Chapter 5: Introduction to the Nli AidNucleic Acidsfaculty.ycp.edu/~jthompso/Biochemistry...

Chapter 5: Introduction to the N l i A idNucleic Acids

DNA, RNA, and the Flow of G i I f iGenetic Information

• DNA and RNA are long polymersg p y– Carry information that is passed on to the next

generationG ti i f ti i t d i th f• Genetic information is stored in the sequence of bases along a nucleic acid chain

• Base pairing occurs• Base pairing occurs• Base pairs provide the mechanism for copying

the genetic information in an existing nucleic g gacid chain to form a new chain.

Central Dogma of Information FlowCentral Dogma of Information Flow

DNA

DNA RNA P t i F ti

DNAWhat is this?

• DNA RNA Protein Function

What is this? What is this? What is this?What is this?

Th G ti C d i C i l!The Genetic Code is Crucial!

General Schematic of a NucleicGeneral Schematic of a Nucleic Acid polymer.

Sugar DifferencesDifferences

Nitrogen Bases in the Nucleic Acids

Making a NucleosideMaking a Nucleoside

N-glycosidicN-glycosidic bond

Nucleosides• Combining Nitrogen bases with sugars

• RNA– AdenosineAdenosine– Guanosine– CytidineCytidine– Uridine

• DNADNA– Deoxy- prefix– ThymidineThymidine

Making a NucleotideMaking a Nucleotide

Adding a phosphate to the nucleoside structureAdding a phosphate to the nucleoside structure.

Nucleotide NomenclatureNucleotide Nomenclature

• 5’- nucleoside phosphate5 nucleoside phosphate• 5’- nucleotide

Adenosine 5’-triphosphate

A.K.A

3’- deoxyguanosine monophosphatemonophosphate

Tedious Method to show the polymerpolymer…

Short-Hand Method to show the polymerpolymer

The Very Short-Hand Method to

• P-5’ACG 3-OHshow the polymer

P 5 ACG 3 OH• By convention: nucleic acid polymers are

always written with the 5’ end to the leftalways written with the 5 end to the left and the 3’end to the right.P l it t th l l 5’ 3’• Polarity to these molecules 5’ 3’

• ACG is DIFFERENT than GCA

Anatomy of the DNA helixAnatomy of the DNA helix

Launch animation

htt // j h k k /DNA t ht lhttp://www.johnkyrk.com/DNAanatomy.html

Visit this link as a study guide!!!

Billions of nucleotides join to form G

• ProkaryotesGenomes.

– Contain genes (coding regions)– Control areas (regulatory regions)

• Eukaryotes– Contain genes (coding regions)g ( g g )– Control areas (regulatory regions)– “Useless” stretches of DNA (noncoding Use ess st etc es o ( o cod g

regions)• Introns – intervening sequences in DNA• Exons - are the coding regions in Eukaryotes.

An E. coli’s genomegenome exposed!

Structure of DNA

• A 1950’s Race

Structure of DNA

A 1950 s Race• Maurice Wilkins and Rosalind Franklin

J W t d F i C i k• James Watson and Francis Crick– Building a structural model from scientific data

d h th !and hypotheses!

– Read their Paper!!! (link is on the class website)

X-ray DiffractionDiffraction of DNA…R li dRosalind Franklin’s

Data

Watson-Crick Model from the data

• 1 two helical polynucleotides coiled

Watson Crick Model from the data

1. two helical polynucleotides coiled around a common axis

• 2 The sugar phosphate backbones are• 2. The sugar-phosphate backbones are on the outside and the bases lie on the insideinside

• 3. bases are perpendicular to the axis of th h li 34 A t t 10the helix. 34 Angstrom repeat 10 bases/turn (bases separated by 3.4 Ang.)

• 4. diameter is 20 Angstroms.

Chargaff’s Results on NucleotideChargaff s Results on Nucleotide Ratios

Paper scissorsPaper, scissors, and Hydrogen

B dBonds…

The secret of the Base Pairs!Base Pairs!

Nitrogen “Base Stacking”Stacking”

helps stabilize the helixthe helix.

W kWeak forces…

Genetic Molecule• Copies are made of the DNA before

Genetic Moleculep

each MITOSIS event.• The enzyme that copies the DNA for theThe enzyme that copies the DNA for the

daughter cells is called DNA polymerasepolymerase– For humans, 3 billion bases have to be

copied to form the new strands of DNAp– Very rapid, very accurate…– Only 1 mistake in every 1 million baseOnly 1 mistake in every 1 million base

pairs.

What was the mechanism of DNA R li i ?Replication?

• PossibilitiesPossibilities– Conservative

Semiconservative– Semiconservative• How can you find out?

S i C tiSemi-Conservative Replication Model…Replication Model…

Meselson and Stahl E i tExperiment

Animation link: http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter14/animations.html#

Density Gradient equilibrium Sedimentation

Heavy N-15 isotopelight N-14 isotope

Hybrid…1/2 Heavy…½ light.

Semi-Conservative R li tiReplication

Uses the following amazing enzymes:Uses the following amazing enzymes:

1. Helicases/topoisomersase – help to open up the double helixdouble helix

2. RNA primase – lays down a short RNA primer to provide replication enzymes with a 3’-OH.

3. DNA polymerase – builds off of the RNA primers p y pto incorporate nucleotide triphosphates into the new daughter strands….both quickly and accurately!

4. Exonucleases – Removes the RNA primer from the daughter strands

5. Ligase – will fill in the gaps and establish a new phosphodiester linkage bet een the neighboringphosphodiester linkage between the neighboring DNA fragments making all of the separate fragments one continuouse nucleic acid strand.

S i C tiSemi-Conservative Replication inReplication in

Action!Animation of DNA Replication

http://www.johnkyrk.com/DNAreplication.html

Another animation of DNA replication

Another animation of DNA replication

REALLY COOL ANIMATION OF DNA PACKAGING AND REPLICATION!DNA PACKAGING AND REPLICATION!

HypochroismHypochroism of DNA

Helicases “melt” the helix in the cell!

Here is melting outside the cell using heatg g

Circular DNA…l

DNA can Supercoil….enzymes called TopoisomerasesDeal with the supercoiling inside the cellDeal with the supercoiling inside the cell.l

Stem Loop and Hairpin structures ithi i l t d d l i idcan occur within single stranded nucleic acids

Single StrandedSingle Stranded RNA can take on a variety of complex

structures!structures!(and Functions)( )

Magnesium Ions often help stabilizeMagnesium Ions often help stabilizeThe structures….

Same Molecule in “3-D”Same Molecule in 3 D

DNA is Replicated by P l EPolymerase Enzymes

What are the requirements?

Phosphodiester BridgePhosphodiester Bridge

RNA Genomes…a carry-over f i t d ?from ancient days?

Retrovirus Mechanismhttp://www.whfreeman.com/kuby/content/anm/kb03an01.htm

Gene Expression…and RNAGene Expression…and RNA

Transcription Start Signals in prokaryotes

Transcription Start Signals in eukaryotes

Terminator sequenceTerminator sequenceIn prokaryotes…

The end of the geneC t i h i iContains a hair pinStructure that tells the RNA polymerase to Stop transcription.p p

Rho factor may alsoBe involved

Methyl Guanosine cap added to 5’ end

PolyA tail added to 3’ endPolyA tail added to 3 end

Molecular ushers…theMolecular ushers…the Transfer RNAs

Hydrogen Bonding is the link between mRNA and protein sequences.

1. Three nucleotides encode an amino acid2. The Code I nonoverlapping3 The Code has no “punctuation”3. The Code has no punctuation4. The Genetic Code is degenerate.

First amino acids inThe prokaryotes

Translation Start Signals in prokaryotes

Translation Start Signals in eukaryotes

Animation of Translation:

http://www johnkyrk com/DNAtranslation htmlhttp://www.johnkyrk.com/DNAtranslation.html