AP bio unit 6

DNA base pairs

C, G, A, T

RNA base pairs

C, G, A, U

purines

A, G - double rings

pyrimidines

T, U, G - single ring

which way is DNA replicated

5’ - 3’

why is DNA replication a semiconservative process

daughter molecules will have one strand of DNA from parent, and one new strand

helicase

unzips

primase

makes RNA primer

DNA polymerase

builds DNA in okazaki fragments and proofreads

ligase

seals fragments of DNA

topoisomerase

unwinds DNA at replication fork and prevents supercoiling

leading vs lagging strand

leading - built continuously (5’-3’ strand of DNA)

lagging - built in okazaki fragments (3’-5’ strand)

DNA and sometimes RNA are …

the primary source of hereditary information

many viruses use RNA to encode genetic information

prokaryotic chromosomes

circular

normally have smaller genomes than eukaryotes

plasmids

additional DNA

both eukaryotes and prokaryotes can carry them

pro. in cytosol and euk. in nucleus

phosphate terminus

5’

hydroxyl terminus

3’

transcription

DNA → mRNA (nucleus)

translation

mRNA → protein (ribosome)

transcription - initiation

• RNA polymerase binds to TATA

• RNA polymerase + transcription factors = transcription initiation process

• DNA partially unwinds and unzips so polymerase can begin matching base pairs

transcription - elongation

• complementary RNA strand grows

• non-template strand = mRNA, template strand = DNA

• RNA polymerase reads DNA 3’-5’ but creates mRNA 5’-3’

transcription - termination

• polyadenylation signal (AAUAAA) causes proteins to cut pre-mRNA from RNA polymerase

• DNA strands rejoin

mRNA post transcription

• addition of poly-A-tail

• addition of GTP cap

• splicing (remove introns by spliceosomes)

alternative splicing

removing introns can cause different patterns of exons which can result in different mRNA sequences

poly-A-tail

long chain of A’s

increases stability and helps mRNA leave nucleus

GTP cap

protects transcript

introns

don’t code for anything

exons

code for amino acids

translation - initiation

• small ribosomal subunit attaches to 5’ end of mRNA at start codon

• chemical initiation factors present

• tRNA attaches to A site

• large ribosomal subunit attaches

• GTP provides energy to join subunits

• first amino acids moved to P site

translation - elongation

• complementary tRNA attaches to A site

• peptide bonds form btw amino acids (needs GTP)

• amino acids moved to P site (GTP needed)

• “empty” tRNA moves to E site (released)

• process repeats until stop codon is reached

translation - termination

• release factors bind to stop codon

• polypeptide freed

• ribosomal subunits detatch

post translational modifications

• proteins can fold into 3D shape

• some proteins need additions before they are functional

  • lipid/phosphate group

  • parts of protein removed

  • quaternary shape

  • secretion of proteins

point mutations

change in 1 nucleotide

• silent: amino acid stays the same

• missense: amino acid changes

• nonsense: early stop codon

frameshift mutation

add/delete one nucleotide

• 1 or 2 base changes: reading frame changes

• 3, 6, or 9 base changes: amino acid removed

mutagens

increase rate of mutation

• UV exposure

• radiation

• chemicals

horizontal acquisition

exchange of hereditary material btw prokaryotes

• transformation: take in DNA from outside

• transduction: virus transfers genetic information btw bacterias

• conjugation: bacteria transfer genetic material by contact

transposition

movement of DNA segments btw/within DNA molecules

• inversion

• translocation

• deletion

• duplication

retrovirus transtation

introduces viral RNA which gets converted to DNA

• results in more viral proteins

protein synthesis - common ancestry

same nucleotides used to construct RNA and DNA

start codon

AUG

errors with chromosomes

• triploidy: 3 copies of chromosome

• polyploidy: multiple homo. chromosomes (makes plant bigger)

regulatory gene

gene in DNA that regulates another

regulatory sequence

found just above gene, allows polymerase to bind

parts of DNA that promote/inhibit protein synthesis

positive control

inducers, “on/off” switch

when repressor attached, operon is off

ex) lactose binds to repressor - repressor changes shape - unbinds to regulatory sequence - polymerase can bind

negative control

repressors

when protein is present, genes deactivate because more of the protein is not needed

initiator

contains operator and promoter site

bioluminescence in nature

• attracts mates

• allows animals to see (hunting)

• defense

bioluminescence in lab (GFP)

• tag cells

• reporter gene (link to gene expresion)

restriction enzyme

cuts DNA at specific restriction sequence

why do bacteria produce restriction enzymes

defense against bacteriaplages

operons

closely linked genes that produce single mRNA molecule - under same regulatory sequence

normally turned off, turned on by inducer

turned off by compressor

methyl tags

silence genes or keep them turned off

• block transcription machinery from binding

• recruit proteins to bind to methylated DNA - causes supercoil

acetylation

turns on genes

• loosen interactions between DNA and histones - transcription is easier

too little methylane

can cause cancer due to fewer blocked genes

too much methylane

can cause cancer due to regulatory/proofreading genes blocked

why is gene control important

• efficiency (save energy by expressing only whats needed)

• cell differentiation

activator

protein that bonds to enhancer region

what percentage of genes do cells use

5-10

purpose of different activators

different gene expression

• cell signals recruit correct transcription factors for specific genes

DNA bending

how bound activators come in contact with mediator proteins

mediatory proteins interact with other proteins at promoter forming transcription initiation complex

microRNA

single strand RNA that can bind to mRNA and prevent protein from being made

level of regulation/protection in protein synthesis

gene expression

DNA → protein

histones

proteins used to wrap DNA around

chemical modifications of DNA/histones cause tight/loose DNA packing

tissues

group of cells with same function due to presence of specific proteins

operator

sequence that inhibits or promotes transcription by binding w/ regulatory proteins

lac operon

positive control example

what charge does DNA have

negative

in electrophoresis, DNA moves to positive end, smaller molecules moving faster and farther

PCR

allows scientists to create large samples of DNA when initially just given a small sample

• DNA is denatured

• primers added

• DNA replicated (get twice as much DNA as originally)