Chapter 7, 15, CRISPR, GMFs

sexual differentiation

male and females are phenotypically different

heteromorphic chromosome

chromosomes that indicate sex

i.e. XX vs XY

heterogametic sex

sex that makes gametes which can be for either sex

XY can create X and Y

homogametic sex

sex that can only make gametes of the same sex

XX can only make X

klinefelter syndrome

XXY
-male genitalia
-some female traits
-tall
-sterile

turner syndrome

X
- less feminine appearance
- low fertility
- short

mosaic organism

cells have different genotypes

triplo-X syndrome

XXX
- low secondary sex characteristics
- low fertility
- language and motor skill difficulties

47, XYY

- tall
- less intelligent and more violent (possibly)

gonadal ridges

become the kidneys

bipotential gonads

can become male of female sex organs

primary sexual differentiation

gonas

secondary sexual differentiation

phenotypic appearance of sex
- glands
-genitals
-appearance

pseudoautosomal region

section of Y chromosome which matches X

male-specific region of Y (MSY)

section of Y chromosome that only males have

Includes: x transpond region, X-degenterative region, and ampliconic region

sex-determining region of Y (SRY)

makes gonads turn into testes by producing SRY protein which makes TDF and signaling SOX9

testis determining factor (TDF)

transcription factor that causes testicular development

Sawyer syndrome

XY females
-SRY is nonfunctional/missing from Y chromosome

SOX9

autosomal genes which activates stesticular development

X-transpond region

region on MSY that is the same as X chromosome

X-degenerative region

region of MSY that is slightly related to X chromosome

ampliconic region

region of MSY that has no relation to X chromosome

primary sex ratio

number of males and females conceived

secondary sex ration

number of males and females born

dosage compensation

prevents the difference in females and male gene quantity from influencing character/expression of females

barr body

inactivated X chromosome chromatin body

number of Barr bodies

N-1

N=number of X chromosomes

imprinting

only affects 1 homolog

X inactivation center (XiC)

X-inactive specific transcript (Xist)

mRNA that coats X chromomse and prevents its transcription

mutation

base pair change

point mutation

1 base substitution

missense mutation

code for a different amino acid

nonsense mutation

code for a stop codon

silent mutation

codes for the same amino acid n

neutral mutation

does not change transcription of gene expression
-in noncoding region or a silent mutations

transition mutation

different base replaces but the class of base is maintained
- pyrimidine stays pyrimidine but went from C to T

frameshift mutation

changes the reading frame

loss of function mutation

decreased capacity of protein

dominant mutation

expresses the mutant phenotype

gain of function mutation

increased capacity of protein

supressor mutation

a second mutation which prevents the expression of the original mutation

somatic mutation

mutation in body cell (no heritable) a

autosomal mutation

mutation of any chromosome but a sex chromosome

homogametic sex

has one type of sex chromosome

homozygous sen

has two types of sex chromosomest

tautomer

version of nitrogenous base with a 1 H+ shift

replication slippage

polymerase stutters os the template escapes leading to an insertion or deletion

translesion DNA polymerase

replicates skipped/damaged DNA leading to possibly the wrong nucleotide being inserted

automatic shift

moving the H+ to make a tautomer

depurination

losing a purine from a double helix

apurinic site

where the purine is missing from

deamination

going from an amine to ketone

- C becomes U
- A becomes G like

transposable elements

cis elements that can move within a genome

mutagen

agent that increases the mutation reate

base analog

compound like a regular N base that take the place of a regular purine or pyrimidine

alkylating agent

adds alkyl groups

intercalating agents

molecules that insert themselves between nucleotides causing a change in the double helix shape
- i.e. ethidium bromide

abduct forming agent

molecule that binds to DNA preventing replication

DNA polymerase III

possesses 3' to 5' exonuclease activity

mismatch repair

fixes insertion, deletions, incorrect base pair matching

DNA methylation

the regular addition of methyl groups to newly synthesized strands

DNA adenine methylase

actively adds methyl groups to DNA strands

post replication repair

filling in the gaps on DNA strains synthesized from unrepaired strands

homologous recombination repair

1) remove a piece of DNA from a homolog
2) insert section into new strand to fill gap
3) fill the gap left on homolog during regular synthesis

SOS repair system

replicating highly damaged DNA (mismatched/gaps) to create strands that still have the damage

photylase

fixes pyrimidine dimers that have extra bonds because of UV damage restoring proper helix structure

excision repair

1) endonuclease removes mistakes and neighboring nucleotides
2) DNA Pol adds nucs to 3' of gap
3) Ligase seals

base excision repair

replaces incorrect base pairs

1) DNA glycolase cuts N base from sugar
2) AP endonuclease cutes out sugar without base
3) DNA polymerase inserts correct nucleotides
4) Ligase seals

apyrimindic site

section on a sugar from a nucleotide where the N base is missing

nucleotide excision repair

replaces incorrect nucleotides influencing helix structure

1) uvr proteins cut nuc+neighbors
2) DNA pol fills in using opp strands as template
3) ligase seals

uvr protein

UV repair protein

heterokaryon

having two nuclei in 1 cell (shared cytoplasm)

double stranded break

when both strands of DNA are cut

homologous recombination

fixing a double stranded break using a sister chromatids

1) enzyme exposes 3' end
2) broken chromosome finds a sister chromatid
3)each broken strand uses the opposite strand on the sister as a template to fill in gap (3' to 5' aligns with 5' to 3')

nonhomologous end joining

fixing a double stranded break by sealing gap with relatively random insertions and deletions

indel

insertion or deletion caused by nonhomologous end joining

innate immunity

defense used against all pathogens

adaptive immunity

defense used against a pathogen seen before because of learning

virus

can be a phage or bacteriophage

CRISPR locus

where spacers and direct repeats are stored

spacer

sections of the virus genome

Cas

CRISPR associated

CRISPR-Cas

system that creates virus immunity in bacteria

spacer acquisition

taking in the viral sequence in bacterial genome
1) Cas9 searched for PAM sequences
2) Cas9 cuts after one PAM and before the next
3) Cas1 and Cas2 carry/insert the viral piece into bacterial genome behind the leader sequence

cRNA biogenisis

transcription and usage of cRNA to fight a virus
1)RNA polymerase transcribes all of CRISPR locus
2) Cas9, tracrRNA, and cRNA attach together
3) cRNA is cleaved
4) cRNA, Cas9, and tracrRNA find viral DNA
5) cleave viral DNA by using PAM or cRNA
6) produces a double stranded break

HNH

cuts viral DNA based on cRNA sequence

RuvC

cuts viral DNA on 5' end of PAM

Cas9

a nuclease complex that is essential to CRISPR

CRISPR-Cas Type I

has stem loops and cascade nuclease activity

CRISPR-Cas Type III

uses Cas10 nuclease

CRISPR-Cas Type II

uses Cas9, tracrRNA, HNH, and RuvC

homology directed repair

using a sister chromosome or homolog as a template to fix damage

sgRNA

manufactured length to RNA that includes cRNA and tracrRNA

transgenic organism

has genes of two unrelated species

golden rice

rice that allows humans to get additional vitamin A

biolistic gene modification

Method of gene modification that is very inefficient

1) coat target plasmid in metal
2) shoot plasmid at cell with gene gun
3) hope DNA incorporates into chromosome

agrobacterium mediated gene modification

More accurate method of gene modification

1) insert Ti plasmid into tumor causing bacteria
2) insert T-DNA into plant cell

Ti plasmid

has localization signal, eukaryotic promoter, Cas1/Cas2 type genes, and target gene

marker gene

an additional gene inserted along with the target that can be easily tested for to track gene incorporation