Chapter 16 Notes: Chapter 16 Notes: Molecular Basis of Molecular Basis of

InheritanceInheritance

• ______: Genetic Material______: Genetic Material– Search for Genetic Material: T.H. MorganSearch for Genetic Material: T.H. Morgan

• Discovered that genes are located on Discovered that genes are located on _____________________._____________________.

• Chromosomes are made of _____ chemical Chromosomes are made of _____ chemical components, two possibilities to be genetic material:components, two possibilities to be genetic material:

– _____- very little known about nucleic acids whose _____- very little known about nucleic acids whose properties seemed too uniform to account for the properties seemed too uniform to account for the large amount of inherited traits to be genetic large amount of inherited traits to be genetic material.material.

– __________- Until 1940, proteins seemed to be the __________- Until 1940, proteins seemed to be the more likely option since biochemists had identified more likely option since biochemists had identified them as a class of much heterogeneity and them as a class of much heterogeneity and specificity of function.specificity of function.

• Study of bacteria and _____________ helped discover Study of bacteria and _____________ helped discover the role of DNA in heredity.the role of DNA in heredity.

DNA

CHROMOSOMES

TWO

DNA

PROTEINS

VIRUSES

– Evidence that DNA can _____________ BacteriaEvidence that DNA can _____________ Bacteria

• Frederick Griffith (1928) and (1928) and streptococcus pneumoniaestreptococcus pneumoniae– Griffith had two strains of bacterium: a Griffith had two strains of bacterium: a

________________ (disease-causing) and a ________________ (disease-causing) and a nonpathogenic (harmless)nonpathogenic (harmless)

– Griffith ____________ the pathogenic bacteria with Griffith ____________ the pathogenic bacteria with heat and mixed the remains with living bacteria of heat and mixed the remains with living bacteria of the nonpathogenic strain.the nonpathogenic strain. Some living cells became _______________.Some living cells became _______________.

– This new trait was inherited by all the This new trait was inherited by all the __________________ of the transformed bacteria.__________________ of the transformed bacteria. Conclusions:Conclusions: Some component of the _______ pathogenic cells Some component of the _______ pathogenic cells

caused this change.caused this change. Griffith called this _____________________: now Griffith called this _____________________: now

defined as a change in genotype and phenotype defined as a change in genotype and phenotype due to the assimilation of external DNA by a cell.due to the assimilation of external DNA by a cell.

TRANSFORM

PATHOGENIC

KILLED

PATHOGENIC

DESCENDENTS

DEAD

TRANSFORMATION

Live S- mouse diesLive S- mouse dies Live R- mouse livesLive R- mouse lives

Heat killed S- mouse livesHeat killed S- mouse lives Heat killed S + Live R- Heat killed S + Live R-

mouse dies!mouse dies!

• Oswald Avery (1944)Oswald Avery (1944)– Avery ____________ various types of molecules Avery ____________ various types of molecules

from heat-killed pathogenic bacteria and tried from heat-killed pathogenic bacteria and tried to transform live nonpathogenic bacteria with to transform live nonpathogenic bacteria with each type.each type. Only ________ worked.Only ________ worked. Conclusion: DNA was the __________________ Conclusion: DNA was the __________________

agent.agent.

PURIFIED

DNA

TRANSFORMING

• Hershey and Chase: Evidence Viral DNA can Hershey and Chase: Evidence Viral DNA can ___________ Cells ___________ Cells – Virus: simpler than cells, just DNA (or _______) Virus: simpler than cells, just DNA (or _______)

enclosed by a protective coat (______________).enclosed by a protective coat (______________). To reproduce, a virus must _________ a cell To reproduce, a virus must _________ a cell

to take over the cell’s metabolism.to take over the cell’s metabolism.– _____________________ (phages)- ___________ _____________________ (phages)- ___________

that infect bacteria.that infect bacteria.– Hershey and Chase took a phage (T2) to infect Hershey and Chase took a phage (T2) to infect

E. coliE. coli to discover which component: protein to discover which component: protein or DNA was ________________ to reprogram the or DNA was ________________ to reprogram the host cell to produce viruses.host cell to produce viruses.

PROGRAM

RNAPROTEIN

INFECT

BACTERIOPHAGES VIRUSES

RESPONSIBLE

– ExperimentExperiment First they grew T2 with E. coli in the First they grew T2 with E. coli in the

presence of radioactive ___________. Since presence of radioactive ___________. Since protein, not DNA contains ___________, the protein, not DNA contains ___________, the radioactive atoms were incorporated only radioactive atoms were incorporated only into the protein.into the protein.

The DNA of a separate group of T2 was The DNA of a separate group of T2 was labeled with radioactive _________________ labeled with radioactive _________________ (phage’s phosphorus is in DNA) and left (phage’s phosphorus is in DNA) and left protein unlabeled.protein unlabeled.

The two groups: protein-labeled and DNA The two groups: protein-labeled and DNA labeled T2 infected ______________ samples labeled T2 infected ______________ samples of nonradioactive E. coli cells.of nonradioactive E. coli cells.

Cultures were mixed in a blender to shake Cultures were mixed in a blender to shake loose any parts of the phages that were loose any parts of the phages that were ____________ the bacterial cells.____________ the bacterial cells.

SULFURSULFUR

PHOSPHORUS

SEPARATE

OUTSIDE

Mixtures then spun in a centrifuge to create Mixtures then spun in a centrifuge to create a ________ at the bottom with bacterial cells a ________ at the bottom with bacterial cells and separating the lighter parts (free phages and separating the lighter parts (free phages and parts of phages) to remain suspended in and parts of phages) to remain suspended in the supernatant. the supernatant.

The pellet was then tested for The pellet was then tested for ________________.________________.

•Hear about their cool experiment

PELLET

RADIOACTIVITY

– Results:Results: When bacteria was infected with T2 phage When bacteria was infected with T2 phage

with radioactive proteins most of the with radioactive proteins most of the radioactivity was found in the radioactivity was found in the _________________ which contained phage _________________ which contained phage particles (no bacteria)particles (no bacteria)

Protein of the phage did not Protein of the phage did not _________________ host cells._________________ host cells.

When bacteria was infected with T2 phage When bacteria was infected with T2 phage with radioactive DNA, most of the with radioactive DNA, most of the radioactivity was found in the ________, radioactivity was found in the ________, where the host DNA was.where the host DNA was.

Phage _________ entered the host cells.Phage _________ entered the host cells. E. coli released phages that contained E. coli released phages that contained

radioactive phosphorus.radioactive phosphorus.

SUPERNATANT

ENTER

PELLETDNA

– Conclusion: Conclusion: DNA of the virus is ___________ into the host DNA of the virus is ___________ into the host

cell during infection, leaving the __________ cell during infection, leaving the __________ outside.outside.

Injected DNA provides genetic information Injected DNA provides genetic information that makes cells produce new viral DNA and that makes cells produce new viral DNA and protein which makes new _________________.protein which makes new _________________.

INJECTED

PROTEIN

VIRUSES

• More Evidence: ChargaffMore Evidence: Chargaff– It was known that DNA is a polymer of It was known that DNA is a polymer of

_________________._________________.– Nucleotide Components: Nucleotide Components:

_________________base_________________base 5-carbon _________________5-carbon _________________ _________________ group._________________ group.

– Nitrogenous Bases for DNA: Nitrogenous Bases for DNA: _________________ (A)_________________ (A) _________________ (T)_________________ (T) _________________ (G)_________________ (G) _________________ (C)._________________ (C).

NUCLEOTIDES

NITROGENOUS

SUGAR

PHOSPHATE

ADENINE

THYMINEGUANINE

CYTOSINE

– After analysis, _________________reported that After analysis, _________________reported that DNA composition varies from one species to DNA composition varies from one species to another.another. Humans: 30.3% nucleotides have base __Humans: 30.3% nucleotides have base __ DNA from DNA from E. coliE. coli has ______% base A. has ______% base A. This is evidence of molecular _______________ This is evidence of molecular _______________

among species (more credible as genetic among species (more credible as genetic material).material).

The number of A approximately equaled the The number of A approximately equaled the number of ____ and the number of ___ number of ____ and the number of ___ approximately equaled the number of G. approximately equaled the number of G. This became known as This became known as ______________________.______________________.

– Nucleotide Structure:Nucleotide Structure:

CHARGAFF

A

26.0

DIVERSITY

T C

CHARGAFF’S RULES

– Building a Structural Model of DNABuilding a Structural Model of DNA

•Watson and Crick- First to discover the 3D Watson and Crick- First to discover the 3D ____________ of DNA____________ of DNA

– Watson saw Rosalind _________________ x-ray Watson saw Rosalind _________________ x-ray diffraction image of DNA while visiting Wilkins diffraction image of DNA while visiting Wilkins at King’s College.at King’s College.

– From a glance, Watson was able to identify From a glance, Watson was able to identify DNA was _________________ in shape and was DNA was _________________ in shape and was able to deduce the _____________of the helix and able to deduce the _____________of the helix and ____________ of the nitrogenous bases along it.____________ of the nitrogenous bases along it.

The width suggests that DNA was made of The width suggests that DNA was made of ______ strands (contrary to 3-strand model ______ strands (contrary to 3-strand model by Pauling)by Pauling)

This leads to the term: ____________________.This leads to the term: ____________________.

STRUCTURE

FRANKLIN’S

HELICALWIDTH SPACING

TWO

DOUBLE HELIX

• Watson and Crick built models of a double helix Watson and Crick built models of a double helix to _________________ the x-ray measurements and to _________________ the x-ray measurements and what they knew about the _________________ of what they knew about the _________________ of DNA.DNA.

• Knowing Franklin’s work, they knew she had Knowing Franklin’s work, they knew she had concluded that the sugar-phosphate concluded that the sugar-phosphate _________________ were on the outside of the _________________ were on the outside of the double helix so it put the _________________ double helix so it put the _________________ nitrogenous bases in the molecule’s interior.nitrogenous bases in the molecule’s interior.

• Watson built a model with nitrogenous bases Watson built a model with nitrogenous bases facing the interior of the double helix facing the interior of the double helix – looks like a rope ladder with rigid _______looks like a rope ladder with rigid _______

The side ropes: ___________________________The side ropes: ___________________________ Rungs: _________________ base pairsRungs: _________________ base pairs

• Through trial and error, Watson and Crick Through trial and error, Watson and Crick discovered that nitrogenous bases have specific discovered that nitrogenous bases have specific combinations: ___ with ___ and __ with __.combinations: ___ with ___ and __ with __.

CONFORMCHEMISTRY

BACKBONES

HYDROPHOBIC

RUNGSSUGAR-PHOSPHATE BACKBONES

NITROGENOUS

AT C G

• More about the Bases (memorize):More about the Bases (memorize):– _________________: Cytosine and Thymine have _________________: Cytosine and Thymine have

a single ringa single ring– _________________: Adenine and Guanine are _________________: Adenine and Guanine are

twice as widetwice as wide– Adenine forms _____ hydrogen bonds with Adenine forms _____ hydrogen bonds with

thyminethymine– Guanine forms _____ hydrogen bonds with Guanine forms _____ hydrogen bonds with

cytosine.cytosine.

PYRIMIDINES

PURINES

23

Purines(2 rings)

Pyrimidines(1 ring)

A

G

C

T

Phosphate group

Deoxyribosesugar

•Watson and Crick’s model explained Chargaff’s Watson and Crick’s model explained Chargaff’s rules: because A-T and C-G, there should be an rules: because A-T and C-G, there should be an _________________ amount of A-T and C-G, _________________ amount of A-T and C-G, respectively.respectively.

•A-T and C-G have to bond but, the ________________ A-T and C-G have to bond but, the ________________ of nucleotides can vary.of nucleotides can vary.

– Example:Example:

•Structure of DNA Strand (Figure 16.5)Structure of DNA Strand (Figure 16.5)– 5’ end (with _________________ group) to 3’ end 5’ end (with _________________ group) to 3’ end

(with ______ group). Numbers 5 and 3 refer to (with ______ group). Numbers 5 and 3 refer to numbers assigned to carbons in the ring.numbers assigned to carbons in the ring.

EQUAL

SEQUENCE

AAA-TTT-CGCTTT-AAA-GCG

PHOSPHATEOH

PURINE + PURINE = TOO WIDE

PYRIMIDINE + PYRIMIDINE = TOO NARROW

PURINE + PYRIMIDINE = WIDTHCONSISTENT WITH FRANKLIN’SX-RAY DATA

• Summary of DNA StructureSummary of DNA Structure– DNA is a ________________: it has two strands that DNA is a ________________: it has two strands that

__________________ around each other.__________________ around each other.– Each strand is made of single strands called Each strand is made of single strands called

__________________.__________________.• The two strands are anti-________________.The two strands are anti-________________.

– It has a ______________________ backbone.It has a ______________________ backbone.– Bases join the two strands by __________________.Bases join the two strands by __________________.

• These bases are:These bases are:– __________________ base pairing is a key idea in __________________ base pairing is a key idea in

genetics: _________________________genetics: _________________________– Each strand of DNA can be millions of Each strand of DNA can be millions of

__________________ in length and is coiled up to __________________ in length and is coiled up to make chromosomes.make chromosomes.

• How is the double helix structure maintained? How is the double helix structure maintained?

DOUBLE HELIXWRAP

NUCLEOTIDESPARALLEL

SUGAR-PHOSPHATE

HYDROGEN BONDSA T C G

COMPLEMENTARYCHARGAFF’S RULES

NUCLEOTIDES

HYDROGEN BONDS, VAN DER WAALS FORCES

• Proteins in DNA Replication and RepairProteins in DNA Replication and Repair– Base Pairing to a Template Strand: Watson and Base Pairing to a Template Strand: Watson and

Crick ______-conservative model (Figure 16.9)Crick ______-conservative model (Figure 16.9)

• The _______________ bonding between the two The _______________ bonding between the two strands of DNA needs to be broken to separate strands of DNA needs to be broken to separate the strands.the strands.

• When cells copy DNA, each strand serves as a When cells copy DNA, each strand serves as a ___________ for ordering nucleotides into new, ___________ for ordering nucleotides into new, _________________ strands._________________ strands.

• As nucleotides line up along the template As nucleotides line up along the template strand according to the _________________ rules, strand according to the _________________ rules, they are linked to form new strands.they are linked to form new strands.

• _____ double-stranded DNA become _____ _____ double-stranded DNA become _____ double-stranded DNA molecules, each double-stranded DNA molecules, each _________________ to the “parent” DNA molecule._________________ to the “parent” DNA molecule.

SEMI

HYDROGEN

TEMPLATECOMPLEMENTARY

BASE-PAIRING

ONE TWOIDENTICAL

– Models of DNA Replication (FIG 16.10 DRAW)Models of DNA Replication (FIG 16.10 DRAW)• Semiconservative model (above)-Semiconservative model (above)-

• Conservative model- two parental strands Conservative model- two parental strands _________________ after acting as templates for new _________________ after acting as templates for new strands, restoring the _________________ double helix.strands, restoring the _________________ double helix.

• Dispersive model- each strand of Dispersive model- each strand of bothboth molecules molecules contains a _________________of old and new DNA.contains a _________________of old and new DNA.

REASSOCIATEPARENTAL

MIXTURE

– DNA Replication: DNA Replication: E. coliE. coli

• _________________ of replication: special sites _________________ of replication: special sites where replication of a DNA molecule where replication of a DNA molecule _________________._________________.

• Bacterial chromosome (circular) has a single Bacterial chromosome (circular) has a single origin, a stretch of DNA that has a specific origin, a stretch of DNA that has a specific sequence of _________________.sequence of _________________.

• Proteins that start DNA replication recognize the Proteins that start DNA replication recognize the sequence and attach to DNA, separating the two sequence and attach to DNA, separating the two strands and opening up a replication strands and opening up a replication “____________.”“____________.”

• Replication starts at the origin and moves in Replication starts at the origin and moves in ____________ directions until the entire molecule ____________ directions until the entire molecule is copied. (Figure 18.14)is copied. (Figure 18.14)

• Prokaryotic DNA Replication

ORIGINSBEGINS

NUCLEOTIDES

BUBBLE

BOTH

– DNA Replication: EukaryotesDNA Replication: Eukaryotes

• Eukaryotic _________________ may vary from Eukaryotic _________________ may vary from hundreds to thousands of replication originshundreds to thousands of replication origins

• _________________ bubbles form and eventually _________________ bubbles form and eventually _______ making replication process very quick._______ making replication process very quick.

• DNA replication proceeds in ________ directions DNA replication proceeds in ________ directions from each origin. from each origin.

• Each end of a replication bubble is a Each end of a replication bubble is a ___________________ (___-shaped region where ___________________ (___-shaped region where new strands of DNA are forming).new strands of DNA are forming).

CHROMOSOMES

MULTIPLEFUSE

BOTH

REPLICATION FORK Y

– Elongating a New strand of DNAElongating a New strand of DNA• At the replication fork, DNA replication is At the replication fork, DNA replication is

catalyzed by _________________ called DNA catalyzed by _________________ called DNA polymerase.polymerase.

• Nucleotides line up along the _________________ Nucleotides line up along the _________________ and are added one by one to the growing new and are added one by one to the growing new DNA strand by DNA _________________. (____ DNA strand by DNA _________________. (____ nucleotides/sec in bacteria and ___ nucleotides/sec in bacteria and ___ nucleotides/sec in humans)nucleotides/sec in humans)– Two types of DNA polymerase in Two types of DNA polymerase in E. coliE. coli: DNA : DNA

polymerase III and DNA polymerase I (DNA polymerase III and DNA polymerase I (DNA ______ III and DNA ______ I)______ III and DNA ______ I)

– Eukaryotes have at least ___ different DNA Eukaryotes have at least ___ different DNA polymerases but they work the same way.polymerases but they work the same way.

ENZYMESTEMPLATE

POLYMERASE 50050

POLPOL

11

•Nucleotides added are _________________ (sugar Nucleotides added are _________________ (sugar and base) triphosphates and base) triphosphates

– Triphosphate monomers are chemically Triphosphate monomers are chemically reactive and as each monomer joins a DNA reactive and as each monomer joins a DNA strand, it ______ two phosphate groups as a strand, it ______ two phosphate groups as a molecule of _________________ which then goes molecule of _________________ which then goes through hydrolysis to become inorganic through hydrolysis to become inorganic phosphate which allows polymerization of the phosphate which allows polymerization of the monomer to the strand.monomer to the strand.

NUCLEOSIDE

LOSES

PYROPHOSPHATE

– ____________________ Elongation____________________ Elongation

• Two ends of DNA strand are different and are Two ends of DNA strand are different and are antiparallel since they are orientated in antiparallel since they are orientated in _________________ directions to each other (one _________________ directions to each other (one ________ and the other ________).________ and the other ________).

• As a result of replication, new stands of DNA are As a result of replication, new stands of DNA are antiparallel to template strand.antiparallel to template strand.

• Effect: DNA polymerase only adds nucleotides to Effect: DNA polymerase only adds nucleotides to the free _____ end of a growing DNA strand and the free _____ end of a growing DNA strand and never to the _____ end.never to the _____ end.– new DNA strand can only new DNA strand can only

elongate in the _______elongate in the _______

direction.direction.– DNA replication

ANTI-PARALLEL

OPPOSITE5’ – 3’ 3’ – 5’

3’5’

5’ 3’

• ____________ Strand:____________ Strand:– At one template strand, DNA polymerase III (DNA At one template strand, DNA polymerase III (DNA

pol III) synthesizes a complementary strand by pol III) synthesizes a complementary strand by _________________ the DNA in the 5’_________________ the DNA in the 5’3’ direction.3’ direction.

– DNA pol III _________ on the template and DNA pol III _________ on the template and _________________ adds nucleotides to the _________________ adds nucleotides to the complementary strand as the fork progresses.complementary strand as the fork progresses.

– Resulting DNA strand is called the _________ strand.Resulting DNA strand is called the _________ strand.

• _________________ Strand (occurs at the same time _________________ Strand (occurs at the same time and pace as leading strand)and pace as leading strand)– To elongate the other new strand of DNA in the To elongate the other new strand of DNA in the

mandatory 5’mandatory 5’3’ direction, DNA pol III must work 3’ direction, DNA pol III must work along the other template strand in the direction along the other template strand in the direction _______ from the replication fork._______ from the replication fork.

– Lagging strand synthesis occurs as a series of Lagging strand synthesis occurs as a series of _________________._________________.

LEADING

ELONGATING

RESTSCONTINUOUSLY

LEADING

LAGGING

AWAY

SEGMENTS

– Once a replication bubble opens far enough, a Once a replication bubble opens far enough, a DNA pol III molecule attaches to the lagging DNA pol III molecule attaches to the lagging strand’s ____________ and moves away from the strand’s ____________ and moves away from the replication fork, synthesizing a short segment replication fork, synthesizing a short segment of DNA.of DNA.

– As _________________ grows, another segment of As _________________ grows, another segment of the lagging strand can be made in a similar the lagging strand can be made in a similar way.way. These segments are called _________________ These segments are called _________________

fragments.fragments. These fragments are ~ 100 to 200 These fragments are ~ 100 to 200

nucleotides long in eukaryotes.nucleotides long in eukaryotes.– _________________ joins the phosphate _________________ joins the phosphate

backbones of the Okazaki fragments to form a backbones of the Okazaki fragments to form a single new strand of DNA.single new strand of DNA.

– Okazaki fragmentsOkazaki fragments

TEMPLATE

BUBBLE

OKAZAKI

DNA LIGASE

– Printing DNA SynthesisPrinting DNA Synthesis

• DNA polymerase cannot _________________ DNA DNA polymerase cannot _________________ DNA synthesis but rather adds nucleotides to the 3’ synthesis but rather adds nucleotides to the 3’ end of an ____________ chain on the template end of an ____________ chain on the template strand.strand.

• _________________- initial nucleotide chain (can _________________- initial nucleotide chain (can consist of DNA or RNA).consist of DNA or RNA).

• Leading StrandLeading Strand– In initiating replication of cellular DNA, primer is In initiating replication of cellular DNA, primer is

a short stretch of _____ with available 3’ end.a short stretch of _____ with available 3’ end.– _________________ can start an RNA chain from _________________ can start an RNA chain from

scratch and joins RNA nucleotides together one scratch and joins RNA nucleotides together one by one to make a primer complementary to the by one to make a primer complementary to the template strand where DNA synthesis occurs.template strand where DNA synthesis occurs.

– DNA pol III adds DNA nucleotides to the ______ DNA pol III adds DNA nucleotides to the ______ end of the RNA primer.end of the RNA primer.

INITIATE

EXISTING

PRIMER

RNA

PRIMASE

3’

• Lagging StrandLagging Strand– Okazaki fragments must be primed Okazaki fragments must be primed

_____________._____________.– DNA pol I replaces the ____________________ of DNA pol I replaces the ____________________ of

the primers with DNA versions, adding them the primers with DNA versions, adding them one by one onto the 3’ end of the adjacent one by one onto the 3’ end of the adjacent Okazaki fragment.Okazaki fragment.

– ______________ joins the final nucleotide of the ______________ joins the final nucleotide of the replacement DNA fragment to the first DNA replacement DNA fragment to the first DNA nucleotide of the Okazaki fragment whose nucleotide of the Okazaki fragment whose _________ was just replaced._________ was just replaced.

SEPARATELYRNA NUCLEOTIDES

DNA LIGASE

PRIMER

– Other Proteins that Help with DNA Replication (We Other Proteins that Help with DNA Replication (We should know DNA polymerase, ligase, primase)should know DNA polymerase, ligase, primase)

• _________________- enzyme that untwists double _________________- enzyme that untwists double helix at the replication forks and separates the helix at the replication forks and separates the two parental strands.two parental strands.

• _________________- the untwisting causes strain _________________- the untwisting causes strain ahead of the replication fork which is lessened ahead of the replication fork which is lessened by topoisomerase.by topoisomerase.

• _____________________________________- binds to _____________________________________- binds to unpaired DNA strands after the parent strands unpaired DNA strands after the parent strands are separated, stabilizing them until they serve are separated, stabilizing them until they serve as templates for DNA synthesis. as templates for DNA synthesis.

• DNA Replication proteins (choose 3)DNA Replication proteins (choose 3)

HELICASE

TOPOISOMERASE

SINGLE STRANDED BINDING PROTEIN

– DNA Replication- StationaryDNA Replication- Stationary

• DNA polymerases are sometimes represented as DNA polymerases are sometimes represented as _________ molecules but are probably stationary. _________ molecules but are probably stationary.

• There are _______ copies of each protein that There are _______ copies of each protein that work together as a “machine”work together as a “machine”

MOVING

MANY

• Proofreading and RepairProofreading and Repair– The accuracy of DNA is not only a result of The accuracy of DNA is not only a result of

______________ rules.______________ rules.– Errors occur about one in ten ________ nucleotides.Errors occur about one in ten ________ nucleotides.– During replication, DNA polymerase ______________ During replication, DNA polymerase ______________

each nucleotide against the template when the each nucleotide against the template when the strand is growing.strand is growing.

• If an ____________ nucleotide is found, it ___________ If an ____________ nucleotide is found, it ___________ the nucleotide and continues synthesis.the nucleotide and continues synthesis.

BASEPAIRING

BILLION

PROOFREADS

INCORRECT REMOVES

– ExceptionsExceptions

•Mismatched nucleotides can _______ proofreading.Mismatched nucleotides can _______ proofreading.

•Mismatching may arise after DNA synthesis is Mismatching may arise after DNA synthesis is completed from _________________ to nucleotide basecompleted from _________________ to nucleotide base

•Mismatch _________________: enzymes are used to fix Mismatch _________________: enzymes are used to fix incorrectly paired nucleotides.incorrectly paired nucleotides.

– What is the effect of missing mismatch repair What is the effect of missing mismatch repair enzymes?enzymes?

– Damage and Change in DNADamage and Change in DNA

•_________________ from the environment and _________________ from the environment and surrounding cells, radioactive emissions, x-rays, ____ surrounding cells, radioactive emissions, x-rays, ____ light can change nucleotides which affect coding of light can change nucleotides which affect coding of DNA.DNA.

•DNA bases can also have spontaneous changes under DNA bases can also have spontaneous changes under normal conditions and are usually corrected by repair normal conditions and are usually corrected by repair enzymes before they become _________________.enzymes before they become _________________.

AVOID

DAMAGE

REPAIR

CHEMICALSUV

MUTATIONS

– Repairing DNA- Nucleotide Excision Repairing DNA- Nucleotide Excision

RepairRepair

•Segment of DNA strand containingSegment of DNA strand containing

damaged is _________________ damaged is _________________

(excised) by _________________ (excised) by _________________

(DNA-cutting enzyme)(DNA-cutting enzyme)

•DNA polymerase (___________) DNA polymerase (___________)

and ligase (_________ DNA) will and ligase (_________ DNA) will

then fill in the gap with nucleotidesthen fill in the gap with nucleotides

that are _________________ to that are _________________ to

the proper strand.the proper strand.

CUT OUTNUCLEASE

FILLS GAPS

COMPLEMENTARY

SEALS

– Example: Skin CellsExample: Skin Cells

•UV rays from the sun can _________ the DNA in our UV rays from the sun can _________ the DNA in our skin cells: skin cells:

•Adjacent _________________ can form a covalent Adjacent _________________ can form a covalent bond between each other which creates a thymine bond between each other which creates a thymine dimer _________ in the DNA strand that can dimer _________ in the DNA strand that can interfere with DNA replication.interfere with DNA replication.

•Xeroderma pigmentosum: individuals who have a Xeroderma pigmentosum: individuals who have a ________ in nucleotide excision repair enzyme________ in nucleotide excision repair enzyme

– Effects: ___________________ to sunlight, Effects: ___________________ to sunlight, mutations in skin cells cause by UV light which mutations in skin cells cause by UV light which are left uncorrected and cause skin _________.are left uncorrected and cause skin _________.

DAMAGE

THYMINE

BUCKLE

DEFECT

HYPERSENSITIVITY

CANCER

• Replicating Ends of DNAReplicating Ends of DNA– DNA polymerase cannot replicate or repair the ___ DNA polymerase cannot replicate or repair the ___

ends of daughter DNA strands. Why?ends of daughter DNA strands. Why?

•DNA polymerase can only add nucleotides to a ___ DNA polymerase can only add nucleotides to a ___ end of a preexisting _________________.end of a preexisting _________________.

– Example: RNA primer on ends of 5’ of template Example: RNA primer on ends of 5’ of template strandsstrands

•Result: More rounds of replication produce Result: More rounds of replication produce ___________ DNA molecules.___________ DNA molecules.

– Prokaryotes do not show this problem since their Prokaryotes do not show this problem since their DNA is ___________ with no ends.DNA is ___________ with no ends.

5’

3’NUCLEOTIDE

SHORTER

CIRCULAR

– Telomeres (_________________only)Telomeres (_________________only)

•Definition: nucleotide sequences that do not Definition: nucleotide sequences that do not contain _________________ but rather multiple contain _________________ but rather multiple _________________ of a short nucleotide sequence._________________ of a short nucleotide sequence.

•Example: TTAGGG can be repeated 100-1,000 Example: TTAGGG can be repeated 100-1,000 times in a telomere.times in a telomere.

EUKARYOTES

GENESREPETITIONS

•Functions:Functions:– telomeric DNA protects genes from being telomeric DNA protects genes from being

__________ through successive rounds of DNA __________ through successive rounds of DNA replication.replication.

– Telomeric DNA and proteins around it prevent Telomeric DNA and proteins around it prevent staggered ends of daughter molecule from staggered ends of daughter molecule from _________________ cell’s systems for monitoring _________________ cell’s systems for monitoring DNA damage (end of DNA with missing piece)DNA damage (end of DNA with missing piece)

– Telomeres do Telomeres do notnot _________ the shortening of _________ the shortening of DNA molecules due to successive rounds of DNA molecules due to successive rounds of replication; they delay the erosion of genes near replication; they delay the erosion of genes near the ______ of DNA molecules.the ______ of DNA molecules.

Telomeres become __________ after every Telomeres become __________ after every round of replication.round of replication.

Some believe that shortened telomeres are Some believe that shortened telomeres are related to the _______ of tissues/organisms.related to the _______ of tissues/organisms.

ERODED

ACTIVATING

PREVENT

ENDS

SHORTER

AGING

CANCERLIMITS THE

SHORT

LENGTHENING

SHORTENING

ZYGOTE

SELF DESTRUCT

• DNA and Chromosome StructureDNA and Chromosome Structure– Nucleosomes hold the DNA together to form the Nucleosomes hold the DNA together to form the

“___________” of chromosomes“___________” of chromosomes– Picture:Picture:

BEADS

– Histone proteins allow DNA to be __________________.Histone proteins allow DNA to be __________________.

•15,000x more dense, so takes up less space in the 15,000x more dense, so takes up less space in the nucleus.nucleus.

•Supercoiled sections of genes cannot be Supercoiled sections of genes cannot be __________________ (cannot be opened up for __________________ (cannot be opened up for transcription).transcription).

•Supercoiling allows for _____________ over which Supercoiling allows for _____________ over which genes are expressed: to express a gene, the genes are expressed: to express a gene, the region of the chromosome must be region of the chromosome must be __________________.__________________.

SUPERCOILED

EXPRESSED

CONTROL

UNCOILED

GENESHERITABLE

CHARACTERISTICSSINGLE COPYREPETITIVE

POLYPEPTIDES

AMINO ACID

EXONSINTRONS

5-45

JUNK

SATELLITE

FINGERPRINTING

MUTATIONS

PHENOTYPE

Homework

•Pg 298 #1-4

•Pg 307 #1-4

•Self Quiz pg 308

Chapter 17 Notes: Gene to Protein

• Genes Specify Proteins Through ________________ and Genes Specify Proteins Through ________________ and ________________________________

– Study of Metabolic Defects: EvidenceStudy of Metabolic Defects: Evidence• Achibald GarrodAchibald Garrod

– Hypothesized that symptoms of inherited Hypothesized that symptoms of inherited disorders reflected the inability to make a disorders reflected the inability to make a particular ________________ which is due to a particular ________________ which is due to a _________._________.

– Example: Alkaptonuria- dark colored urine Example: Alkaptonuria- dark colored urine because the chemical alkapton cannot be because the chemical alkapton cannot be __________________ due to missing enzyme__________________ due to missing enzyme

– Beadle and Tatum Experiment: Beadle and Tatum Experiment: Neurospora crasaNeurospora crasa (bread mold)(bread mold)

• Exposed Exposed NeurosporaNeurospora to X-rays to separate mold to X-rays to separate mold– Wild-type can live in _____________ mediumsWild-type can live in _____________ mediums– Mutants ____________ live in minimal mediums Mutants ____________ live in minimal mediums

but only complete growth mediumsbut only complete growth mediums

TRANSCRIPTIONTRANSLATION

ENZYME GENE

BROKEN DOWN

MINIMALCANNOT

• Wanted to discover the __________________ in Wanted to discover the __________________ in each mutanteach mutant– Separated vials with minimal medium plus a Separated vials with minimal medium plus a

single __________________single __________________– Growth in a vial indicated that mutants had a Growth in a vial indicated that mutants had a

metabolic __________________ for that specific metabolic __________________ for that specific nutrient.nutrient.

– Example: Growth is observed in a vial with Example: Growth is observed in a vial with __________________; can conclude that mutant __________________; can conclude that mutant is defective for the pathway that wild-types is defective for the pathway that wild-types use to synthesize __________________.use to synthesize __________________.

DEFECT

NUTRIENT

DEFECT

ARGININE

ARGININE

– One gene-oneOne gene-one __________________ hypothesis __________________ hypothesis one gene-one polypeptideone gene-one polypeptide Researchers suspected that: Researchers suspected that:

precursor nutrientprecursor nutrient orinthineorinthinecitrullinecitrullineargininearginine

Three classes of mutants: Tested for growth Three classes of mutants: Tested for growth on orinthine and citrullineon orinthine and citrulline

One could grow on _______ and arginineOne could grow on _______ and arginine One only grew on citrulline or One only grew on citrulline or

____________________________________ One only grew with __________________One only grew with __________________ Conclusion: three classes are blocked at Conclusion: three classes are blocked at

__________________ steps for pathway that __________________ steps for pathway that synthesizes arginine: each class lacking an synthesizes arginine: each class lacking an _________ that catalyzes the blocked step._________ that catalyzes the blocked step.

Fig 17.2 pg 311Fig 17.2 pg 311

ENZYME

BOTH

ARGININEARGININE

DIFFERENT

ENZYME

– What is the purpose of transcription and What is the purpose of transcription and translation?translation?

• Genes are __________________ for proteins or Genes are __________________ for proteins or messages.messages.– The cell needs to take the instructions and The cell needs to take the instructions and

__________________.__________________.

• In transcription, the gene is converted into an In transcription, the gene is converted into an ____________ messenger which attaches to the ____________ messenger which attaches to the __________________.__________________.– The ribosomes then translate the message The ribosomes then translate the message

into a __________________. The sequence of into a __________________. The sequence of amino acids is determined by the gene, and it amino acids is determined by the gene, and it determines the properties of the finished determines the properties of the finished __________________.__________________.

INSTRUCTIONS

CARRY THEM OUT

mRNARIBOSOMES

POLYPEPTIDE

PROTEIN

– Examples of proteins:Examples of proteins:

• The Central Dogma of GeneticsThe Central Dogma of Genetics–

• Genes are simply codes for making Genes are simply codes for making __________________.__________________.

• DNA is stored in the nucleus, yet the polypeptide is DNA is stored in the nucleus, yet the polypeptide is produced in the _____________ (by ____________).produced in the _____________ (by ____________).

• mRNA is a message from the nucleus to the mRNA is a message from the nucleus to the ribosome- _______________ for how to put the ribosome- _______________ for how to put the polypeptide together.polypeptide together.

• The genetic code is the ___________ of bases on The genetic code is the ___________ of bases on mRNA- this tells the ribosome which amino acids to mRNA- this tells the ribosome which amino acids to use.use.

POLYPEPTIDES

CYTOPLASM RIBOSOMES

INSTRUCTIONS

SEQUENCE

– Transcription and Translation in BriefTranscription and Translation in Brief• Differences between DNA and RNADifferences between DNA and RNA

– RNA nucleotides contain ________ instead of RNA nucleotides contain ________ instead of deoxyribosedeoxyribose

– Nitrogenous bases are A, G, C, U Nitrogenous bases are A, G, C, U (_______________) instead of A, G, C, T.(_______________) instead of A, G, C, T.

– RNA molecule is ________ stranded (usually), RNA molecule is ________ stranded (usually), while DNA is double strandedwhile DNA is double stranded

RIBOSE

URACILSINGLE

•Transcription (DNA and RNA share a “language” Transcription (DNA and RNA share a “language” ____________________)____________________)

– Location: ___________Location: ___________– Synthesis of RNA under direction of DNA.Synthesis of RNA under direction of DNA.– DNA strand serves as a template for DNA strand serves as a template for

assembling a sequence of RNA nucleotides.assembling a sequence of RNA nucleotides.The result is a transcript of gene’s protein-The result is a transcript of gene’s protein-

building instructionsbuilding instructionsMessenger RNA (mRNA)- carries genetic Messenger RNA (mRNA)- carries genetic

message from DNA to protein-synthesizing message from DNA to protein-synthesizing organelles of the cell.organelles of the cell.

NUCLEOTIDES

NUCLEUS

• Translation (change in “language” from Translation (change in “language” from ______________ ______________ __________________) __________________)– Location: ______________Location: ______________– Synthesis of a polypeptide under direction of Synthesis of a polypeptide under direction of

______________.______________.

• Why is RNA used as instructions for protein synthesis Why is RNA used as instructions for protein synthesis as opposed to DNA?as opposed to DNA?– Using RNA instead of DNA ______________ DNA in the Using RNA instead of DNA ______________ DNA in the

nucleusnucleus Example: ______________ and building plansExample: ______________ and building plans

– RNA allows ______________ copies of a protein to be RNA allows ______________ copies of a protein to be made as many RNA can be made from one gene.made as many RNA can be made from one gene.

• ____________________________: Transcription : Transcription Translation: DNA Translation: DNA mRNA -mRNA - polypeptide polypeptide

• ______________: Transcription ______________: Transcription RNA Processing RNA Processing Translation: DNA Translation: DNA pre-mRNA pre-mRNA mRNA mRNA polypeptide polypeptide

AMINO ACIDSNUCLEOTIDESRIBOSOMES

mRNA

PROTECTS

ARCHITECT

MORE

PROKARYOTES

EUKARYOTES

– Genetic CodeGenetic Code

• Codons: ______________of BasesCodons: ______________of Bases– ______________code: genetic instructions for ______________code: genetic instructions for

polypeptides are written in DNA as a series of polypeptides are written in DNA as a series of ________-nucleotide fragments.________-nucleotide fragments.

– Example: AGT codes for construction of the Example: AGT codes for construction of the amino acid ______________.amino acid ______________.

• Code in TranscriptionCode in Transcription– ______________ strand: one of the two DNA ______________ strand: one of the two DNA

strands transcribed to make mRNA.strands transcribed to make mRNA.– Coding strand- _______________ DNA strandCoding strand- _______________ DNA strand– mRNA is ___________________ to DNA template mRNA is ___________________ to DNA template

because RNA also follows base-pairing rules with because RNA also follows base-pairing rules with the exception that ____ substitutes for ____ (U-A)the exception that ____ substitutes for ____ (U-A)

– mRNA is _______________ to the template strand.mRNA is _______________ to the template strand.

TRIPLETS

TRIPLET

THREE

SERINE

TEMPLATE

NON TEMPLATECOMPLEMENTARY

U T

ANTIPARALLEL

– mRNA read in the ___________ directionmRNA read in the ___________ direction mRNA base triplets are called mRNA base triplets are called

____________________________– Translation: codons are decoded Translation: codons are decoded

(______________) into a sequence of amino (______________) into a sequence of amino acidsacids

– Example: 3’ ACCAAACCGAGT 5’Example: 3’ ACCAAACCGAGT 5’

– ______________ frame- correct groupings of ______________ frame- correct groupings of codonscodons Need to use correct reading frame to Need to use correct reading frame to

receive intended ________________.receive intended ________________.

5’ 3’

CODONS

TRANSLATED

READING

POLYPEPTIDES

• Universality of genetic codeUniversality of genetic code– all living things have the ________________code.all living things have the ________________code.– all living things have the same all living things have the same

________________.________________.– codons code for the same ___________________, codons code for the same ___________________,

no matter what organismno matter what organism

• The universal code is degenerate (redundant)The universal code is degenerate (redundant)– There are ___ codons but only ___ amino acids There are ___ codons but only ___ amino acids

(plus stop)(plus stop)– The same amino acid may be coded for by The same amino acid may be coded for by

____________________ codon.____________________ codon.– Reduced impact of base-substitution Reduced impact of base-substitution

________________, as amino acid produced ________________, as amino acid produced could still be the ________________.could still be the ________________.

SAME

BASESAMINO ACID

64 20

MORE THAN ONE

MUTATIONSAME

• Transcription in detailTranscription in detail

– Terms to know:Terms to know:

• RNA polymerases (each has a specific promoter RNA polymerases (each has a specific promoter sequence it recognizes)sequence it recognizes)– RNA polymerase IRNA polymerase I

only transcribes ______________genesonly transcribes ______________genes makes ______________makes ______________

– RNA polymerase IIRNA polymerase II Transcribes genes into ______________Transcribes genes into ______________

– RNA polymerase IIIRNA polymerase III only transcribes ______________genesonly transcribes ______________genes

rRNA

RIBOSOMES

mRNA

tRNA

• Promoter: DNA sequence where RNA polymerase Promoter: DNA sequence where RNA polymerase attaches and ______________ transcription attaches and ______________ transcription (binding site)(binding site)

• Terminator- sequence that signals the Terminator- sequence that signals the ______________ of transcription______________ of transcription

• Transcription unit- area of DNA transcribed into Transcription unit- area of DNA transcribed into RNA moleculeRNA molecule

• Transcription ______________- mediate binding of Transcription ______________- mediate binding of RNA polymerase and ______________ of RNA polymerase and ______________ of transcriptiontranscription– Need specific factors to bind to the promoter Need specific factors to bind to the promoter

before RNA polymerase II ______________.before RNA polymerase II ______________.

BEGINS

END

FACTORSINITIATION

BINDS

• Transcription initiation complexTranscription initiation complex– Transcription ______________Transcription ______________– RNA polymerase II bound to ______________RNA polymerase II bound to ______________

______________ box: promoter DNA ______________ box: promoter DNA sequence important in forming sequence important in forming transcription initiation complex.transcription initiation complex.

– Transcription Steps:Transcription Steps:• InitiationInitiation

– The promoter region which starts with a TATA The promoter region which starts with a TATA box has _________________ factors bind to the box has _________________ factors bind to the DNA strand (one binds to the TATA box).DNA strand (one binds to the TATA box).

– RNA polymerase II and additional transcription RNA polymerase II and additional transcription factors bind to DNA forming the transcription factors bind to DNA forming the transcription ______________ complex.______________ complex.

– Fig 17.8 pg 316Fig 17.8 pg 316

FACTORSPROMOTER

TATA

TRANSCRIPTION

INITIATION

• RNA polymerase II ______________ DNA and RNA polymerase II ______________ DNA and begins to synthesize RNA at the ______________ begins to synthesize RNA at the ______________ point (part of the promoter) of the template point (part of the promoter) of the template strand.strand.– RNA is synthesized by adding ______________ RNA is synthesized by adding ______________

triphosphates which become nucleotides that triphosphates which become nucleotides that are bound by a __________________ bond are bound by a __________________ bond between nucleotides.between nucleotides.

• ElongationElongation– RNA polymerase II adds nucleotides to the RNA polymerase II adds nucleotides to the

________ end of the growing RNA molecule as ________ end of the growing RNA molecule as it ______________ along the strand.it ______________ along the strand.

– RNA separates from the DNA template (and RNA separates from the DNA template (and RNA polymerase) allowing the double helix to RNA polymerase) allowing the double helix to ______________.______________.

UNTWISTSSTART

NUCLEOSIDE

PHOSPHODIESTER

3’MOVES

RE-FORM

• Termination of Transcription (________________)Termination of Transcription (________________)– Transcription moves through a ______________ Transcription moves through a ______________

sequence in DNA.sequence in DNA.– The transcripted terminator (RNA sequence) The transcripted terminator (RNA sequence)

acts as the termination ______________.acts as the termination ______________.– This causes RNA polymerase to ______________ This causes RNA polymerase to ______________

from the DNA and release the ______________ from the DNA and release the ______________ molecule.molecule.

PROKARYOTES

TERMINATOR

SIGNALDETACHmRNA

• Termination of Transcription (eukaryotes)Termination of Transcription (eukaryotes)– Pre-mRNA is ______________ from the growing RNA Pre-mRNA is ______________ from the growing RNA

chain while RNA polymerase II continues to chain while RNA polymerase II continues to transcribe DNA.transcribe DNA.

– Polymerase transcribes a sequence on DNA called Polymerase transcribes a sequence on DNA called polyadenylation signal (AAUAAA) sequence in pre-polyadenylation signal (AAUAAA) sequence in pre-mRNA.mRNA.

– About 10-35 nucleotides away from AAUAAA signal, About 10-35 nucleotides away from AAUAAA signal, proteins cut the RNA transcript free from proteins cut the RNA transcript free from polymerase and release the ______________.polymerase and release the ______________.

– Polymerase ______________ transcribing for Polymerase ______________ transcribing for hundreds of nucleotides where pre-mRNA was hundreds of nucleotides where pre-mRNA was released.released.

– Transcription is Transcription is ______________ ______________ when when polymerase falls off DNA (reason unknown). polymerase falls off DNA (reason unknown). (no terminator sequence)(no terminator sequence)

– RNA processing follows.RNA processing follows.

CLEAVED

PRE-mRNA

CONTINUES

TERMINATED

• How does transcription occur?How does transcription occur?– Since RNA polymerase II is moving along the Since RNA polymerase II is moving along the

DNA strand, it allows ______________ molecules DNA strand, it allows ______________ molecules of RNA polymerase II molecules to follow each of RNA polymerase II molecules to follow each other.other.

– This allows the ________________ production of This allows the ________________ production of RNA.RNA. more mRNA = more ______________more mRNA = more ______________

MANY

SIMULTANEOUS

PROTEIN

See anothertranscriptionanimation

Transcription animation Transcription animation too

• RNA ProcessingRNA Processing– Diagram of RNA ProcessingDiagram of RNA Processing

– RNA Splicing (fig. 17.10 pg 318)RNA Splicing (fig. 17.10 pg 318)• RNA has segments that do not have genes.RNA has segments that do not have genes.

– Introns (intervening)- ______________segments Introns (intervening)- ______________segments of nucleic acid ______________the coding regionsof nucleic acid ______________the coding regions

– Exons (expressed)- coding regions that will be Exons (expressed)- coding regions that will be coded into ________________ sequences.coded into ________________ sequences.

• RNA polymerase II ______________both introns and RNA polymerase II ______________both introns and exons from DNA but mRNA that enters the exons from DNA but mRNA that enters the cytoplasm has the introns cut out allowing exons cytoplasm has the introns cut out allowing exons to __________ together (RNA ______________).to __________ together (RNA ______________).

• RNA Splicing EnzymesRNA Splicing Enzymes– ______________- small nuclear RNA, proteins______________- small nuclear RNA, proteins– SpliceosomeSpliceosome

several ______________several ______________ recognize ______________site sequence; cut recognize ______________site sequence; cut

and ______________ geneand ______________ gene

NONCODINGBETWEEN

AMINO ACIDTRANSCRIBES

JOINSPLICING

snRNPs

snRNPsSPLICE

PASTE

• ______________ -RNA molecules that function as ______________ -RNA molecules that function as enzymes enzymes (In some organisms pre-RNA can (In some organisms pre-RNA can ______________its own introns)______________its own introns)

– Alternative SplicingAlternative Splicing

• Alternative mRNAs produced from same geneAlternative mRNAs produced from same gene– when is an intron not an ______________when is an intron not an ______________– different segments treated as ______________.different segments treated as ______________.

RIBOZYMES

REMOVE

INTRON

EXONS

– Modifying mRNA EndsModifying mRNA Ends•The ends of a pre-mRNA molecule is modified.The ends of a pre-mRNA molecule is modified.

– ____ Cap- 5’ end (transcribed first) of mRNA is ____ Cap- 5’ end (transcribed first) of mRNA is capped with a modified ______________ capped with a modified ______________ nucleotide.nucleotide.

– ______________ tail- 3’ end has 50-250 A ______________ tail- 3’ end has 50-250 A nucleotides.nucleotides.

•Functions:Functions:– Facilitate export of mature mRNA to nucleusFacilitate export of mature mRNA to nucleus– Protect mRNA from ________________ by Protect mRNA from ________________ by

enzymesenzymes– Both help ______________attach to 5’ end of Both help ______________attach to 5’ end of

mRNA.mRNA.

5’GUANINE

POLY-A

DEGRADATIONRIBOSOMES

• TranslationTranslation– mRNA (message in codons) is interpreted into mRNA (message in codons) is interpreted into

_______________________ that will later fold into a _______________________ that will later fold into a ______________.______________.

– Transfer RNA (tRNA)- transfer amino acids to the Transfer RNA (tRNA)- transfer amino acids to the growing end of a _________________ from pool of growing end of a _________________ from pool of amino acids to a ______________.amino acids to a ______________.

• Structure : contains an amino acid at one end Structure : contains an amino acid at one end and an _______________ at the other end.and an _______________ at the other end.

– Anticodon- nucleotide ______________that can Anticodon- nucleotide ______________that can pair with a complementary ______________ on pair with a complementary ______________ on mRNA.mRNA.

– Example: Example:

AMINO ACIDSPROTEINS

POLYPEPTIDERIBOSOME

ANTICODONTRIPLETCODON

– tRNA is transcribed from _______, made in the tRNA is transcribed from _______, made in the ______________ and needs to travel from the ______________ and needs to travel from the nucleus to the _________________ (location of nucleus to the _________________ (location of translation).translation).

– tRNA can be used _________________ by picking tRNA can be used _________________ by picking up its specific amino acid in the ______________ up its specific amino acid in the ______________ and depositing the amino acid at the and depositing the amino acid at the ribosome, leaving to pick up another amino ribosome, leaving to pick up another amino acid.acid.

– tRNA has a 3D structure (__-shaped) that folds tRNA has a 3D structure (__-shaped) that folds back upon itself due to ______________ bonding.back upon itself due to ______________ bonding. Loop ______________ from one end of the Loop ______________ from one end of the

structure.structure. 3’ end of tRNA is location where amino acid 3’ end of tRNA is location where amino acid

______________.______________.

DNANUCLEUS

RIBOSOME

REPEATEDLYCYTOPLASM

LHYDROGEN

PROTRUDING

ATTACHES

– As mRNA molecules move through the As mRNA molecules move through the ______________, tRNA ______________amino acids in ______________, tRNA ______________amino acids in the order of codons of mRNA and they are joined the order of codons of mRNA and they are joined ______________ by the ribosome.______________ by the ribosome.

– tRNA is known as the ______________because it can tRNA is known as the ______________because it can read nucleic acids (__________) and interpret it to read nucleic acids (__________) and interpret it to ______________ (amino acid).______________ (amino acid).

RIBOSOMEDEPOSITS

TOGETHER

TRANSLATORmRNA

PROTEIN

– Translation requires two ______________ stepsTranslation requires two ______________ steps

• Correct match between ______________and an Correct match between ______________and an amino acid: tRNA that binds to an mRNA codon amino acid: tRNA that binds to an mRNA codon coding for a particular amino acid must only carry coding for a particular amino acid must only carry that amino acid.that amino acid.– Amino acids are joined to correct tRNA by an Amino acids are joined to correct tRNA by an

enzyme called aminoacyl-tRNA ______________.enzyme called aminoacyl-tRNA ______________. Active site of each aminoacyl-tRNA Active site of each aminoacyl-tRNA

synthetase fits a ______________ amino acid synthetase fits a ______________ amino acid and tRNA (___ different synthetases).and tRNA (___ different synthetases).

Synthetase catalyzes the covalent bond Synthetase catalyzes the covalent bond between the amino acid to the tRNA driven between the amino acid to the tRNA driven by the hydrolysis of _______.by the hydrolysis of _______.

aminoacyl tRNA is released from the aminoacyl tRNA is released from the enzyme and delivers amino acid to the enzyme and delivers amino acid to the ______________.______________.

RECOGNITION

tRNA

SYNTHETASE

SPECIFIC 20

ATP

RIBOSOME

• Correct match between tRNA anticodon and an Correct match between tRNA anticodon and an __________ codon.__________ codon.– 45 possible _________: some tRNA are able to 45 possible _________: some tRNA are able to

bind to more than _____ codon.bind to more than _____ codon.– This is a result of the rules for base paring This is a result of the rules for base paring

between third base of a ______________ and between third base of a ______________ and corresponding base of a tRNA anticodon not corresponding base of a tRNA anticodon not being as ______________ as for DNA and mRNA.being as ______________ as for DNA and mRNA. Example: base U at 5’ end of a tRNA Example: base U at 5’ end of a tRNA

anticodon can pair with either A or G (3’ anticodon can pair with either A or G (3’ end) of a mRNA codon.end) of a mRNA codon.

This relaxation of base-pairing rules is called This relaxation of base-pairing rules is called ______________.______________.

Explains why codons can differ in a third Explains why codons can differ in a third base but can code for the ______________ base but can code for the ______________ amino acid.amino acid.

mRNAtRNA’sONE

CODON

STRICT

WOBBLE

SAME

– RibosomesRibosomes

• Diagram:Diagram:

Ribosomes are made up of two Ribosomes are made up of two ______________: large and small.______________: large and small.

Ribosomal subunits are made of proteins and Ribosomal subunits are made of proteins and ______________.______________.

For eukaryotes, subunits are made in the For eukaryotes, subunits are made in the ______________.______________.

SUBUNITS

rRNA

NUCLEOLUS

• Ribosomal RNA genes on the chromosomal DNA Ribosomal RNA genes on the chromosomal DNA are ______________, RNA is processed and are ______________, RNA is processed and assembled with proteins and are then exported assembled with proteins and are then exported to the ______________.to the ______________.

• Both prokaryotes and eukaryotes have their Both prokaryotes and eukaryotes have their subunits join to from a functional ______________ subunits join to from a functional ______________ only when they attach to an mRNA molecule.only when they attach to an mRNA molecule.

• 2/3 of the mass of a ribosome is ________, most 2/3 of the mass of a ribosome is ________, most cells contain thousands of RNA, rRNA is most cells contain thousands of RNA, rRNA is most ______________ type of RNA.______________ type of RNA.

TRANSCRIBED

CYTOPLASM

RIBOSOME

rRNA

ABUNDANT

• Structure: Structure: – ______________ site: ribosome binds to mRNA ______________ site: ribosome binds to mRNA

and it (ribosome) moves through as codons and it (ribosome) moves through as codons are matched with tRNA anticodons.are matched with tRNA anticodons.

– P site (______________-tRNA site)- holds tRNA P site (______________-tRNA site)- holds tRNA carrying the growing polypeptide carrying the growing polypeptide ______________.______________.

– A site (______________-tRNA site)- holds tRNA A site (______________-tRNA site)- holds tRNA carrying the next amino acid to be carrying the next amino acid to be ______________.______________.

– E site (______________)- discharged _____ leave E site (______________)- discharged _____ leave the ribosome from this site. the ribosome from this site.

• As polypeptide becomes ______________ (and As polypeptide becomes ______________ (and eventually complete), it passes through exit eventually complete), it passes through exit tunnel in ribosome’s large subunit.tunnel in ribosome’s large subunit.

BINDING

PEPTIDYLCHAIN

AMINOACYLADDED

EXIT tRNA

LONGER

• Building a Polypeptide (Three Stages analogous to Building a Polypeptide (Three Stages analogous to _________________)_________________)

– InitiationInitiation

• ________ ribosomal subunit binds to an mRNA ________ ribosomal subunit binds to an mRNA molecule and a specific initiator tRNA (carries molecule and a specific initiator tRNA (carries ______________). ______________).

• Small subunit moves downstream along mRNA until it Small subunit moves downstream along mRNA until it reaches ______________ codon (_____).reaches ______________ codon (_____).

– Start codon is important because it establishes a Start codon is important because it establishes a ____________ frame for mRNA.____________ frame for mRNA.

• Then the large ribosomal subunit attaches completing Then the large ribosomal subunit attaches completing a _______________ initiation complex. Initiation factors a _______________ initiation complex. Initiation factors (___________) are needed to bring these parts together.(___________) are needed to bring these parts together.

• Cell must spend energy (_____) to from the complexCell must spend energy (_____) to from the complex

• At the end of initiation, the initiator tRNA sits in the At the end of initiation, the initiator tRNA sits in the ___ site of the ribosome and vacant ____ site is ready ___ site of the ribosome and vacant ____ site is ready for the next aminoacyl tRNA.for the next aminoacyl tRNA.

TRANSCRIPTION

SMALLMETHIONINE

START AUG

READING

TRANSLATIONPROTEINS

GTPP

A

– Elongation- Amino acids are added one by one to Elongation- Amino acids are added one by one to the ______________ amino acid.the ______________ amino acid.

• Codon recognition- ______________ of an incoming Codon recognition- ______________ of an incoming aminoacyl tRNA pairs with a mRNA ______________ aminoacyl tRNA pairs with a mRNA ______________ in the A site. GTP goes under hydrolysis to in the A site. GTP goes under hydrolysis to increase accuracy and efficiency.increase accuracy and efficiency.

• ______________ bond formation- rRNA molecule of ______________ bond formation- rRNA molecule of the large subunit catalyzes formation of a peptide the large subunit catalyzes formation of a peptide bond between new amino acid in A site and bond between new amino acid in A site and ______________ end of growing polypeptide in ___ ______________ end of growing polypeptide in ___ site. This attaches polypeptide to tRNA in A site.site. This attaches polypeptide to tRNA in A site.

• Translocation- Translocation- – ribosome translocates ______ in A site to P siteribosome translocates ______ in A site to P site– Empty tRNA in P site is moved to E site where it Empty tRNA in P site is moved to E site where it

is ______________. is ______________. – mRNA moves along with bound tRNAs bringing mRNA moves along with bound tRNAs bringing

next _______ to be translated.next _______ to be translated.

PREVIOUSANTICODON

CODON

PEPTIDE

CARBOXYLP

tRNA

RELEASED

CODON

– TerminationTermination

• Elongation continues until a ______________ codon Elongation continues until a ______________ codon in mRNA reaches A site.in mRNA reaches A site.– Stop codons: UAG, UAA, UGA act as a Stop codons: UAG, UAA, UGA act as a

______________ to stop translation______________ to stop translation– Release factors bind to stop codon in the A Release factors bind to stop codon in the A

site and causes addition of a water instead of site and causes addition of a water instead of an amino acid to the polypeptide chain which an amino acid to the polypeptide chain which ______________ the polypeptide and releases it ______________ the polypeptide and releases it through the exit tunnel.through the exit tunnel.

– Translation assembly will then come Translation assembly will then come ______________.______________.

STOP

SIGNAL

HYDROLYZES

APART

• Completing a Functional ProteinCompleting a Functional Protein– Protein ______________Protein ______________

• During synthesis a chain begins to coil and fold During synthesis a chain begins to coil and fold _________________ forming a functional protein _________________ forming a functional protein with secondary and ______________ structure.with secondary and ______________ structure.

• Gene determines ______________ structure which Gene determines ______________ structure which will determine conformation.will determine conformation.

• Chaperone protein assist in ______________.Chaperone protein assist in ______________.

FOLDING

SPONTANEOUSLYTERTIARY

PRIMARY

FOLDING

– Post-translational modificationsPost-translational modifications

•Amino acids may be chemically ______________ by Amino acids may be chemically ______________ by the attachment of sugars, lipids, phosphate the attachment of sugars, lipids, phosphate groups, etc.groups, etc.

•Enzymes may ______________ one or more amino Enzymes may ______________ one or more amino acids from leading (amino) end of polypeptide acids from leading (amino) end of polypeptide chain.chain.

•Single polypeptide chain may be ______________ Single polypeptide chain may be ______________ into at least two pieces.into at least two pieces.

– Ex: Insulin is only active after an enzyme cuts Ex: Insulin is only active after an enzyme cuts out a central part of __________.out a central part of __________.

MODIFIED

REMOVE

CLEAVED

CHAIN

– Targeting Polypeptides to specific locationsTargeting Polypeptides to specific locations

• ______________ ribosomes make proteins of ______________ ribosomes make proteins of endomembrane system and proteins secreted endomembrane system and proteins secreted from the cell.from the cell.

• Ribosomes are ______________and switch Ribosomes are ______________and switch between bound and ______________.between bound and ______________.

• Polypeptide synthesis always begins in the Polypeptide synthesis always begins in the ______________ when a free ribosome begins to ______________ when a free ribosome begins to translate an mRNA molecule.translate an mRNA molecule.– It moves to completion unless the polypeptide It moves to completion unless the polypeptide

______________ the ribosome to attach to the ______________ the ribosome to attach to the ______.______.

– Polypeptides of proteins in the Polypeptides of proteins in the endomembrane system or for secretion are endomembrane system or for secretion are ______________ by a signal peptide.______________ by a signal peptide.

BOUND

IDENTICALFREE

CYTOSOL

SIGNALSER

MARKED

– Signal peptide is recognized as it emerges by Signal peptide is recognized as it emerges by a protein-RNA complex called a signal a protein-RNA complex called a signal recognition particle (_____) which functions as recognition particle (_____) which functions as an ______________ that brings ribosome to a an ______________ that brings ribosome to a receptor protein in the ER membrane. receptor protein in the ER membrane.

– Polypeptide synthesis continues as the Polypeptide synthesis continues as the polypeptide snakes across the membrane into polypeptide snakes across the membrane into the ER lumen via protein ______________.the ER lumen via protein ______________.

– Signal peptide is removed by an ______________ Signal peptide is removed by an ______________ and the polypeptide is released into the and the polypeptide is released into the solution or embedded in the ER membrane.solution or embedded in the ER membrane.

SRPADAPTER

POREENZYME

Translation 1

Translation animation-step by step

TRANSLATION VIDEOThe Best!

translation 4

• What can go wrong during the previous processes?What can go wrong during the previous processes?

• Point Mutations (______________ mutation)Point Mutations (______________ mutation)– Mutations- changes in ______________ material of a Mutations- changes in ______________ material of a

cell (or virus).cell (or virus).– ____________ mutations- chemical changes in just ____________ mutations- chemical changes in just

one ________ pair of a gene (do not confuse with one ________ pair of a gene (do not confuse with chromosomal mutations)chromosomal mutations)

– Point mutations that occur in gametes lead to Point mutations that occur in gametes lead to these mutations to be passed on to offspring with these mutations to be passed on to offspring with the same mutations and if it affects phenotypes, the same mutations and if it affects phenotypes, it is a ______________ disorder.it is a ______________ disorder.

– Example: Sickle-cell disease- mutation Example: Sickle-cell disease- mutation

SPONTANEOUS

GENETIC

POINTBASE

GENETIC

– Types of Point MutationsTypes of Point Mutations

• Base-pair __________________- replacement of one Base-pair __________________- replacement of one nucleotide and its partner with another nucleotide and its partner with another ______________ of nucleotides.______________ of nucleotides.– ______________mutations- due to redundancy of ______________mutations- due to redundancy of

genetic code, it has _____ effect on the encoded genetic code, it has _____ effect on the encoded protein.protein. Example: 3’-CCG-5’Example: 3’-CCG-5’ 3’-CCA-5’3’-CCA-5’

– ______________ mutations- altered codon still ______________ mutations- altered codon still codes for an amino acid and makes sense, but codes for an amino acid and makes sense, but not the ______________ sense.not the ______________ sense.

– Nonsense mutation- translation is terminated Nonsense mutation- translation is terminated prematurely and the resulting polypeptide will prematurely and the resulting polypeptide will be ______________ than normal.be ______________ than normal. Almost all nonsense mutations lead to Almost all nonsense mutations lead to

nonfunctional ______________.nonfunctional ______________.

SUBSTITUTION

PAIR

SILENTNO

MISSENSE

RIGHT

SHORTER

PROTEINS

• Insertions and DeletionsInsertions and Deletions– Additions or losses of nucleotide pairs in a gene Additions or losses of nucleotide pairs in a gene

that have ______________ effects on resulting protein that have ______________ effects on resulting protein more so than substitutions.more so than substitutions.

– Reason: mRNA is read as a series of ______________ Reason: mRNA is read as a series of ______________ (codons) during translation and an insertion or (codons) during translation and an insertion or deletion may shift the __________________ deletion may shift the __________________ (frameshift mutation).(frameshift mutation).

– Frameshift mutations occur whenever the number Frameshift mutations occur whenever the number of nucleotides inserted or deleted is not a multiple of nucleotides inserted or deleted is not a multiple of ______________.of ______________.

– The rest of the nucleotides after the error will be The rest of the nucleotides after the error will be improperly ______________ into codons which will improperly ______________ into codons which will lead to ______________ and premature termination.lead to ______________ and premature termination.

– Frameshift almost always leads to nonfunctional Frameshift almost always leads to nonfunctional proteins unless the frameshift is at the very proteins unless the frameshift is at the very ________ of the gene.________ of the gene.

DISASTROUS

TRIPLETS

READING FRAME

THREE

GROUPEDNONSENSE

END

– MutagensMutagens

• Definition- physical and chemical agents that Definition- physical and chemical agents that interact with DNA to cause ______________.interact with DNA to cause ______________.

• Effect: can pose hazards to Effect: can pose hazards to ______________material of organisms.______________material of organisms.

• Mutagenic radiation (______________)- UV lightMutagenic radiation (______________)- UV light

• Chemical mutagens- base analogs (bases that Chemical mutagens- base analogs (bases that pair incorrectly during DNA replication), pair incorrectly during DNA replication), chemicals that can change base ______________ chemicals that can change base ______________ rules, chemicals that can interfere with DNA rules, chemicals that can interfere with DNA replication,replication,

MUTATIONS

GENETIC

PHYSICAL

PAIRING

• What is a gene?What is a gene?– A region of DNA whose final product is either a A region of DNA whose final product is either a

polypeptide or RNA molecules.polypeptide or RNA molecules.