Genes to Proteins Exam 1

Chromosome

a very long DNA molecule genetic information is packed into

Intergenic regions

the non-coding DNA in between genes

Polyploid

multiple sets of chromosomes that are found at certain life-stages in some organisms

Eukaryotic cells can have __ to the chromosomal DNA found in the nucleus

additional DNA

__ have their own chromosome

mitochondria & chloroplasts

The origins of mitochondria and chloroplasts:

thought to have derived from ancestral free-living bacteria that were absorbed and maintained by other single-celled organisms

Plasmids

small circular DNA molecules

__ often have additional DNA within their cells & typically encode a few proteins for a selective advantage (antibiotic resistance)

bacterial cells

__ are infectious agents and carry genetic information as small DNA or RNA chromosomes

viruses

G1 (gap phase 1):

cells grow to a minimum size required for the next stage

S (synthesis phase):

DNA is copied, duplicating the chromosomes; the 2 copies (sister chromatids) remain associated with one another

G2 (gap phase 2):

the cell prepares for mitosis

M (mitotic phase):

sister chromatids are separated & a full set of chromosomes is moved to each pole of the cell

Anuploidy:

abnormal chromosome count

Karyotype:

a display of the chromosomes from an individual derived from microscopy images prior to separation of sister chromatids

Chromatin:

the DNA-protein complex that makes up chromosomes

The 4 core histones:

H2A, H2B, H3, & H4

__ of the sister chromatids bind to microtubules from each pole

centromeres

On entry to M phase, the __

nuclear membrane breaks down

Chromosomes consist of __ that help condense the DNA into a smaller space and protect the genome

DNA + packing proteins

The first packing stage:

the binding of small positively charged proteins along the DNA

Histones are rich in __

lysine and arginine

The Lys & Arg in histones have positive charges, what does this do?

stabilize the DNA-histone interaction

Nucleosome:

DNA wrapped around a histone complex in a left handed manner

The __ associates with DNA

H3-H4 heterotetramer

The __ associate to form the octamer

two H2A-H2B dimers

About __ of DNA wraps around the octamer to form the nucleosome

146 bp

__ makes strand separation easier, which is required for replication and transcription

negative supercoiling

Histone tails are up to __ and have undefined structure

25 amino acids

The tails interact with other nucleosomes to __

help compact DNA further

Linear chromosomes:

• found in eukaryotes

• enclosed in nucleus

• has histones

• telomeres as ends

• divides by meiosis and mitosis

Circular chromosomes:

• found in prokaryotes

• in nucleoid region of cytoplasm

• lacks histones

• no ends

• do binary fission

Euchromatin:

• less condensed & dense

• transcriptionally active

• has more acetylation

• where the work happens in the interior of the nucleus

Heterochromatin:

• highly condensed & dense

• transcriptionally silent

• more resistant to nuclease digestion

• nuclear envelope region

Neocentromere

CENP-A can bind to other DNA regions

Methylation

turns genes off

Acetylation

turns genes on

Chromodomain

binds methylated lysine

Bromodomain

binds acetylated lysine

ISWI family

positions nucleosomes during chromatin assembly

DNA methyltransferases (HMTs)

acts as a placeholder to correct the base without disrupting DNA stability

Global conformational change

nucleosome remodeling that creates torsional stress that allows the DNA to change position

Tug of War

nucleosome remodeling where an enzyme pushes one end of the DNA to create slack around the nucleosome and pulls the other end too change position

5-methyl cytosine

• less stable

• undergo deanimation

• changed to thymine

• is restored back to cytosine by dna methyltransferases

Gene silencing example

translocation in a fruit fly

• translocation of heterochromatin to brown locus

• gene silenced due to proximity to heterochromatin

What triggers histone modifications

• external- diet, stress

• internal- DNA damage, metabolism

• oxidative stress

Why is lysine used for modifications

• the amino group is versatile

• fewer potentila H-bonds

• positive charge

Phosphorylation

provides additional regulatory signals

CENP-A

centromere-specific histone H3 variant marking the domain where the kinetochore assembles

Kinetochore

protein structure built on the centromere that attaches chromosomes to spindle microtubules

Shelterin

the human protein complex that protects and regulates telomere length

TAD

a self-interaction chromatin region, often bounded by CTCF/cohesin sites

FACT/CAF1/ASF1

histone chaperones that help disassemble nucleosomes ahead of and reassemble them behind the replication fork

Hetero-chromatin rich regions include __

telomeres, centromeres and high repetitive DNA

30 nm fiber requires __

linker histone H1

__ is phosphorylated at DNA double-strand breaks to recruit repair machinery

H2A.X

Acetylation creates docking sites for __ at acetylated lysines

bromodomain proteins, which recruit further complexes

Heterochromatin is __ to nuclease digestion than euchromatin

more resistant

How does chromatin state affect replication?

origins in heterochromatin replicate late and recombination protects regions like rRNA genes

How does acetylation work?

removes pos charge from lysine, loosens DNA-histone interactions

Methylation is assocated with __

transcription activation or repression, depending on the residue

Methylation of __ is associated with silent chromatin

lysine 9 on H3 tail

Methylation of __ is associated with active chromatin

H3 lysine 4

Chromodomains bind to __ and are associated with transcriptional silencing

specific methylated lysines

Phosphorylation of __ allows cell growth transcription

H3 Serine 10

Phosphorylation of __ correlate with chromosome condensation in mitosis

H3 serine 10 & serine 28

Phosphorylation at Ser10 __

promotes acetylation of lysine 14

Acetylation of Lys14 __

inhibits methylation of lysine 9

Ubiquitin:

76 AA protein tag

Ubiquitin role

• affect transcription regulation & DNA repair

• can target histones for proteolysis

How do ATP-dependent nucleosome remodeling complexes increase accessibility of DNA?

• sliding histone octamer along DNA

• removing/relocating octamer

• introducing transient DNA loops

SWI/SNF family:

disrupts nucleosome positioning

Why is DNA methylation risky?

• methylated cytosines are less chemically stable; mutating to thymine

• recognized as DNA damage

DNA methyltransferases use “base-flipping” how?

• cytosine ins flipped out of the DNA double-helix

• amino acid is inserted to stack in double-helix as a placeholder

• cytosine is methylated and reinserted into the double-helix

Methylation allows bacteria to __

distinguish genomic DNA from invading bacteriophage DNA

Eukaryotic methylation is usually at __; used for epigenetic silencing

CpG or CpXpG

__ is an example of silencing in mammals

X-chromosome inactivation

__ bind specifically to methylated DNA

histone modification enzymes and nucleosome remodeling complexes

Genomic imprinting:

parent-of-origin-specific silencing of certain genes; if active copy in father is missing, there is no gene expression at all

Centromeres all have a defined region where the nucleosomes have a __

histone H3 variant (CENP-A in humans)

Human centromeres are made of __

alpha-satellite repeats (tandem repeats)

What happens when there is an extra alpha-satellite repeat in a chromosome?

the 2nd potential centromere is inactivated through chromatin structure and a neocentromere is formed

A neocentromere is __

self-propagating

It is possible that __ are more likely to recruit CENP-A

AT rich

Telomere function:

protect chromosome ends and help overcome the end-replication problem

Telomere DNA consists of __

single tandem repeats with one C-rich & one G-rich strand

Human telomere repeats:

TTAGG

The G-rich strand always extends __

5’ → 3’ toward the chromosome end

What happens in organisms with long telomeres

the single-stranded region will overhang and form a t-loop by base pairing with the double strand region

Telomeres have a single-stranded overhand region on the __

GC rich 3’ strand

Telomerase:

a special DNA polymerase that has protein and RNA components

Telomerase function:

extends the 3’ end; the complementary strand is filed in by regular repair polymerases

Telomere elongation alternative:

3’ end of one chromosome invades an identical telomeric sequence and use it as a template

Telomere binding proteins:

• end-binding proteins (protect G-rich overhang)

• double-stranded binding proteins

• proteins that associate with the DNA binding proteins

Boundary elements:

• physical barrier; proteins bind and block spreading of successive histone modifications

• anchor large chromatin loops, possibly forming TAD anchors