Review 16-18Review 16-18 The search for the genetic material The search for the genetic material

involved many experimentsinvolved many experiments

Griffin-transformationGriffin-transformation Hershey/Chase –Sulfur/PhosphorusHershey/Chase –Sulfur/Phosphorus

Franklin & Wilikins/Watson & Crick-double Franklin & Wilikins/Watson & Crick-double helix w/bases in middle held together by helix w/bases in middle held together by H-bondsH-bonds

Antiparallel Antiparallel

Chargoff’s base-pairing rules-A/T & C/GChargoff’s base-pairing rules-A/T & C/G

Transformation-assimilation of external Transformation-assimilation of external DNA into a cellDNA into a cell

DNA replication:DNA replication:

Begins @ origin of replication (bubbles)Begins @ origin of replication (bubbles)

Helicase- separates strandsHelicase- separates strands

Ss binding proteins stabalize strandsSs binding proteins stabalize strands

Leading strand is made by DNA pol adding Leading strand is made by DNA pol adding nt’s 1 by 1 in the 5’ to 3’ directionnt’s 1 by 1 in the 5’ to 3’ direction

Primase attaches to other strand & Primase attaches to other strand & makes RNA primer for Okazaki makes RNA primer for Okazaki fragmentsfragments

DNA pol adds nt’s to the primer DNA pol adds nt’s to the primer fragment fragment

Ligase binds the fragments together Ligase binds the fragments together by covalent bondsby covalent bonds

DNA pol’s proofread nt’s & if 1 is DNA pol’s proofread nt’s & if 1 is found to be wrong it takes it out & found to be wrong it takes it out & replaces itreplaces it

Mistakes not caught right away are Mistakes not caught right away are cut out later by enzymes called cut out later by enzymes called nucleasesnucleases

This is called nt excision repairThis is called nt excision repair

Telomeres-nt seq’s at the ends of Telomeres-nt seq’s at the ends of chromosomeschromosomes

They protect DNA from being eroded They protect DNA from being eroded after many cycles of replicationafter many cycles of replication

They protect the genes on the end of They protect the genes on the end of chromosomeschromosomes

They get shorter w/each replication & They get shorter w/each replication & are shorter in older people’s cellsare shorter in older people’s cells

Telomerase-lengthens the telomeres Telomerase-lengthens the telomeres in germ cells & compensates for the in germ cells & compensates for the shortening that occurs w/replicationshortening that occurs w/replication

Not active in most somatic cellsNot active in most somatic cells

Germ cells give rise to gametesGerm cells give rise to gametes

Ch 17Ch 17 From gene to proteinFrom gene to protein

DNA- A T C G; dsDNA- A T C G; ds RNA- A U CG; ssRNA- A U CG; ss

Adenine is in DNA, RNA, & ATPAdenine is in DNA, RNA, & ATP

1 gene 1 pp1 gene 1 pp

Txn-in the nucleus it is written from Txn-in the nucleus it is written from DNA templateDNA template

mRNA processing-then the introns mRNA processing-then the introns are cut out & a cap & tail is addedare cut out & a cap & tail is added

In the cytoplasm it is translated at the In the cytoplasm it is translated at the ribosome into a ppribosome into a pp

Codons-3 letter words that code for Codons-3 letter words that code for each aa during tslneach aa during tsln

Look at pg 314Look at pg 314

What is the possible seq of nt’s in the What is the possible seq of nt’s in the template strand of DNA that would template strand of DNA that would code for the pp phe-leu-ile-ala-val?code for the pp phe-leu-ile-ala-val?

Aaa-gaa-taa-cga-caaAaa-gaa-taa-cga-caa

What pp will be made fromWhat pp will be made from

Aug-ucu-uca-uua-ucc-uuu?Aug-ucu-uca-uua-ucc-uuu?

Met-ser-ser-leu-ser-pheMet-ser-ser-leu-ser-phe

Txn 3 stagesTxn 3 stages

Initiation, elongation, terminationInitiation, elongation, termination

Initiation begins w/initiation complexInitiation begins w/initiation complex A promoter region on DNAA promoter region on DNA Including the TATA box ~25 nt’s Including the TATA box ~25 nt’s

upstream from start pointupstream from start point

Txn factors bind to help RNA pol bindTxn factors bind to help RNA pol bind

DNA strands unwindDNA strands unwind RNA pol transcribes mRNARNA pol transcribes mRNA

Remember way back to cell Remember way back to cell signaling?signaling?

Txn factors can be signals from Txn factors can be signals from hormones or other moleculeshormones or other molecules

Used to turn genes on or off by Used to turn genes on or off by blocking txnblocking txn

ElongationElongation

RNA pol moves downstream RNA pol moves downstream unwinding DNA and elongating RNA unwinding DNA and elongating RNA transcript in 5’transcript in 5’→3’ direction→3’ direction

Double helix reforms as RNA pol moves Double helix reforms as RNA pol moves on down the lineon down the line

TerminationTermination

Eventually RNA is released and RNA Eventually RNA is released and RNA pol falls off pol falls off

Not yet completely understood what Not yet completely understood what mechanism causes thismechanism causes this

Modification of RNA B4 leaving Modification of RNA B4 leaving nucleusnucleus

Introns (non-coding regions) are cut Introns (non-coding regions) are cut outout

A polyA tail is added to 3’end & a cap A polyA tail is added to 3’end & a cap is added to 5’ endis added to 5’ end

Evolutionary role of introns:Evolutionary role of introns:

Some have seq’s that control gene activitySome have seq’s that control gene activity

Some genes code for more than 1 pp Some genes code for more than 1 pp depending on which segments are treated depending on which segments are treated as exons during RNA processingas exons during RNA processing

This is alternative RNA splicingThis is alternative RNA splicing

**The presence of introns allows **The presence of introns allows exons to be moved around more exons to be moved around more easily (exon shuffling) making new easily (exon shuffling) making new proteins w/new combinations of proteins w/new combinations of functional domainsfunctional domains

Tsln also 3 parts:Tsln also 3 parts: Initiation, elongation, teminationInitiation, elongation, temination

The players: mRNA, tRNA, The players: mRNA, tRNA, aminoacyl-tRNA synthetase, aminoacyl-tRNA synthetase, ribosomesribosomes

Structure of tRNAStructure of tRNA aa at 1 end & anticodon on other endaa at 1 end & anticodon on other end Anticodon is complemetary to codonAnticodon is complemetary to codon

The function of the ribosome in pp The function of the ribosome in pp synthesis is :synthesis is :

To hold the mRNA & tRNA together,To hold the mRNA & tRNA together, catalyze the addition of aa’s form catalyze the addition of aa’s form

tRNA’s to the pp chain, tRNA’s to the pp chain, & to move the mRNA along & eject & to move the mRNA along & eject

tRNA during translocationtRNA during translocation

initiation stage of tslninitiation stage of tslnBrings together mRNA, tRNA Brings together mRNA, tRNA

bearing the 1bearing the 1stst aa of the pp, & 2 aa of the pp, & 2 subunits of a ribosomesubunits of a ribosome

The small ribosomal subunit binds The small ribosomal subunit binds w/mRNAw/mRNA

An aminoacyl-tRNA binds to the A An aminoacyl-tRNA binds to the A sitesite

A peptide bonds forms b/w new aa & A peptide bonds forms b/w new aa & pppp

tRNA translocates to P sitetRNA translocates to P site tRNA leaves P site & P site is vacant tRNA leaves P site & P site is vacant

until another tRNA has given up their until another tRNA has given up their aaaa

TerminationTermination

The final stage of tsln is terminationThe final stage of tsln is termination the ribosome reaches a stop codon the ribosome reaches a stop codon

in the mRNAin the mRNA

The pp may undergo further The pp may undergo further modification B4 it becomes a modification B4 it becomes a functional proteinfunctional protein

A polyribosome is a group of A polyribosome is a group of ribosomes the read a single mRNA at ribosomes the read a single mRNA at the same timethe same time

While it’s being made the pp will start While it’s being made the pp will start to fold & coil spontaneouslyto fold & coil spontaneously

But…b4 it can do it’s job some aa’s But…b4 it can do it’s job some aa’s made be modified by the addition of made be modified by the addition of sugars, lipids, phosphate groups, sugars, lipids, phosphate groups, etc….etc….

Sometimes the pp is cut into pieces Sometimes the pp is cut into pieces b4 it is functionalb4 it is functional

If the pp is destined for the If the pp is destined for the endomembrane system or secretion endomembrane system or secretion it’s marked by a signal peptideit’s marked by a signal peptide

This targets the pp to the ERThis targets the pp to the ER

The signal peptide is recognized by The signal peptide is recognized by by SRP’s (signal-recognition particle)by SRP’s (signal-recognition particle)

The signal is usually removed & then The signal is usually removed & then the rest of the pp is finishedthe rest of the pp is finished

If it is to be secretory protein it is If it is to be secretory protein it is released into ER solnreleased into ER soln

Mutations- Mutations- point mutationspoint mutations are the are the most common kindmost common kind

They are the change of 1 ntThey are the change of 1 nt Substitutions usually missense Substitutions usually missense

(codes for aa but not the right one)(codes for aa but not the right one)

Nonsense mutation (point mutation Nonsense mutation (point mutation that codes for a stop codon where that codes for a stop codon where there should not be one)there should not be one)

Pro’s vs Euk’sPro’s vs Euk’s Prok have circular DNA & so don’t Prok have circular DNA & so don’t

have telomeres & has only 1 origin of have telomeres & has only 1 origin of replicationreplication

Txn & tsln take place at the same Txn & tsln take place at the same time in prok’s (prok’s have no time in prok’s (prok’s have no nucleus)nucleus)

Prok’s don’t have introns!Prok’s don’t have introns!

Ch 18Ch 18 Viruses have a genome but can only Viruses have a genome but can only

replicate w/in a host cellreplicate w/in a host cell

Viruses are obligate parasites b/c Viruses are obligate parasites b/c they cannot reproduce outside of a they cannot reproduce outside of a host cellhost cell

Phages can have 2 types of life cyclesPhages can have 2 types of life cycles

lysogenic- viral DNA is replicated w/host lysogenic- viral DNA is replicated w/host DNADNA

Lytic cycle- (virulent phages) host is Lytic cycle- (virulent phages) host is destroyed after making many baby virusesdestroyed after making many baby viruses

Viral structure is a nucleic acid which Viral structure is a nucleic acid which can by ss or ds DNA or RNAcan by ss or ds DNA or RNA

surrounded by capsid (protein shell)surrounded by capsid (protein shell) ** ONLY some viruses have a viral ** ONLY some viruses have a viral

envelopeenvelope

Viruses that use ssRNA & reverse Viruses that use ssRNA & reverse transcriptase are retrovirusestranscriptase are retroviruses

Vaccines & nucleoside analogs Vaccines & nucleoside analogs (interfers w/viral nucleic acid (interfers w/viral nucleic acid synthesis) are the only effective synthesis) are the only effective weapons against virusesweapons against viruses

Viroids are the simplest infectious Viroids are the simplest infectious biological systemsbiological systems

Prions are misfolded versions of Prions are misfolded versions of normal brain proteinsnormal brain proteins

Gene transfer & recombination in Gene transfer & recombination in bacteriabacteria

Transformation-external DNA is Transformation-external DNA is assimilated by a cellassimilated by a cell

Transduction-DNA is transferred from Transduction-DNA is transferred from 2 bacteria to another by a virus2 bacteria to another by a virus

Transposition-A seq of DNA is moved Transposition-A seq of DNA is moved to alternate locations in the genometo alternate locations in the genome

Conjugation-a group of F+ bacteria is Conjugation-a group of F+ bacteria is mixed w/group of F- bacteria (after mixed w/group of F- bacteria (after days all are F+)days all are F+)

Also a plasmid is exchanged via a Also a plasmid is exchanged via a piluspilus

What is an operon?What is an operon? A promoter, operator, & the genes A promoter, operator, & the genes

they controlthey control They are all part of the DNAThey are all part of the DNA

An operon can be turned off by a An operon can be turned off by a repressor (protein) that binds to the repressor (protein) that binds to the operator & blocks txn by blocking the operator & blocks txn by blocking the attachment of RNA polattachment of RNA pol

The repressor is a product of a The repressor is a product of a regulatory gene (in this case called regulatory gene (in this case called trpR) trpR)

Regulatory genes are always on at a Regulatory genes are always on at a low ratelow rate

An inducer inactivates the repressorAn inducer inactivates the repressor

What is a ligand?What is a ligand?

EXPLAINEXPLAIN replication in detail replication in detail EXPLAINEXPLAIN how a gene in a eukaryotic cell is how a gene in a eukaryotic cell is

transcribed & translated to produce a transcribed & translated to produce a protein. protein. DrawDraw these processes & label RNA these processes & label RNA Polymerase, pre-mRNA, mRNA, introns, Polymerase, pre-mRNA, mRNA, introns, exons, spliceosome, ribosome, tRNA, exons, spliceosome, ribosome, tRNA, codon, anticodon codon, anticodon

EXPLAIN EXPLAIN what changes may occur to the what changes may occur to the mRNA b4 it leaves the nucleusmRNA b4 it leaves the nucleus

EXPLAIN EXPLAIN how the genetic material from 1 how the genetic material from 1 bacterial cell enters another via bacterial cell enters another via transformation, transduction, or conjugationtransformation, transduction, or conjugation

In fruit flies, the phenotype for eye color & In fruit flies, the phenotype for eye color & wing shape is determined by certain loci. wing shape is determined by certain loci. EE indicates the dominant allele and indicates the dominant allele and ee indicates the recessive allele for eye color indicates the recessive allele for eye color and and WW is normal wings and is normal wings and ww is vestigial is vestigial wings. The cross between a fruit fly with wings. The cross between a fruit fly with wild-type eyes and vestigial wings & sepia wild-type eyes and vestigial wings & sepia eyes with normal wings (wild-type) yielded eyes with normal wings (wild-type) yielded the following results for the F1 generation:the following results for the F1 generation:

Wild-typeWild-type sepia/normal sepia/normal wild-type/vestigial wild-type/vestigial sepia/vestigialsepia/vestigial

F1F1 100100 00 00 00

F2F2 5252 1616 2323 99

Determine the genotypes of the Parental (P) generation.Determine the genotypes of the Parental (P) generation. Show a Punnett square cross of the P generation and Show a Punnett square cross of the P generation and

the F1 generation (to show the expected F2 results)the F1 generation (to show the expected F2 results) Use the Chi-square test to determine your chi-square Use the Chi-square test to determine your chi-square

value of the observed vs. expected ratios.value of the observed vs. expected ratios. How many degrees of freedom is there in this analysis?How many degrees of freedom is there in this analysis?

A virus is an infectious particle that A virus is an infectious particle that replicate using the metabolic machinery of replicate using the metabolic machinery of their bacterial, animal, or plant host. Viral their bacterial, animal, or plant host. Viral infections may destroy the host cell and infections may destroy the host cell and cause disease within the host organism.cause disease within the host organism.

Describe the basic structure of a virusDescribe the basic structure of a virus Why are they not considered alive?Why are they not considered alive? What is a prion?What is a prion? How does a vaccine work?How does a vaccine work?