AP Bio units 6.3-6.8

central dogma

flow of genetic info from DNA to RNA to a protein

DNA

• stores genetic info

• 2x stranded helix

• deoxyribose sugar & phosphate backbone

• AGCT

• cell nucleus & mitochondria

RNA

• transmit & copy genetic info

• 1 stranded helix

• ribose sugar & phosphate backbone

• AGCU

• cytoplasm

mRNA structure

• single strand of RNA

• code copied form DNA template

mRNA function

carry code to ribosome to create protein

tRNA structure

• 1 strand RNA

• looped to expose anticodon on 1 side & AA binding site on other

tRNA function

carry specific AA to ribosome when anticodon matches mRNA codon

rRNA structure

• 1 strand RNA

• interacts w/ proteins to form ribosome

rRNA function

catalyze the addition of AAs to polypeptide chain during protein synthesis

transcription

cell makes mRNA to copy DNA code

gene is expressed when…

transcription factors recruit RNA polymerase to the promoter region of said gene

RNA polymerase

• does transcription

• reads 3’ → 5’ direction

antisense strand

• aka template strand

• complementary to mRNA

sense strand

• aka nontemplate strand

• same sequence as mRNA

prokaryotes transcription

• transcription & translation can occur simultaneously

• ribosomes start translating the RNA before RNA polymerase is done transcribing

transcription in eukaryotes

• RNA transcript is called pre-mRNA

• must be modified by other enzymes before it leaves the nucleaus

RNA processing in eukaryotes steps

1. capping

2. polyadenylation

3. splicing

capping

• GTP added to the 5’ end

• helps ribosome recognize the mRNA

polyadenylation

• bunch of As added to 3’ end

• makes RNA more stable

splicing

• introns (noncoding segments) are excised (cut out)

• coding segments left called exons

alternative splicing

exons of (some) genes can be spliced together in different combos to make diff versions of a protein from 1 gene

reverse transcriptase in viruses

• retroviruses

  • have reverse transcriptase enzyme

• copies virus’ RNA genome into DNA

• viral DNA is in host genome where it can be transcribed & translated to assemble new viral progeny

translation

• occurs at the ribosome

• mRNA dictates sequence of AAs in the polypeptide via codon-anticodon matches w/ tRNA

ribosomes

• present in the cytoplasm of all cells

• eukaryotes have ribosomes on rough ER

  • transport proteins to the Golgi for modification & export

• mitochondria & chloroplasts have their own ribosomes

codons & anticodons

• mRNA read in codons

• each codon codes for 1 AA via genetic code

• codons match w/ anticodons on tRNAs → correct seq of AAs bound 2gether

where do AAs come from

• made in metabolic pathways or from diet

• hang around in cytoplasm waiting to be picked up by tRNA

3 steps of translation

1. initiation

2. elongation

3. termination

initiation

• rRNA recognizes mRNA start codon AUG

  • AUG codes for AA methionine (met)

elongation

• ribosome moves along the mRNA

• tRNA brings in AAs as directed by codons

• AAs added to growing polypeptide via peptide bonds

termination

• ribosome reaches on of 3 mRNA stop codons

• polypeptide released

• may/may not need to undergo further modifications to be a functional protein

codon charts

used to decode mRNA codons

universality of genetic code

• we can take a gene from 1 species & integrate it into another

  • it will still make the same protein

• all living organisims use the same genetic code

• evidence for common ancestry of life

mutation

any alteration in a DNA sequence

• can change structure or amount of a protein

effects of mutations

• may or may not lead to actual changes in a protein &/or phenotype

• can be beneficial/detrimental/neutral

neutral mutation reasons

• location

  • occurs in noncoding region that doesn’t affect gene regulation

• silent mutation

  • changes nucleotide sequence w/o changing AAs

• no effect on phenotype

  • type/amount of protein changes but in a way that doesn’t effect the phenotype

mutation causes

• errors in DNA replication or DNA repair mechanisms

• external factors (mutagens)

  • radiation & reactive chemicals

if a mutation is on an intron…

mutation will be cut out → no effect

if mutation is on a regulatory region…

may/may not affect the level of transcription based off how it affects binding of transcription factors

if mutation is on coding region…

may/may not affect affect structure &/or protein function depending on how AA seq is affected

point mutation

• when 1 nucleotide has been substituted for a different nucleotide

• can have variety of effects depending on how it changes the AA at that location

types of point mutations

1. nonsense

2. silent

3. missense

nonsense point mutation

codon mutates to a premature stop codon→ shortened protein, severity depends on location

silent point mutation

codon codes for same AA → no effect on protein

missense point mutation

codon codes for a different AA if AA is …

• similar → little effect on protein

• dissimilar → large change in protein structure & function

frameshift mutations

1+ nucleotides inserted/deleted causing reading frame to be shifted

natural selection& mutations

• new gene variations & combinations may increase fitness(ability to pass on genes) of an individual

• lets pops adapt via natural selection

mutations & the environment

• if a mutation is beneficial detrimental or neutral depends on env contest

• ie sickle cell anemia allele beneficial in malarial regions not in others

processes that increase genetic variation

• all organisms: mutation

• eukaryotes: sexual reproduction

• prokaryotes: horizontal gene transfer

mutations in unicellular organisms

all mutations contribute to genetic variation (passed on through offspring)

mutations in multicellular organisms

only mutations in germline cells will be passed to offspring

mutations in somatic cells will either

• have no effect

• lead to apoptosis

• lead to cancer

horizontal gene transfer

prokaryotes exchange genes

methods of horizontal gene transfer

1. transformation

2. transduction

3. conjugation

4. transposition

transformation

• bacterial cells take up foreign DNA from their environment

• scientists use it to introduce plasmids into study bacteria

transduction

• bacteriophages (viruses) infect bacteria

• can transmit DNA from one bacterial cell to another

conjugation

bacterial have structures called pili which can connect to other bacteria & form tubes to transfer DNA

transposition

• transposable elements=chunks of DNA that “jump” from one place to another

  • can help genes jump into a plasmid so they are more easily shared via conjugation or transformation

viral recombination

related viruses can recombine genetic info if they infect same host cell →new hybrid virus

a gene is expressed when…

it is transcribed & translated into a protein

housekeeping genes

• on all the time (constiutively expressed)

• needed 24/7 for cell maintenance

inducible genes

• can be turned on/off depending on circumstances in the cell

• often occurs via transcription factors

transcription factors

• proteins that bind to regulatory regions of a gene & influence transcription

• may upregulate or downregulate transcription

activators

transcription factors that increase RNA polymerase binding

repressors

transcription factors that decrease RNA polymerase binding

cell specialization

• diff tissues have tissue-specific transcription factors → cell differentiation → cells can perform specific functions

coordinate regulation

• one transcription factor controls multiple genes at 1 time

• prokaryotes & eukaryotes

prokaryotic operons

• groups of genes under the control of 1 promoter

• all transcribed together

• contain an operator region where a repressor protein can bind to block transcription

Lac operon

• contains genes for breaking down lactose sugar

• no lactose present → repressor active → transcription off

• lactose present → lactose binds to repressor → repressor inactivated (can’t bind to operator anymore)→transcription on

Trp operon

• genes needed to synthesize AA tryptophan

• trp present → binds to repressor → activates → transcription off

• no trp present (cell used it up)→ no trp to bind to repressor→ repressor inactive→ transcription on

non transcriptional regulation

• epigenetics

• miRNA/siRNA

• post-translational modifications

epigenetics

• reversible modifications of the structure of DNA or histone proteins

  • ex: DNA Methylation & Histone Acetylation both change how accessible a gene is for transcription

miRNA/siRNA

miRNA (micro RNA) & siRNA (small interfering RNA) are small RNA mols that bind to mRNA after transcription & target it for degradation preventing translation

post -translational modifications

different things added to proteins after translation

genetic engineering techniques can be used to…

analyze & manipulate DNA & RNA

genetic engineering techniques

1. PCR

2. Gel Electrophoresis

3. DNA sequencing

4. Bacterial transformation

Short Tandem Repeats

short sequence of DNA repeated over & over in multiple regions of a person’s DNA

• ppl have diff # of STR repeats → diff # used to identify/compare individual’s DNA

PCR (polymerase chain reaction) main idea

DNA fragments amplified so millions of copies of the targe DNA sequence are produced

PCR steps

1. DNA denaturation

2. primer annealing

3. primer extension

DNA denaturation

DNA heated to separate 2 strands

primer annealing

short primer strands added which are complementary to the start of the target sequence

primer extension

replication enzymes added to extend the primers & produce a 2x stranded DNA molecule

taq polymerase

• replication enzyme that works in extreme heat

• used in PCR

restriction enzymes

enzymes that cut at particular palindromic DNA sequences

gel electrophoresis

separates DNA fragments by size & charge

Steps of Gel electrophoresis

1. DNA samples cut w/ restriction enzymes - each DNA sample has a unique sequence → each cut at diff places & produce diff length segments

2. DNA samples loaded into gel

3. electric current applied to gel- DNA is neg charged so samples will move towards the + charged end, smaller segments will move quicker

4. analyze bands - each DNA segment will produce a unique “DNA fingerprint”

DNA fingerprint analysis steps

1. from child’s bands cross out all that could have been from mom

2. choose father that matches all leftover bands

DNA sequencing

determines the order of nucleotides in DNA molecule

bacterial transformation

• introduces foreign DNA to bacterial cells

• natural process we use to introduce genes of interest into bact via plasmids

  • often use plasmids that also carry an antibiotic resistance gene to select out transformed bacteria