• Promoter - lies close gene initiation site
• Enhancer - can lie far away from a gene, can be pointing in any direction, Augment or repress basal levels of transcription

• a tool for studying gene regulation
• identify promoters and enhancers

test used for finding cis elements?

trans elements?

• promoter trap
• mapping, biochemical studies for transcription factors

promoter trap?

transcription factors are?

Enhancesome?

• repeatedly cloning sections of DNA b4 a gene to find one that causes a difference in transcription( Enhancer trap as well)
• protein that binds to target genes' cis acting elements (block enhancesome)
• repressor or actvator

1. makes rRNA
2. recognizes promoter with one or more enhancers
3. tRNA and other small RNA's(snRNA)

1. TBP (TATA box binding protein) binds to promoter
2. then TAF to TBP
3. then RNA pol II to TAF

• TF's
• interact with other proteins to activate and increase transcription of DNA by as much as 100 fold

• DNA binding domain
• transcription-activator domain

• steroid hormone
• steroid binds to receptor to change its shape to allow it to bind to enhancer
• zinc finger
• helix-turn-helix

Co-Activator

co-repressor

take apart activator protein gene into sections and insert b4 a reporter gene

then see which section produces transcription

homomer

heteromer

• multimeric proteins that contain identical subunits
• multimeric proteins that contain nonidentical subunits

1. They can stop the activation of the gene, but the expression remains at basal levels
2. they can completely stop transcription by binding to promoter

Activator - repressor competition?

Quenching?

• Activator and repressor compete for who binds the enhancer. if repressor binds, there is no activation
• Quenching -1) the repressor binds to the activators DNA binding site  2)repressor binds to activation domain of activator

• cell type
• gene it is regulating

Chromatin structure?

Genomic imprinting? epigenetic?

• hypercondensation slows transcription
• silendces transcription selectively if inherited from one parent. whatever is causing the silencing of the gene, it is not encoded in the DNA, but inherited from outside the gene

• Protein modification
• RNA splicing
• RNA stability

What do methyl groups do?

how can they be detected?

insulator?

• get in the way of RNA pol
• use restriction enzymes that usually cut DNA but dont this time becuase DNA is methylated. RUn southern blot see differnces in length
• insulated promoter blocks gene from enhancer activity

promoter

DNase hypersensitive sites

RNA interference  is?

miRNA's composed of?

• trans acting single stranded microRNA's that regulate eukaryotic gene expression
• 60-120 base pairs of sequence complimentiarity. regualtes after transcription

1. after transcription Drosha recognizes pri-miRNA and crops it out
2. Actively transported into cytoplasm and recognized by dicer
3. dicer forms a di-miRNA complex that is quickly turned into functional miRNA by RISC

1. if miRNA is completely complementary to other RNA than it cleaves the RNA and it is rapidly degraded by RNase
2. if miRNA is only partially complementary then it stays bound to the RNA and represses its espression

• carries 37 genes, 16.5 kb in length, no introns
• four times longer, 25% introns, spacers separate genes

endosymbiont theory?

evidence?

• the theory that eukaryotes engulfed bacteria cells and are living symbiotically together today

• mt and cpDNA are similar to that of bacteria
• inhibitors of bacterial translation have same effect on cp and mtDNA but not nuclear DNA.

• COXII gene - gene found in nuclear DNA in some plants and mt DNA in other plants
• nuclear copy lacks introns suggesting an RNA intermediate

• chunks of cpDNA are found in mtDNA

heteroplasmic

homoplasmic

contain a mixture of organelle DNA

contain one type of organelle

different

same

• degradation of male gametes
• paternal organelle genomes are distributed to cells that are destined to be destroyed
• after fertilization the paternal organelle is destroyed

1. infinite population
2. no mutation
3. no immigration/emmigration
4. random sex
5. no selection

evolution

micro?

macro?

• changing of allele frequency over time
• micro - generation to generation within a species
• over geological time among species

fitness

natural selection

• ability to survive and pass on gene's
• individuals with higher fitness reproduce more often than individuals with lower fitness

Waht is W?

s?

• recalibrating allele frequency due to selection
• selection coefficient that subtracts from 1

• becuase the recessive allele can be maintained in heterozygotes who have no disadvantage, or may even have an advantage(malaria)

• is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population
• could lead to speciation and evolution of new species (forms new equilibrium for sure)

1. fast life cycle
2. strong selection by antibiotics
3. human error
4. large population densities
5. variety of ways genes are transfered

multifactorial

quantitative

polygenic

• multiple factors that contribute to a trait either biological or environmental
• continous trait that varies of a range measurement
• quantitative trait that is controlled by two or more genes

difference from curve to mean in identical plants is?

difference from curve to curve is?

environmental variance

genetic variance

• straight line - correlation between parent and offspring having the same attributes
•  random no correlation between parent and offspring

• combination of markers
• look for combination between haplotype and disease phenotype
• helps narrow down chromosome function and markers that are linked to disease