Genetics Exam 2

genetic material

• contains information

  • expression determines all traits and functions of organisms

  • this is what is leading to the traits that we observe, phenotypes

• is stable, but must also have the ability to change

  • variation in many traits without lethality to organism

  • being passed to one generation to the next and being passed to one cell to 2 daughter cells during cell division

• is carried on chromosomes

  • contain proteins and DNA (deoxyribonucleic acid)

  • meiosis where the chromosomes are organized at the metaphase plate so we wend up dividing the chromosomes up equally into the daughter cells that eventually become the gametes

helicase

unwinds DNA double helix

single-stranded binding protein

• prevents the reannealing of DNA strands

DNA replication order

• each genomic origin of replication assembles a prereplication complex

• the initiation complex creates an active replication fork as helicase unwinds DNA

• RNA primers are added to provide a 3’ end for elongation

• DNA polymerase synthesizes both the leading and lagging strands from 5’ to 3’

• RNA is replaced with DNA, and lagging strands are joined

• active telomerase can extend the lost telomere region

Hershey-Chase experiment sequence

• radiolabel phage DNA and phage protein

• mix each type of phage with separate bacteria

• agitate to separate cells from phage bodies

• centrifuge to separate bacteria into a pellet

• measure pellet and liquid for radioactivity

Initiator protein

• bind to the oriC and unwind the DNA, allowing for the binding of

  DNA helicase and single-stranded binding proteins to the DNA.

• If these proteins are unable to bind, then DNA replication initiation will not occur, so DNA synthesis will not take place

Griffith’s Experiment

• Smooth (S)

  • colonies are smooth and shiny

  • cells are enclosed in polysaccharide capsule

  • virulent (infectious)

  • wild-type

• Rough (R)

  • colonies are rough with jagged edges because there is no polysaccharide capsule

  • nonvirulent (easy to engulf and destroy)

  • mutant

• experiment

  • S (virulent) → dead mouse → S bacteria was recovered

  • R (nonvirulent) → alive mouse → no bacteria recovered

  • boiled S → alive mouse → no bacteria recovered

  • boiled S and living R → dead mouse → S bacteria was recovered

    • protein denatured when boiled

• Conclusion

  • living cells are necessary for virulence

transformation

• conversion of rough → smooth

• inject living R strain into an S strain

Avery, MacCleod, McCarty

• experiment

  • boiled S → split into 3 samples

    • add RNase (destroys RNA) → add to R → transformation principle destroyed

    • add protease (destroys proteins) → add to R → transformation principle destroyed

    • add DNase (destroys DNA) → add to R → transformation principle was NOT destroyed

• conclusion

  • transforming principle is made of DNA

  • transformed bacteria remained virulent in subsequent generations → transformed traits are heritable (passed to one gen to the next)

Hershey and Chase

• studied Bacteriophage T2

  • virus that infects bacteria

  • DNA core surrounded by protein coat

    • protects core that has DNA

  • structure

    • phage = attaches to the outside of cell, take over machinery of host and use machinery to make more copies of itself

    • protein coat remains on the outside of the bacterial cell

• knew T2 is ~50% protein, ~50% DNA

• infection steps

  • adsorption

    • phage attaches to bacteria via tail fibers

  • phage material enters bacteria

    • production of new viruses within bacterial cell

    • this must be the genetic material of the phage … it is necessary to make new phage

      • because this material is allowing the phage to make more copies of itself

  • bacterial lysis

    • new phage progeny released

• radioactive labeling is used to “see” molecules

  • sulfur (³⁵S) marks proteins

  • phosphorus (³²P) marks DNA

• experiment

  • phage with labeled protein or DNA → infect with E. coli (genetic material must enter cells here) → blend (shears off what’s left on outside of bacteria because want to get rid of any phage that is left) → spin (infected bacteria will pellet)

    • protein (³⁵S) radioactive in liquid

    • DNA (³²P) radioactive in pellet

• conclusion

  • DNA is genetic material

purines

• adenine (A)

• guanine (G)

• nitrogenous base has 2 rings

pyrimidines

• cytosine (C)

• thymine (T)

• nitrogenous base has 1 ring

nucleotides

• made up of phosphate, sugar, and a base

  • they are bonded covalently

• basic building block of DNA

deoxyribose structure

• C1’ has N-base attached

• C2’ has H in DNA OH in RNA

• C3’ has OH group

• C5’ has phosphate attached

Erwin Chargaff

• studied composition of DNA from many organisms

• total pyrimidine (T+C) = total purine (A+G)

• T = A and G = C but A+T ≠ G+C

Rosalind Franklin and Maurice Wilkins

• studied X-ray diffraction of DNA

• conclusion

  • DNA is made of 2 parallel parts

  • DNA is helical

  • helix contains 10 nucleotides (nt) per turn

  • measured helix diameter

Watson and Crick

• DNA is a double helix

  • 2 strand of DNA wound around each other

  • each strand is one chain of nucleotides

• 5’ phosphate of one nucleotide is linked to the 3’ OH of another

• covalent bonds that are joining each nucleotide to its neighbor

• complementary bases

  • A pairs with T

    • 2 hydrogen bonds holding it together

  • C pairs with G

    • 3 hydrogen bonds holding it together

• 2 strains are antiparallel

  • runs in opposite directions

  • 5’→3’ and 3’ → 5’

• DNA structure is likely important for replication

  • complementary strands → each strand could be template for the other

  • specific base-paring → only one sequence is possible from a template

DNA Structure

• two strands of DNA form one helix

  • antiparallel

• sugar-phosphate backbones of each strand are on the outside of helix

  • covalent bonds between sugar and phosphate hold nucleotides together in a single chain

• Bases (A, G, C, T) are stacked inside

  • hydrogen bonding between complementary bases keeps 2 DNA strands together

• major and minor grooves are formed

  • important for protein binding

  • minor = distance between two backbones

  • major = area between turns of double helix

A form DNA structure

• less hydrated

• more compact (10.9 bp/turn)

• right-handed

• seen under high salt concentrations

• in test tube → in vitro

B form DNA Structure

• more hydrated

• less compact (10bp/turn)

• right-handed

• typically in vivo (in cell)

• proposed by Watson and Crick

Z form DNA Structures

• left-handed

• zig-zag sugar phosphate backbone

• seen in short DNA pieces with alternating purine/pyrimidine

oligonucleotide

• short chain of nucleotides

• single-stranded DNA

denaturing

• separating 2 strands of DNA

• also called “melting”

  • make single stranded

• can be done by heating DNA, which breaks H-bonds between strands

• G/C rich DNA has higher melting temp than A/T-rich DNA

  • the H bonds that are only hold two bonds are less stable sot they are easier to break when heating

annealing

• when 2 complementary single strands of DNA H-bond back together

DNA

• sugar: deoxyribose

• bases: A, G, C, T

• structure: double-stranded

• relative stability: more

RNA

• sugar: ribose

• Bases: A, G, C, U

• structure: single-stranded

• relative stability: less

• synthesized as single stranded nucleic acid

• hairpins, bulges, stems, loops, etc fold on each other

  • create binding sites for proteins

• overall molecule will be most stable if complement base pairing is allowed to happen

• fold into complex secondary and tertiary structures

hairpin

• sequences on same strand are inverted complements

• sequence between inverted repeats forms loops

• found in single-stranded nucleic acid

  • more often in RNA than DNA

stem

• hairpin with no loop

• found in single-stranded nucleic acid

  • more often in RNA than DNA

conservative model of DNA replication

• 1st round of replication

  • 2 strands original

  • 2 strands new

• 2nd round of replication

  • 1 helix original

  • 3 helices new

• old strands back together and new strands back together

semi-conservative model of DNA Replication

• 1st round of replication

  • 1 strand original; 1 strand new

  • 1 strand original; 1 strand new

• 2nd round of replication

  • 2 helices new

  • 2 helices old + new strands

• the two experiments that proved this model

  • Meselson-Stahl experiment (in prokaryotes)

    • studied E. coli → 1 circular chromosome

    • used heavy isotope of Nitrogen (¹⁵N) to label DNA

    • “normal” Nitrogen is ¹⁴N

  • Taylor experiment (in eukaryotes)

• all DNA in the sample consists of one heavy strand and one light strand

dispersive model of DNA replication

• 1st round of replication

  • 2 strands mixed

  • 2 strands mixed

• 2nd round of replication

  • 4 helices mixed

• here long chromosomes gets chopped up into smaller pieces and each piece has 2 strands separate so that each strand acts as a templet and then somehow the whole long chromosome gets reassembled

• the chopped up pieces come back together

Meselson-Stahl experiment (in prokaryotes)

• studied E. coli → 1 circular chromosome

• used heavy isotope of Nitrogen (¹⁵N) to label DNA

• “normal” Nitrogen is ¹⁴N

• used density gradient centrifugation

  • take their cell samples at various time points during the process of DNA replication

  • chop DNA up so they can analyze it and they are going to put it onto a gradient

  • basically the light DNA sits on the top and the heavy DNA sits on the bottom

• consistent with the semi-conservative model because 2 different populations of DNA present

density gradient centrifugation

• DNA is extracted from cells cut into pieces and added to a gradient of Cesium Chloride (CsCl)

• samples are centrifuged at high speeds

• at equilibrium, DNA concentrates within the gradient where its density is equivalent to that of CsCl

• see DNA by straining with ethidium bromide and shining uv light

  • binds to DNA and can see where etBr is for where the DNA is located

• method

  • take from their cell samples at various time points during the process of DNA replication

  • chop DNA up so they can analyze it and they are going to put in onto a gradient

  • DNA moves so it matches density with the CsCl

  • lighter DNA sits at the top while the heavier DNA sits on the bottom

• conservative model

  • 1st round: will have a band at ¹⁴N and ¹⁵N

• semi-conservative model

  • 1st round: one at the intermediate

  • 2nd round: will have a band at ¹⁴N and one at the intermediate

• dispersive model

  • will have one band at the intermediate that progressively shifts towards the light

Taylor Experiment

• studies bean root tups (eukaryotic cells)

• followed cells through mitosis (2 rounds)

• labeled DNA with tritiated (³H) thymidine → radioactive

• the conservative model would suggest only one chromatid containing 2 newly synthesized strands would be radiolabeled

• meiosis 1

  • G1 → (goes through S, G2, prophase)

  • Metaphase (DNA is most condense, stop cells from growing here)

  • anaphase (all chromosomes are lined up and sisters are separating from each other)

    • chromatids migrate into separate cells

  • both sister chromatids are radioactive

• meiosis 2

  • G1 unlabeled thymidine and chromosome goes through S, G2, prophase

  • metphase

    • only 1 chromatid is labeled

• autoradiography

  • exposed DNA to film dark areas = radioactivity

DNA polymerase

• enzyme that synthesizes DNA

• in E coli Pol 1 and Pol 3 do most work during DNA replication

• more types in eukaryotes

• makes new DNA strand 5’ → 3’

  • only works in one direction

• needs 3’-OH group to begin

  • cant do it by itself

DNA synthesis

• is synthesized in 5’ → 3’

• polymerase moves down template in 3’ → 5’ direction

• anti-parallel

theta replication

• circular chromosome

• autoradiographs

  • you radiolabeled the DNA and then put piece of film on that, develop the film, and where you see the dark signal that is where the DNA is present

• in prokaryotes

rolling circle replication

• plasmids

  • extrachromosamal, circular piece of DNA that is present in one bacterial cell

  • if present, bacterial cell will replicate it at the same time it replicates circular chromosomes before cell division

origin of replication

• where replication begins

• eukaryotic chromosomes have many

• only 1 in e. coli → OriC

• A/T rich

  • important because at ORiC, the two strands have to begin synthesizing the new DNA

    • easier to do it lots of A’s and T’s becase A and T only have 2 hydrogen bonds

      • required less energy to do this

• sequence is recognized by initiator proteins

• recognize tha there is a group of proteins that bind to the OriC and begin this process by melting the DNA

theta model in prokaryotes

• starting at oriC, DNA is melted so single stands can act as templates

• DNA synthesis happens simultaneously in both directions (bidirectional)

• 1 replication bubble made of 2 replication forks

• product = 2 circular chromosomes with 1 old + 1 new DNA stand

theta replication in eukaryotes

• many replicons on eukaryotic chromosomes

  • replicons = point of origin + area of DNA replicated

• 1 bubble (2 forks) from each origin

• bidirectional DNA synthesis

• final product = 2 linear chromosomes

  • 1 old and 1 new DNA strand

• contains

  • leading strand

    • each fork will have only 1 strand made continuously

  • lagging stand

    • made discontinuously

    • contains ozaki fragments

leading strand

• since DNA polymerase makes DNA 5’ → 3’, each fork will only have 1 strand made continuously

lagging strand

• made discontinuously

• short pieces are called the Okazaki Fragments

DNA Replication

• overall sequence

  • initiator proteins bind oriC

  • DNA melts at A/T rich regions

  • DNA Helicases bind and continue denaturing

  • single-strand-binding proteins (SSBs) keep DNA melted

• RNA Primer Removal and DNA Ligase

  • RNA primers are removed by DNA Pol 1 in prokaryotes

    • has 5’ → 3’ exonuclease activity

    • has 5’ → 3’ polymerase activity to replace RNA primer with DNA

    • has 3’ → 5’ exonuclease activity for proofreading

  • DNA Ligase

    • seals final hole (nick) in sugar/phosphate backbone

DNA gyrase

• important for initiation of replication

• its a specific topoisomerase (enzyme)

• works ahead of replication fork to reduce strain due to helix unwinding

  • prevents supercoiling

• functions upstream of replication fork

primase

• RNA polymerase

• needs no free 3’-OH group to work

• makes an RNA primer using ssDNA as template

RNA primer

• short oligonucleotide

• provides free 3’-OH for DNA polymerase to add onto

DNA Polymerase III

• prokaryotic enzyme

• does most of DNA synthesis

• elongates RNA primer by adding new DNA

• very fast (~1,000 nucleotides/sec)

• has 3’ → 5’ exonuclease activity to correct mistakes

3’ → 5’ exonuclease

• enzymatic activity that destroys nucleic acid such as DNA

• destruction from end and not middle

• start at 3’ end and destory it

• catch some mistake right after the fact but will not catch all mistakes

• only works for nucleotides just added

  • called proof-reading

• base pairing not correct, will realize it and step backward to remove it (3’ → 5’)

DNA Polymerase 1

• 5′ → 3′ exonuclease activity = Removes RNA primers

  • destroys RNA primer

• 5′ → 3′ polymerase activity = Adds DNA nucleotides

• 3′ → 5′ exonuclease activity = Proofreading

5′ → 3′ exonuclease activity

• remove RNA primer

• if mutant, RNA primers cannot be removed

3′ → 5′ exonuclease activity

• proofreading, step back and take away

• if mutant, more mistakes will be in the newly made DNA

5′ → 3′ polymerase activity

• used to synthesize new DNA to replace RNA primers

• if mutant, RNA primers will not be replaced by DNA Pol 1 with DNA

DNA ligase

• seals final hole (nick) in sugar/phosphate backbone

• creates final covalent bond that joins the two Ozakai fragments together so RNA fragments has been replaced by DNA primer

• creating covalent bond between 5’ phosphate and 3’ OH to join together 2 nucleotides in their newly synthesized DNA strands

DNA replication eukaryotes

• these chromosomes have many DNA packing proteins bound to DNA

  • histones

    • making more of DNA packing proteins so DNA can be packaged properly

  • must be synthesized during this

• have many replicons/chromosome

• have many DNA polymerases

  • different DNAPs function at specific times, with varying speeds, error rates and ability to handle mismatches and distortions in DNA

• use replication licensing factor (RLF) to control timing of replication initiation

  • RLF help keep track where DNA replication has happened and where it needs to happen still

  • contains several proteins that bind to OriC during G1 phase of cell cycle

  • marks an OriC as ready for DNA replication

  • once replication begins, different proteins will bind to maker that OriC as already replicated

• have linear chromosomes with telomeres (contain repetitive sequence that doesn’t code for anything) on the ends

  • difficult to replicate the end of a lagging strand

  • length is linked to aging and disease

    • chromosomes shortening

    • DNA gets shorter and shorter by RNA primer length

DNA replication prokaryotes

• have 5 DNA polymerase

replication licensing factor (RLF)

• helps keep track where DNA replication has happened and where it needs to happen

telomeres

• contain highly repetitive DNA

• contains repetitive sequence of DNA that doesn’t code for anything

end-replication of linear chromosomes

• when RNA primer on 5’ end is removed, there’s no 3’-OH for DNA Polymerase to use

  • very end of chromosome can’t be replicated

  • chromosome should get shorter after every round of replication

• there is a cap left by removal of primer

  • cant add to it because DNA primer needs a free 3’-OH, cant go in opposite direction, must go in 5’ → 3’ direction

• happens in DNA replication of eukaryotes

single-stranded DNA overhang

• happens when there is __ on the 3’ side

• to fix this problem

  • telomerase enzyme extends DNA at chromosome ends and has a protein and RNA component

    • protein part synthesizes new DNA

    • RNA part acts as template for DNA synthesis

  • telomerase moves down and continues extending 3’ overhang

  • primase makes primer

  • DNA Polymerase fills in

  • primer removed

  • telomerase solves the problem of the chromosome shortening after every round of DNA replication

telomerase enzyme

• extends DNA at chromosome ends to help with DNA overhang

• has protein and RNA components

  • protein

    • synthesizes new DNA

  • RNA

    • acts as template for DNA synthesis

• expressed in

  • germ cells

    • gives rise to gametes

  • stem cells

    • immortal cells that aid in such things as wound healing

telomerase protein part

• synthesizes new DNA to help with DNA overhang

telomerase rna part

• acts as template for DNA synthesis

• helps with DNA overhang

why does our body cells have finite life span?

• because telomerase doesn’t work on them so once it gets too short, the self-death of cell is activated

• is useful because can help get rid of mutations that have occurred in our DNA

DNA packing in prokaryotes

• formation of loop domains

  • each loop is held in place by DNA binding proteins

• supercoiling

  • happens within loop domains

  • allow DNA to be more condense so more can get added

  • superpacked ≠ gene expression

• relaxed DNA ←(topoisomerases)→ supercoiled DNA

topoisomerases

• enzymes that add or remove rotations from DNA helix

• super coiling from looped domains

• relaxes supercoiled DNA

chromatin

• DNA + proteins

  • DNA is always existing as chromatin, bound by protein

  • example is nucleosomes by histones

  • DNA is never really by itself

chromosome

• chromatin that is highly condensed

  • DNA complex during G₁, S, G₂, prophase → chromatins

heterochromatin

• remains highly condensed (tightly packed) throughout cell cycle

• no gene expression here because chromatin is tightly packed in these regions so its difficult for all machinery to come in and access the DNA in order for gene expression to happen

• can be

  • constitutive

    • always condensed

    • examples: centromeres and telomeres

  • facultative

    • condensed at certain times

    • example:

      • inactivation X chromosome

        • happens early on in development

          • ½ moms inactivated and ½ dads inactivated

euchromatin

• packaging changes during cell cycle

• contains expressed genes

  • more losely packed when gene expression happens

centromeres are made out of

• heterochromatin

• part of chromosome that attaches to spindle fibers

• required for proper segregation of chromatids

• no genes present here; DNA sequence is highly repetitive

  • # of repeats on each chromosome varies

• DNA remains tightly packaged throughout cell cycle

telomeres are made up of heterochromatin

• POT (Protection of Telomere) proteins bind single stranded overhang

  • provide stability

  • prevent ends from degrading and/or sticking together

• sometimes ends fold over to form triple-stranded structure

• DNA remains tightly packaged throughout cell cycle

histones

• “beads on a string”

• simplest level of chromatin structure

• visible under low salt conditions

• small, positively charged (R groups)

  • Arg and Lys amino acids

  • bind tightly to DNA

• bind tightly to DNA

where is the tightest packaging seen?

• at the metaphase plate

• and anaphase so that DNA or chromatin can go to daughter cells

• chromosomes

nucleosome

• simplest level of chromatin structure

• contains histone proteins

  • small, positively charged

    • Arg and Lys amino acids

    • bind tightly to DNA

• Five types:

  • H1

    • linker histone

  • H2A

    • core histone

  • H2B

    • core histone

  • H3

    • core histone

  • H4

    • core histone

  • need 2 of each of the core histones since 8 histones make one bead

net charge of DNA is

• negative because of the phosphate groups in the backbone

epigenetics

• study of phenotypic variation caused by variation in gene expression … NOT caused by variation in nucleotide sequence

• changes in gene expression due to changes in chromatin structure

  • can be stable through cell divisions (mitosis)

  • can be stable over generations (meiosis)

  • can be influenced by environment

  • chromatin structure is always changing and are reversible but can be maintained because they are heritable

chromatin structure is altered by

• chemical modification on DNA and histones

• reversible

• important for regulating gene expression

• modified by

  • DNA modification

  • histone modification

DNA modification

• one type: methylation of nucleotide base (mostly Cytosine)

  • frequently CpG dinucleotides

  • both strands of DNA are modified

• associated with lower gene expression

• happens where there is repeat of C’s and G’s

histone modification

• several types: phosphorylation, methylation, acetylation, ubiquitination

• affects binding to DNA

• often happens in positively charged “tails”

  • groups of amino acids at end of histone proteins

  • wrap around DNA and interact with phosphates in backbone

    • tail becomes a littler arm

      • can interact tightly with backbone → giving it a little hug essentially

  • can act strongly with the negative charge in the sugar phosphate backbone of DNA

• acetylation can mask positive charges

  • often stimulates gene expression

• methylation can create binding sites for transcription factors

  • stimulates gene expression

  • it can mark on area for increased or decreased gene expression

histone acetylation

• can mask positive charges

  • makes binding to DNA weaker

    • not hugging it as tightly

  • makes chromatin structure more open

    • losely packed

  • often stimulates gene expression

• remember: open chromatid structure and increased gene expression

histone methylation

• can create binding sites for transcription factors

  • stimulates gene expression

• can “mark” an area for increased or decreased gene expression

  • specific amino acid in certain histones

• this is heritable

  • enzymes are recruited by transcription factors, pre-existing epigenetic marks, noncoding RNAs

    • are recruited during S-phase

      • new histones being made

  • mechanisms for maintenance during cell division are not well understood

how is level of DNA Methylation maintained after DNA replication?

• DNA replication

  • melt DNA
    2 olds strands act as template

• both DNA molecules are hemimethylated

  • methylated on 1 DNA strand

  • DNA repair machinery can distinguish old and new DNA strands at this point

  • helps DNA repair machinery because if they are scanning and see base pairs not proper, strand not methylated is the new strand so that must be where the mistake is

  • G2 cell cycle

    • enzymes that will check DNA and correct any mistakes that were made during DNA replication

• special methyltransferase enzymes recognize hemimethylated DNA

• can see where methyl group is supposed to be by looking at the old strand and add methyl groups on the appropriate place on the new strand

chemical modifications are

• heritable

  • can be passed on to one cell to the daughter cell during mitosis and can be passed on to parent to progeny when we create gametes

DNA methylation and gene expression

• it down-regulates gene expression

• how it does it

  • methyl group in major groove prevents binding of proteins that stimulate transcription (transcription factors → important for turning on gene expression, which increases gene expression)

  • creates binding site for histone deacetylase enzymes

    • removes acetyl groups from histone proteins

• it will ALWAYs lead to down regulation of gene expression by preventing transcription factors from binding because methylation of DNA

histone deacetylase

• remove acetyl groups from histone proteins

  • histones bind DNA more tightly

  • chromatin structure is more condensed

  • gene expression downregulated

    • harder for machinery to get in and read DNA in order to start the process of gene expression

DNA methylation in honeybees

• queen and work bees develop from genetically identical eggs

• queen

  • female

  • larger body

  • functional ovaries (just means fertile)

  • behavior includes mating flight and egg production

• worker bees

  • female

  • smaller body

  • sterile

  • behavior includes collecting nectar and pollen, tending the queen, raising babies

• differences between the two are caused by changes in gene expression and diet

• queen’s diet

  • queen is the only one that eats royal jelly or siRNAs

    • is an RNA silencer

  • Dnmt3 gene repressed

    • gene codes for methyltransferase enzyme

  • less methylation in genome, increased gene expression

• this is an example of epigenetics

X-inactivation epigenetics

• random even that happens early in development

  • either moms or dads X is inactivated

• leads to stable change in gene expression

• passed on to daughter cells after mitosis

  • will have the same x-inactivation gene

• histone modification is important

x-inactivation center

• segment of X-chromosome where inactivation begins

• contains several important genes:

  • X-inactivation-specific transcript (X-ist)

  • Tsix

    • important for keeping one X-chromosome activated

  • Jpx

    • important for keeping one X-chromosome activated

  • Xite

    • important for keeping one X-chromosome activated

X-ist gene

• encodes long RNA that does not code for protein that doesn’t get translated

  • bind X-chromosome from which it was made

  • attracts protein complexes (PRC2; PRC1)

    • methylate histones to turn off gene expression

    • create “epigenetic mark” for repressed gene expression

      • because of long non-coding RNA binding

        • recruit proteins that will modify histones

        • methylated histones create the signal (the epigenetic mark) that results in a decrease in gene expression

• the long noncoded RNA will bind to chromosome where it wasn’t synthesized

  • when RNA binds, it will attract protein complexes

• Tsix is complement to this gene

  • meaning they are 2 genes that are opposite from one another

• part of x-inactivation center

Tsix gene

• keeps active x chromosome from being inactivated

• encodes long RNA that does not code for protein

  • anti-sense to X-ist RNA

    • reverse complement

    • complementary antiparallel sequence

      • the interaction prevents the Xist chromosome from binding to one x-chromosome

      • can hydrogen bond with one another

  • prevents X-ist expression/function on activated X

• part of x-inactivation center

Jpx gene

• encodes lon RNA that does not code for protein

  • stimulates (increases) synthesis of Xist on inactive chromosome

• part of x-inactivation center

Xite gene

• encodes long RNA that does not code for protein

  • sustains Tsix expression on active X chromosome

• part of x-inactivation center

genomic imprinting

• gene expression affected by whether gene comes from Mom or Dad

• results in autosomal traits that show different results for reciprocal crosses

• genes often in clusters of 3-12

  • encode proteins and noncoding RNAs

    • key to process basically

  • chromatin modification differ between alleles

    • tightly or more loosely packed

• genetic conflict hypothesis attempts to explain

  • dad might benefit more when certain genes are turned on than mom would benefit if it was turned on

    • example

      • growth factor of baby

        • dad wants big baby while mom wants a small baby for giving an easier birth

• it matters which parent supplies gene to progeny

  • mom and dad each give one and one is turned on while the other is off

• example

  • A1 allele (reciprocal cross)

    • A1 allele only expressed if from Dad

    • moms A1 gene is not expression (as shown on the right side of the picture

  • reciprocal crosses between donkey and horse produce hybrid animals with very different phenotypes

    • female donkey x male horse → hinny

      • more like a horse than a donkey

    • male donkey x female horse → mule

      • more like a donkey than a horse

• THIS IS AN EXAMPLE OF EPIGENETICS

behavioral epigenetics

• The study of how environmental experiences influence gene expression through epigenetic modifications without changing the DNA sequence, potentially affecting behavior.

• Example: Maternal care in rats can alter DNA methylation and stress responses.

variations in chromosome structure

• chromosomal rearrangements

• changes in parts of chromosomes

• involve 1 or more breaks in chromosomes

  • means that the free ends of DNA are unable

    • can be degraded by exonucleases (enzymes that destroy nucleic acid from the end)

    • can bond with other free ends (sometimes telomers)

    • can be repaired by cellular DNA repair machinery

      • mistakes here can create rearrangements

• may also be caused by unequal genetic recombination

  • prophase 1 of meiosis

• includes

  • deletion

    • loss of chromosomal segment

    • break, then degradation

  • duplication

  • inversion

  • translocation

chromosomal deletion

• loss of chromosomal segment

• break, then degradation

• effects

  • phenotype depends on which genes/gene parts are deleted

  • in het (diploid)

    • __ dominat allele → expression of recessive allele

      • this is called psuedodominance

    • gene dosage effects may occur

      • haploinsufficiency

    • looped out structure forms during meiosis prophase 1

  • if its only one region and that region does not influence genome, could see no phenotypic variation

  • deletion of one or more genes depending on what those genes code for, you will see a resulting phenotype

intercalary deletion

• deletion of an internal region of the chromosome

• example

  • wt: A B C · D E F G

  • mutation: A B C · D G

terminal deletion

• deletion of the end of the chromosome

• example

  • wt: A B C · D E F G

  • mutation: A B C · D E