can DNA polymerase initiate DNA synthesis

not by itself, it requires an RNA primer (needs to bind to double strand)

what direction does DNA polymerase synthesize in

5’ → 3’

what direction is the template strand read in DNA replication

3’ → 5’

how do nucleotides join in the DNA backbone

3’ hydroxyl to 5’ carbon

phosphodiester bond forms, phosphate ions released

leading strand

DNA pol reads 3’ → 5’ into the replication fork, no breaks