BIOB11 midterm lec 1-6

learning objectives and more

Identify differences in the process and function of mitosis vs meiosis (4 things that meiosis has that met doesn’t)

meiosis ends up with ½ the gen mat as mitosis

Mei includes recombination

Mei includes Synapsis: pairing of homo chromosome

Mei includes reduction division

Identify similarities in the process and function of mitosis vs meiosis (2)

they both begin with replication of chromosomes, and creation of sister chromatids

functions of the mitotic spindle in meiosis

organizes chromosome and pulls them to opposite poles (and is organized by centrosomes)

microtubules fxn in meiosis

main component of the mitotic spindle apparatus

kinetochore fxn meiosis

proteins that connect spindle fibres to chromo’s centromeres.

cohesions fxn in meiosis

all along the chromosomes ensuring sister chromatids stay together. (also at centromeres)

centromere fxn in meiosis

where the spindle apparatus connects to the chromosomes (by kinetochore Ps)

Law of segregation

an indv’s Mat and pat’s chromosome segregate from e/o during gamete formation

law of independent assortment

Segregation of a pair of alleles for one trait (gene) has no

effect on the segregation of alleles for another trait

what steps in meiosis allow laws of inheritance to apply

crossing over and synapsis

what is crossing over (genetic recombitiations) and when does it happen

allows for gametes to have new allele combos!

chromosome from one parent crosses over with chromosomes from other parent exchanging some bits.

prophase I

components of DNA ___+____+____=________

sugar, phosphate, nitrogen base= nucleotide

purines

A and G

pyrimidines

C and T

nucleotide vs nucleoside

Nucleosides:

Sugar + nitrogenous base (no phosphate!!)

Nucleotides:

Nucleoside + phosphate group(s)

DNA 3 functions, and how structure allows them to happen

1. Storage of genetic information: linear bases sequences code for genes.

2. Replication and inheritance: strands can be pulled apart, and since strands can be templates.

3. Expression of genetic message: strands can be separated for RNA synthesis (transcription) to make proteins= expression

Identify which organisms use DNA as the keeper of their heritable information (3)

bacteria, archea, eukaryotes

Explain why mutations in germline vs somatic cells have different effects on offspring

only mutations in the gremlin cells will be passed on to offspring

Describe the flow of information in the Central Dogma of Biology (Directionality in the flow of information)

DNA, RNA, Protein

a gene is a:

vessel for heritability and change

Major and Minor grooves of DNA are:

protein binding sites

each spiral of DNA is how many bases?

10

phosphate is on what prime?

5’ phosphate (on carbon 5)

hydroxyl on what prime?

3’ hydroxyl (on carbon 3)

what end is the red box on?

5’

what end is grey box

3’

what are the 3 main genetics discoveries in order?

inheritance exists, chromosomes, DNA

what is chiasma

site of crossing over between 2 chromosomes during genetic recombination.

who are these cuties

homochromos/ bivalents/ a tetrad

prokaryote genome and a result

double stranded circular DNA in nucleotide region

results in lots of horizontal gene transfer= lots of external DNA

eukaryote genome shape

double stranded, in nucleus

pathogens, chloroplasts and mitochondria’s dan can be infused into a eukaryotes DNA T or F

true

explain viral DNA

singe or double stranded, needs to use host to replicate and protein synthesis (not alive!)

as gene density increases, gene coding % ____

increases too

gene density in prokaryotes vs eukaryotes

high in Process

low in euks

does genome size correlate with complexity?

no (called c value paradox apparently)

how can we have a larger genome size and smaller amt of genes encoding Ps?

lots of repetition!

is genome size correlated with number of genes?

no. most of it is noncoding DNA with other fxns, ex: regulatory (the actual gene section is so small and P coding regions even smaller!)

• Identify the % of human DNA that encodes protein vs other types of sequences

1-2%

does the number of protein coding genes indicate complexity of an organism?

no! g-value paradox

an x shaped chomosome indicates that ____ has occurred

replication

genes are all the same size T or F

FALSA: can be all sizes

positive supercoiling (to relieve strain) occurs which direction of a DNA strand being unwound?

in front, overwinding

negative supercoiling (to relieve strain) occurs which direction of a DNA strand being unwound"?____

behind, underwinding

Topoisomerases

enzyme that uncoils DNA poisitive supercoiling, while it is being unwound.

DNA charge and why is it important

- because of the P group

• can easily interact with histone’s positive charge

what are the 4 parts of the histone octamer

H2A, H2B, H3, AND H4, connected in a histone handshake

chromatin ARE MADE OF (3)

dna wrapped around histones, which then package themselves into nucleosomes

which histone serves as a linker of nucleosomes and what is the new shape it forms called?

H1, Histone H1 can line up nucleosomes end-to-end into two stacks called 30nm fibre (increases ration 6 fold)

how many nucleotides in a nucleosome

around 200

after the 30nm fibre is created, it can be folded even further with he help of what P? how?

• 30 nm fiber may further be gathered into a series of large loops

• These loops are attached to protein scaffolds

DNA-packaging ratio in a

mitotic chromosome is ————

fold!

10000

function of histone N-terminal tails

subject to covalent modifications and site of methylation and acetylation of histones

Euchromatin vs heterochromatin

Euchromatin: DNA that is less compacted and functionally active (accessible for

protein binding and transcription). Genes here can be expressed

Heterochromatin: DNA that is highly compacted and has little to no functional

activity

two types of heterochromatin and function

Constitutive heterochromatin

• Permanently silenced DNA

• Includes regions around telomeres and

centromeres

• Contains DNA repeats and few genes

Facultative heterochromatin

• Inactivated during certain phases of

organism’s life

what’s this

The inactive X chromosome is condensed as

heterochromatin (Barr body)

what is X inactivation and when does X inactivation occur?

an example of facultative heterochromatin. when either the mat or pat chromosome is inactivated in almost all somatic cells.

early on in development(but when there are already a bunch of cells), and all daughter cells have the same one silencenced

explain x inactivation in calico cats and clones with identical genetics, but physical differences.

in heterozygous individuals, in some cells the orange colour can be silenced and in some the black colour will be silenced, and as these multiply, it results in different colour patches.

clones can have different chromosomes silenced.

epigenetics vs. genetics

genetics: permanent and inheritable changes in DNA that result in different traits.

epigenetics: reversible covalent modifications that change the expression of DNA without altering it. can be influenced by environmental factors.

what’s euchromatin and what’s heterochromatin in the photo?

where’s the histone P, and the histone modification?

what are the three covalent modifications that can occur on the histone code on the N terminal tails?

acetylation, methylation, phosphorylation

acetylation does what

more open, increased transcription

methylation does what?

compaction, repression.

acetylate histone proteins by transferring acetyl group from

acetyl-CoA to specific lysine residues.

Histone acetyltransferases (HATs)

what removes remove the acetyl group

ONLY Histone deacetylases (HDACs)

Histone methyltransferases (HMTs)

add methyl group(s) (1, 2, or 3) to lysine or arginine

residues.

remove methyl groups.

histone/DNA demethylases

chromatin has way better memory in ______ than in _______

eukaryotes, prokaryotes

euchromatin or heterochomatin? (3)

euch, het, het

active or repressed gene

repressed

active or repressed gene

active

CpG

epigenetic marker that allows DNA methyltransferase to add a methyl group between the C and G (the p spot)

when is DNA methylated and why?

during replication so its methylation patterns can be passed on to its daughter strand.

do you inherit all your epigenetics from your parents?

no, zygote erases is all previous epigenetics and the blastocyst is fresh

exception: genomic imprinting, but thats only a tiny bit

role of reader-writer complexes

reads histone code, positions and activates “writer” enzymes, that attach it to other components in nucleus responsible for expressing, silencing, etc.

which basically means AFTER REPLICATION, histone modifications are scattered throughout, the RW complexes read them, and mark spots that need to be filled in order for it to be identical as parent. then the correct heterochromatin proteins are added to all the spots with midficwations.

how does the initial recruitment of these enzymes occur?

often occurs through a transcription factor protein binding to a specific DNA sequence

heterochromatin doesn’t go across whole chromosome because:

Barrier sequences on DNA that Barrier proteins bind to.

three kinds of barrier proteins

brown: physical protection

purple: linking scaffold P and nuc pore to make wall

blue: mechanism that directly opposed RW activity,

• Explain why some regions/sequences of the genome are likely to be exhibit faster or slower rates of change

more important sequences are more conserved (less change). generally exons and protein coding sequences

point mutation, and explain an example

switching one nucleotide for another

(Changes in the nucleotide sequence of DNA can

be caused by errors in DNA replication or repair)

Ex: SNPs, a common version that usually is not detrimental=not selected against, persists.

Of the five large scale rearrangements: Insertions, Deletions, Duplications, Inversions, Translocations

Which of these are likely to result

in loss/mutation of genes?

Deletion, by far!!

(not translocations because it would need to cut right in the middle of the gene, which is unlikely)

synteny

regions where genes are in conserved order, but are now at a diff position.

_____% of human genome is conserved across species

5, and 1.5% of that is P-coding

• Apply an understanding of genome composition and rates of change to select the type of sequence a researcher should look at if identifying closely related individuals within a species vs constructing a phylogenetic tree

help

name them

what do you think is

more highly conserved: sequences within

exons or the positions of genes on particular

chromosomes?

sequences within

exons

just know this

Satellite DNA

highly repetitive, (generally found at centromeres and telomeres) - 5-500 bp in tandem

repeats of up to 100 kb that can form very large clusters. Base composition is distinct from

bulk DNA

Minisatellite DNA

highly repetitive, 0-100 bp with up to 3000 repeats → highly variable (polymorphic),

therefore # repeats differs between individuals– basis for DNA fingerprinting in criminal

and paternity tests

Microsatellite DNA

highly repetitive, 1-5 bp in clusters of 10-40 bp scattered quite evenly throughout the

genome → highly variable (# of repeats changes fast!), can be used to compare closely

related populations.

12

Name two kinds of Moderately repetitive DNA, 20-80% of the genome

genes: ribosomal RNAs and Histone genes

non-coding: SINES and LINES caused by transposons

Protein coding DNA Is likely

Non repetitive

what are the two forms of slippage, and what does it cause?

( what are the 2 forms of slippage??) expansion and deletion causes misalignment of DNA during replication

transposons vs retrotransposons method of locomotion, and details

transposon: cut and paste, by transposase enzyme results in a direct repeat behind it

retrotransposon: copy paste, by RNA intermediate, use and can encode a reverse transcriptase enzyme to catalyze production of

DNA from RNA.

Example: LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements)

what percentage of genetic change is due to transposons?

40%

why do humans have more transposon events than bacteria

because humans have less density, less of a chance of it hitting smog important

• Explain 4 mechanisms that can contribute to creating new genes/alleles and explain how gene families and pseudogenes could form

1. segment shuffling, exon shuffling is when transposition includes exons

2. Horizontal gene transfer: viruses inserting their DNA

3. Gene duplication (ex: unequal crossing over ): different versions of the same gene!

4. Mutations: point mutations etc..

genes always come from pre-existing genes. T or F

T

what is exon shufflring?

when the exons from different areas combine due to transpositional activity. results in the creation of new proteins

what is the result of unequal crossing over

a way of gene duplication resulting in the expansion of multigenerational families. how? the chromosomes aren’t perfectly aligned during crossing over, so one gets a deletion and another gets extra. if it occurs consecutively, duplications and stuff.