biological chemistry chapter 8

Nucleotides and NucleotidesChapter 8

Some basics

Nucleic Acid Structure

Nucleic Acid Chemistry

Other functions of Nucleotides

Learning Outcomes

Structure and function of nucleic acids

Draw and ID purine and pyramidine nitrogeneous bases

Draw and understand the mechanism for formation of ring inpentose ring in nuclotides

Draw the mechanism for formation and cleavage of N-glycosidic bond

ID and draw the mechanism for the formation ofphosphodiester bond which links nucleotides together in DNA

What are the major characteristics of DNA that highlight theimportant chemical interactions that impart structure andfunctionality

Nucleotides: Building Blocks of Nucleic Acids

DNA = _________________ acid

Nucleotide sequences in DNA provide _____________

for ______ ____ sequence in all proteins in cells

For nucleotide sequence in ______

Section of DNA containing nucleotide information iscalled ____________

Many _________ of genes and DNA molecules in cells

Only known function of DNA is _________ and______________ of biological information

AdministratorTypewritten TextS

AdministratorTypewritten TextDeoxyribonucleic

AdministratorTypewritten Textinformation

AdministratorTypewritten TextAmino Acids

AdministratorTypewritten TextGenes

AdministratorTypewritten Textstorage

Nucleotides: Building Blocks of Nucleic Acids

RNA = _____________ acid

RNAs have several functions:

____________ RNAs (rRNAs) are part of ribosomes

Ribosomes are where proteins are synthesized

_____________ RNAs (mRNAs) carry informationfrom one or more genes to the ribosome

______________ RNAs (tRNAs) are moleculeswhich translate mRNA sequence into a specificamino acid

Other RNAs exist and have other purposes

AdministratorTypewritten TextRibonucleic acid

AdministratorTypewritten TextMessenger

Definitions:Nucleotides, nucleosides and nucleobases

Nucleotide = ______________, ____________, and ____

to ____ _____________ groups

Nucleoside = ____________ base and ____________

Nucleobase = ______________ base

Fig 8.1a

AdministratorTypewritten TextNitrogeneous

AdministratorTypewritten Text3

AdministratorTypewritten TextPhosphate


AdministratorTypewritten TextNitrogeneous Base

AdministratorTypewritten TextPentose (sugar)

Definitions:D-Ribose and 2-

deoxy-D-Ribose

D-Ribose has ______ at 2 (and is used in ________)

2-deoxy- D-Ribose has _____ at 2 (and is used in______)

Pentose has 1 to 5 numbers to _________ thenumbered elements from the ____________ base

Fig 8.1a

AdministratorTypewritten TextOH group

AdministratorTypewritten Text2 prime

AdministratorTypewritten TextDNA

AdministratorTypewritten Textdistinguish

b-furanose(closed 5 membered

ring of pentose)

In solution free forms of __________ _______(aldehyde) and _______ (b-furanose) exist in _________

RNA contains b-D-_______________

DNA contains b-2-________-D-____________Fig 8.3a

AdministratorTypewritten Textequilibrium

AdministratorTypewritten TextStraight

AdministratorTypewritten TextRing

AdministratorTypewritten TextRibose

AdministratorTypewritten TextDeoxy

AdministratorTypewritten TextRibose

AdministratorTypewritten TextKnow how to draw the sugar

Puckered b-furanoseconformations(endo or exo)

In ribofuranose ring formation 4 of 5 atoms are in_________ plane

_____ or _____ are either on the same side (______) oropposite side (_____) the plane relative to C-5

____________ base usually attached to ______

__________ group is usually attached to _____Fig 8.3b

AdministratorTypewritten TextC2



AdministratorTypewritten TextNitrogenous

Definitions:Nitrogenous bases (purine or pyrimidine)

________ in nitrogeneous bases are not _________

Purine is parent compound of _________ (A) and __________ (G)

_____________ is parent compound of ________(C), __________ (T) and ________ (U in RNA)

Bases are __________ compounds (contain N and C)

Fig 8.1b

AdministratorTypewritten TextNumbers

AdministratorTypewritten Textprimed

AdministratorTypewritten TextAdenine

AdministratorTypewritten TextGuanine

AdministratorTypewritten TextPyrimidine

AdministratorTypewritten TextCytosine

AdministratorTypewritten TextThymine

AdministratorTypewritten TextUracil

Purine Nitrogenous bases

Purine has 5 C and 4 N and 4 double bonds

___________ has NH2 group at C6

__________ has NH2 group at C2 and ketone (=O) at C6

All purines are good ________donors and ____________

Adenine pKa at N1 is 3.8 Guanine pKa at N7 is 2.4

Neutral molecules at pH 7Fig 8.1b and Fig 8.2

AdministratorTypewritten TextAdenine

AdministratorTypewritten TextHydrogen Bond

Pyrimidine Nitrogenous bases

Pyrimidine has 4 C and 2 N and 3 double bonds

_________ has NH2 at C4, ketone (=O) at C2 and no db N1 - C2

Thymine has _____ at C5, (=O) at ___ & ___ and no db N1 - C2

_______ has ketones (=O) at C2 and C4 and no ____ N1 C2

All pyrimidines are _____ H-bond donors and __________

Cytosine pKa at N3 is 4.5 Thymine pKa at N3 is 9.5

Neutral molecules at pH 7 Fig 8.1b and Fig 8.2

AdministratorTypewritten TextCytosine

AdministratorTypewritten TextMethyl Group

AdministratorTypewritten TextCH3



AdministratorTypewritten TextAcceptors

Deoxyribonucleotidesfree form at pH 7.0

Fig 8.4a

AdministratorTypewritten TextDraw these out, know which are what, what binds where



Ribonucleotidesfree form at pH 7.0

If phosphate group is in a different location, the name will change

Fig 8.4b

Nomenclature

The type of pentose defines the nucleic acid(So 2-deoxy-D-ribose is in DNA even if base is uracil)

Nomenclature for Minor Bases Common names may be used (hypoxanthine for inosine)

Name usually includes the ________ of the ring where thesubstitution occurred (but not the ________ where thesubstitution occurred)

If the substitution is ________ the ring, then the ________is indicated along with its connection to the ring (N6)

Fig 8.5a

AdministratorTypewritten TextNumber

AdministratorTypewritten TextIndicatin the methyl is attatched to the n on the 6th carbon

AdministratorTypewritten TextNumber

Minor Bases in DNA Methylation is common change to major bases for DNA

Viral DNA bases can be hydroxymethylated (-CH2OH) or glucosylated (sugar moiety added to N or C or O group)

Fig 8.5a

Minor Bases in DNA

Changes are often made to the bases after the DNA hasbeen _______________

5methylcytosine is found in ____________ and bacteria

N6-________________ is found in bacteria but noteukaryotes

Epigenetic ____________ (which are not coded on genes

but which are passed on as the cells replicate) are useful

for distinguishing __________ DNA and when to ______

on gene ___________

AdministratorTypewritten TextMade / Synthesized

AdministratorTypewritten TextEukaryotes

AdministratorTypewritten Textmarkers

AdministratorTypewritten TextReplication

AdministratorTypewritten TextForeign

Minor Bases in tRNA Changes are often in the location of ribose attachment

Thiol or methyl groups can also be attached

Fig 8.5b

Minor Bases in RNA

Inosine can be found in the ______ position of anticodonfor tRNA (wobble position is the third base in the codonposition for an amino acid and allows for _______ than61 expected tRNA for the number of codons present)

It is made from de-amination of ____________

Provides richer __________ codes

Pseudouridine is ________ in tRNA and rRNA

Found in _____________ and some eubacteria

Made from uridine by _______________ isomerizationafter RNA ______________

May be used in the _______________ of tRNA structure

May help in the ____________ of rRNA

AdministratorTypewritten TextWobble

AdministratorTypewritten TextAdenosine

AdministratorTypewritten Textfound

AdministratorTypewritten TextEukaryotes

AdministratorTypewritten TextEnzymatic

AdministratorTypewritten TextStab

AdministratorTypewritten TextFolding

AdministratorTypewritten Textilization

AdministratorTypewritten TextSynthesized

Location of Phosphate group on pentose Phosphate groups are usually attached on ____ of ribose

Phosphate can be ____________ at C2

ribonucleoside 2- monophosphate

Phosphate can be attached at the C3 and is the endproduct of ___________ of RNA by some ribonucleases

ribonucleoside 3- monophosphate

Fig 8.6


AdministratorTypewritten TextAttatched

AdministratorTypewritten TextHydrolysis

Location of Phosphate group on pentose Phosphate can be attached at C2 and C3 and is able to

be isolated as an _________________

adenosine 2,3-cyclic monophosphate

Fig 8.6

AdministratorTypewritten TextIntermediate

AdministratorTypewritten TextInsert Drawing here.

Linkages in DNA

b-N-glycosidic bond between_________ ring and the _____________

N-9 of purine (A or G) or N-1 ofpyrimidine base (C or T) is linked tothe C- 1 of the __________

Bond is formed with the anomericcarbon (C with ___________ in the bconfiguration (OH is up in _______ and____________ positions))

Bond is _________ towards hydrolysisespecially in _____________

Bond cleavage is catalyzed by _______

Fig 8.3a

AdministratorTypewritten TextSugar

AdministratorTypewritten TextNitrogeneous Base

AdministratorTypewritten TextAxial

AdministratorTypewritten TextEquitorial

AdministratorTypewritten TextStable

AdministratorTypewritten TextAcid

Conformation about the b-N-glycosidic bond

When nucleotides are free in solution,rotation about the b-N-glycosidic bond ispossible

Torsion angle in bond between N of baseand C1 of pentose is called c

O4-C1-N9-C4 for purine

O4-C1-N1-C2 for pyrimidine

Angle near 0 is syn conformation

Angle near 18 0 is anti conformation

Anti conformation is found in B-DNA

Fig. 8.16a

Anti and Syn Conformation aboutthe b-N-glycosidic bond

Fig. 8.16b

Linkages in DNA

Backbone of DNA and RNA are _____________since theOH groups of pentose form _______ with water in the cell

Phosphate groups have pKa near _____

At neutral pH (pH = 7) phosphate groups are ___________charged

Charges are neutralized by ionic interactions with _______charges on proteins or ________ ions or polyamines

____________ linkages always are oriented 5 to 3 with 5end missing a nucleotide and 3 end missing a nucleotide

5 and 3 ends may have be ______ or have attached____________ groups

AdministratorTypewritten TextHydrophilic

AdministratorTypewritten TextHydrogen Bonds

AdministratorTypewritten Text- ve

AdministratorTypewritten Textmetal

AdministratorTypewritten TextPhosphodiester

AdministratorTypewritten TextFree

AdministratorTypewritten TextPhosphate

Phosphodiester Linkage

Note 5 end and 3 end whichis the orientation of thestrands

Note base differencesbetween RNA and DNA

Covalent backbone of theDNA and RNA is subjected toslow ___________ hydrolysisof phosphodiester bonds

_____ in test tubes undergoesrapid hydrolysis due to theOH on C2 under_______conditions (basic pH)

Fig. 8.7

AdministratorTypewritten TextNon enztmatic

AdministratorTypewritten TextRNA

AdministratorTypewritten TextAlkaline

Cyclic 2,3-monophosphate nucleotidesPhosphodiester Linkage

Cyclic 2,3-monophosphate nucleotides are first products ofthe action of alkali on ______ and _________ further toform a mix of 2 and 3 nucleoside monophosphates

Fig. 8.8

AdministratorTypewritten TextRNA

AdministratorTypewritten TextHydrolysis

Short form to writing the DNA sequence Phosphate groups are in circled P

Deoxyribose is a linear line with ____ at top and _____ at bottom but is in the closed ring __-furanose formation

Phosphate group is linked from ____ of one pentose to _____ of next pentose

Always written 5 end to 3 end, with 5 end on the _____

Fig pg 286

AdministratorTypewritten TextShort cut form





Short form to writing the DNA sequence

pA-C-G-T-AOH pApCpGpTpA

pACGTA

Definition of _____________ is 50 or less nucleotides

___________ are long chains of nucleotides

Fig pg 286

AdministratorTypewritten TextOligonucleotide

AdministratorTypewritten TextPolynucleotide

Properties affecting Nucleotides

Free nucleotides are basic compounds and are called______

Purines and pyrimidines in DNA and RNA are ________compounds (have rings with double bonds)

Presence of _______ ______ influences structure,electron distribution and light absorption

Electron delocalization due to double bonds gives somebonds _______ double character

Presence of double bonds means purines are ________planar in nature and pyrimidines are planar in nature

Bases will exist in one of several __________ statesdepending on pH

AdministratorTypewritten TextNitrogenous bases

AdministratorTypewritten TextAromatic

AdministratorTypewritten TextDouble Bonds

AdministratorTypewritten TextTautomeric

Tautomeric states of Uracil

Uracil has three states when free in solution

Lactam at pH 7

Lactim and double lactim exist in lower pH solutions

Other bases do have these forms but they are rare in solution

Fig. 8.9

Absorption of Common

nucleotides

Abs range is 250 to 270 nm

Absorbance due to p p* electronic transitions

Excited states of common nucleobases decay rapidly viaradiationless transitions

No fluorescence from these nucleic acids

Spectra are nearly identical for all species

Mixture of nucleotides would use Abs at 260 nm formeasurements and analysis Fig. 8.10

Properties affecting Nucleotides

Free nucleobases are ___________ and usually_________ in water at near neutral pH in cells

In acidic or basic environments, the bases become________ and are more ________ in water

Bases are able to ________ with their rings parallel (likestacking coins) which allows for hydrophobic stackinginteractions

Stacking involves van der Waals and ______-dipoleinteractions between bases

Stacking reduces base interaction with water and helps inmaintaining the _______ structure of DNA

AdministratorTypewritten Texthydrophobic

AdministratorTypewritten TextCharged

AdministratorTypewritten TextStack

AdministratorTypewritten TextDipole

AdministratorTypewritten Text3D

Functional groups in Nucleobases

Presence of ring nitrogens, carbonyl groups, andexocyclic amino groups

Hydrogen bonding is very important

Involves carbonyl and amino groups

Interactions between purine and pyrimidine basepairing

Interaction between two (and up to four)complementary strands of nucleic acids

A bonds to T (or U in RNA) and G bonds to C

This base paring allows for duplication of DNA andRNA strands

Nucleobases paring in DNA

Fig. 8.11

Polynucleotides

___________ is phosphodiester linkage based so it isnegatively

The backbone is fairly stable but it can undergo__________ in the presence of enzymes (DNAase)

______ backbones are not as stable (RNA can last foryears in water but only for a few hours inside cells)

The backbone does not contain __________ or branches

You can only read the sequence from 5 to 3

A different ____________ will be created if you readfrom 3 to 5

AdministratorTypewritten TextBackbone


AdministratorTypewritten TextCross Links

AdministratorTypewritten TextSequence

Summary of Basics

Nucleotide has purine or pyrimidine nitrogenous base,pentose sugar and at least one phosphate group

Phosphodiester bonds join the 5 OH of one pentose tothe 3 OH of the next pentose

Two types of nucleic acid: RNA and DNA

RNA has ribose (sugar) and usually Uracil, Cytosine,Adenine and Guanine (bases)

DNA has deoxyribose (sugar) and usually Thymine,Cytosine, Adenine and Guanine (Bases)

Recall it is the sugar that determines the type of nucleicacid not the base

Nucleic Acid Structure

1953 Watson and Crick discovered the structure of DNA

Structure is hierarchial in complexity

__________ covalent structure and nucleotide sequence

__________ regular or stable structure obtained by any or all nucleotides

____________ - folding of large chromosomes or large tRNA or rRNA molecules

AdministratorTypewritten TextPrimary

AdministratorTypewritten TextSecondary

DNA double helix that stores genetic information

1868 DNA first isolated by Friedrich Miescher and wascalled _____________

1940s work by Oswald T Avery, Colin MacLeod, andMacIyn McCarty proved that DNA was genetic basedmaterial

Avery and collegues took DNA from a virulent strain ofStreptococcus pneumoniae bacterium and injected into anon-virulent strain of the bacterium (and the nonvirulentstrain became virulent)

DNA _____________ information about the virulence.

AdministratorTypewritten Textnuclein

AdministratorTypewritten TextContained

DNA double helix that stores genetic information

1952 - Alfred D. Hershey and Martha Chase studiedinfection of bacteria cells by bacteriophage (virus) byradioactive labeled DNA (showed DNA not proteinscontained genetic information)

Late 1940s Erwin Chargaff and colleagues determinedthat there were ________ bases in DNA

Bases occurred at different _______ between differentorganisms


AdministratorTypewritten TextRatios

Chargaffs Conclusions

1. Base composition varies from one species to another

2. DNA from different tissues of the same species havesame base composition

3. Base composition does not change with changes to theorganisms age, nutritional state or surroundingenvironment

4. A = T in number and G = C in number within a specificDNA strand

Sum of pyrine bases = sum of pyrimidine bases

** information above useful in determining 3D structure ofDNA, how info is encoded in DNA and how it passesbetween generations

Use of X-ray diffraction to prove

DNA

1950s Rosalind Franklin and Maurice Wilkins used X-raydiffraction to look at DNA fibers

___________ pattern was found

They deduced that DNA was helical in with two periodicitiesalong their long axis (___________ was 3.4 and_________ was 34 )

Fig. 8.12

AdministratorTypewritten TextReproducable

AdministratorTypewritten TextPrimary

AdministratorTypewritten TextAngstroms

AdministratorTypewritten Text^

How do you get a 3D model to fit this data? Enter Watson and Crick

1953 Watson and Crick proposed a 3D structure DNAusing base pairing and X-ray data

Two helical DNA chains wound around a central axis toform a right handed double helix

Make 2 fists and point your thumbs away from you

Does the helix curve to the right or the left to wrap around your thumb?

Is the spiral going around your right thumb in the direction where there four other fingers curled up (clockwise)?

Box. 4.1

AdministratorTypewritten TextRight handed clockwiseleft handed counterclockwise

AdministratorTypewritten TextBe able to identify :

How do you get a 3D model to fit this data? Enter Watson and Crick

Backbone keep deoxyribose and phosphate groups onthe outside of double helix right beside the water in thecell

Each ____________ is in a C2-endo conformation (ringformation)

Purine and pyrimidine bases are on the inside of the helix

Planar nature allows for close stacking

Rings are _____________ to the long backbone axes

Since bases are inside the helix they are in ahydrophobic environment

AdministratorTypewritten TextDeoxyribose

AdministratorTypewritten TextPerpendicular

Major and Minor Grooves in DNA structure

Smaller groove in the double helix is theminor groove (the backbone is closertogether)

________ groove in double helix is the________ groove (backbone is furtherapart)

Pairing of bases a purine on one strandpairs in the same plane with apyrimidine on the other strand

Fig. 8.13a

AdministratorTypewritten TextLarger

Major and Minor Grooves in DNA structure

A to T has a double H bond

C to G has a triple H bond

Higher the ratio of GC to AT base pairsthe ________ it is to separate thepaired DNA strands

Other pairing of bases will lead to_______________ of the double helix

(b) is ball and stick model of doublehelix

(c) is space filling model of double helix

Fig. 8.13b and c

AdministratorTypewritten TextHarder

AdministratorTypewritten TextDestabilization

Parallel or Antiparallel strands in DNA

Parallel strands would have 3,5 phosphodiester bonds inthe same direction

Antiparallel strands have 3 and 5 running in oppositedirections

Watson and Crick thought the antiparallel orientation wasthe better model

DNA polymerase provided experimental results that thestrands were antiparallel

X-ray diffraction results also confirmed antiparallel strands

Spacing of bases and Turns in the double helix

DNA model has the bases ____________ to the backbone

Bases needed to be 3.4 apart (_________ repeatingfeature in the x-ray analysis)

____ base pairs per turn of the DNA double helix (adistance of 34 ) which was the second repeating featurein the x-ray analysis)

If DNA is in ________ and not in the cell, the bases perturn is about _____

Base pairs are also not identical in the sequence orcomposition but are __________________

A partners (hydrogen bonds) with T

G partners (hydrogen bonds) with C

AdministratorTypewritten Textprimary


AdministratorTypewritten Text10.5

AdministratorTypewritten TextComplimentary

What forces hold DNA duplex together?

Hydrogen bonds between the basepairs

2 H-bonds between A and T

3 H-bonds between C and G

Base stacking interactions

Non specific in nature but makemajor contributions to thestability of double helix

Fig. 8.14

Complimentary nature of the strands

Complementary nature of DNAallows for easy replication

Watson and Crick were able toforesee this feature before therewas confirmatory proof

Two strands separate

Each parent strand is the guidefor making a precisecomplimentary strand with Apairing with T and G pairing withC

Fig. 8.15

A and B and Z forms of DNA

DNA is flexible

Rotation about the____________________ backboneand changes in temperature cancause bending, stretching and_________ of bases through melting

These changes result in differentDNA structure (Form ___) from theone proposed by Watson and Crick

Reagents used to crystallize DNAcause it to ________ and so mostshort DNA molecules will appear inForm A

Fig. 8.17

AdministratorTypewritten Textcovalent

AdministratorTypewritten Textunpairing

AdministratorTypewritten TextDehydrate

AdministratorTypewritten TextB

AdministratorTypewritten Text



A, B and Z forms of DNA:3 changes can occur

Different Structural conformationof deoxyribose (C2 or C3 endoor exo)

Rotation about the bonds in thephosphodeoxyribose backbone

Rotation about the C1-N-glycosylbond

purines (A and G) can beeither _______ or _______

pyrimidines can be only______ (C and T) due to sterichinderance of carbonyl oxygenat C2 Fig. 8.16

AdministratorTypewritten TextAnti

AdministratorTypewritten TextSyn

AdministratorTypewritten TextAnti Conformation

A and B forms of DNA

B form DNA is most stable underphysiological conditions

A form and Z form have been studiedunder crystal form

A form appears in solutions with little H2O

A form is right handed,

wider (11 bases per turn)

plane of bases tilted by 20 from thebackbone

minor groove is shallower and majorgroove is deepened

Fig. 8.17

B and Z forms of DNA

Z form is left handed helix

12 bases per turn (but it looks moreslender and elongated)

Backbone looks zig zag in appearance

Pyrimidine alternating with purine bases fitbetter in to a Left handed helix (alternatingC and G or 5-methyl-C and G residues)

Purines are in the ____ conformation andpyrimidines are in the _____ conformation

Major groove is hard to find in Z form butthe minor groove is narrow and deep

Z form in __________ and eukaryotes Fig. 8.17


AdministratorTypewritten TextSyn

AdministratorTypewritten TextAnti

AdministratorTypewritten TextBacteria

Comparison of A and B and Z forms of DNA

Fig. 8.17

Structures within DNA due to specific base sequences

4 or more Adenosine in a row lead to a bend (6 A = bend of18 )

Bending may assist in binding proteins to DNA

Presence of palindromes (sequences which are the sameforward and backwards like ROTATOR or NURSES RUN) andtheir location influence how a strand of DNA may fold uponitself

Term used when sequences of DNA have inverted repeats ofbase sequence over two strands of DNA

Fig. 8.18


Palindrome on two complementary strands of DNA tosuperimpose, the sequence is rotated by 180 in horizontalaxis and then rotated by another 180 in the vertical axis.

Minor repeat has a repeating sequence on the same strandof DNA and only needs to rotated by 180 in the vertical axis

Fig. 8.17


Since the repeats are within the same strand, they are able to participate in other structures

Hairpin turns can not formed from complementary strands of DNA (only single stranded DNA)

If both strands are participating in the hairpin turn it is called a cruciform (cross shape).

Fig. 8.19


These hairpin and cruciform can be found in all large DNAmolecules

Cruciforms have been found in in vivo E. coli

Single stranded DNA and RNA fold into many hairpinturns when they are in solution

Other unusual structures involve three or four strands ofDNA

Three or four strands can be found in the major groovewhen there is additional hydrogen bonding

Protonated Cytosine can pair with G of

Thymidine can pair with A in A/T base pair

Hoogsteen pairing

Fig. 8.20a


N-7, O6 and N6 of purines (known as Hoogsteen positions)can participate in H-bonding of triplex DNA

Unusual (non Watson-Crick base pairing) base pairingcalled Hoogsteen pairing

These triplex DNAs are most common in low pH (sincecystosine must be protonated)

pKa of cystosine is greater than 7.5 (normal pKa value is4.2)

Triplex DNA

Fig. 8.20b


Triplexes will form when there are long stretches of onlypurine or pyrimidine bases in one strand

These stretches may contain two purine and onepyrimidine strand or (two pyrimidine and one purinestrand)

If there are high content ofguanosine residues thentetraplex DNA strands willform

These strands can beparallel or antiparallel innature

Fig. 8.20e

Guanosine tetraplex

Fig. 8.20c

Four successive tetraplets from a G tetraplex structure

Fig. 8.20d

Structures within RNA due to specific base sequences

RNA is the intermediary carrying the information from thegene in DNA to the _________ where the amino acidsequence is assembled to make functional proteins

1950s RNA was thought to be the molecule which movedthe information from the nucleus to the ribosome

1961 Franois Jacob and Jacques Monod proposedmessenger RNA (mRNA) to carry the information fromDNA to ribosomes

Process of forming mRNA on DNA template is_____________________

AdministratorTypewritten TextRibosome

AdministratorTypewritten TextTranscription

Structures of mRNA

Bacteria and archaea use a single mRNA to encode manypolypeptide chains

One chain is monocistronic

Many chains is polycistronic

Cistron = gene

Fig. 8.21

Structures of mRNA

Minimum length of a mRNA is defined by the length of thegene

If there is are 100 amino acids, the chain would need to beminimum 300 nucleotides (1 amino acid = 3 nucleotides =1 codon)

Chains are always longer because there are ___________sequences for protein synthesis

AdministratorTypewritten TextNoncoding



Structures of other RNA

Transfer RNA (tRNA) is used to bring the amino acids tothe growing protein chain one ________ ______ at a time

tRNA is covalently linked to the amino acid and willpartner with mRNA so that the correct sequence is createdfor the desired protein (from the DNA gene)

Ribosomal RNA (rRNA) are part of the ____________

Ribozymes have enzymatic activity

RNA molecules have a ________ diversity in structure thanDNA

AdministratorTypewritten TextAmino

AdministratorTypewritten TextAcid

AdministratorTypewritten TextRibosomal

AdministratorTypewritten TextRicher

Transcription product is singlestranded (ss) RNA

ss RNA will form a righthanded helix influenced bybase stacking interactions

________-purine is strongerthan _______-pyrimidine or__________-pyrimidine

Pyrimidine bases can be___________ to offer purine-purine stacking to occur

Self complementarysequences in the strand offermore complex structures

Single stranded RNA

Fig. 8.22

AdministratorTypewritten TextSingle stranded are supposed to be right handed

AdministratorTypewritten TextPurine


AdministratorTypewritten TextPyrimidine

AdministratorTypewritten TextDisplaced


Structure Formation of double stranded RNA

____ to have two strands of RNA be 100% complementary

Strands will bond over shorter regions and form a righthanded ________ double helix

Weak interactions involving base stacking help to stabilizethe RNA structures

Z-form RNA has been made in the lab (under ____ saltconcentration or _____ temperature conditions)

No B-form RNA has been made

A-form helix is not continuous due to mismatches (_____in one strand or _______ loop on both strands) or fromhairpin turns from nearby self complementary sequences

AdministratorTypewritten Textrare

AdministratorTypewritten TextA Form

AdministratorTypewritten TextHigh


AdministratorTypewritten TextBulge

AdministratorTypewritten TextInternal

Structure Formation of double stranded RNA

Fig. 8.23

Pairing differences in RNA

In RNA, A pairs with U and Cpairs with G

BUT G can pair with U

Pairing of RNA strands isantiparallel

Hairpins are thepredominant secondarystructure

Fig. 8.24

Hairpin turns in RNA

Short sequences (such as UUGG) make tight turns andare located at the end of a hairpin turn

These sequences are often very stable

It is possible that these sequences will act as startingpoints for 3D folding of RNA molecules

Other stabilizing mechanisms come from non-Watson-Crick bonding of base pairs

2OH of ribose can bond to other groups

Such bonding is seen in phenylanine tRNA of yeast, andtwo RNA enzymes (ribozymes) whose functions dependon their structure

Summary of Nucleic Acid Structure -1

Avery-MacLeod-McCarty experiment showed DNAcarries inheritable characteristiscs

Hershey Chase experiment proved DNA not proteinscarried the information for replication

Watson and Crick used available data to provide thedouble helix model based on B-DNA (A pairs with T and Gpairs with C; bases are perpendicular to the backboneand 3.4 and 10.5 bases per turn)

DNA can be in A-form, B-form or Z-form

Summary of Nucleic Acid Structure -2

DNA can have hairpin turns or cruciforms depending onpalindrome sequences or be in triplex or tetraplexstrands

mRNA carries the genetic information from DNA to theribosome

tRNA and rRNA are involve in protein synthesis

Single RNA can fold into hairpin turns, double strandedsections or complex loops


Genetic information in DNA needs to be _________

Chemical transformations of DNA are slow in _________of enzymatic catalyst activity

Even with the slow changes, DNA alterations can bephysiologically ________________

Slow accumulation of irreversible alterations to DNA maybe linked to ________ and _______________

Non-destructive changes also occur such as ________separation for DNA replication and ______________

Studying DNA has lead to the development of some veryspecific and interesting ___________ which helps inanalysis of DNA base sequences

AdministratorTypewritten TextStable

AdministratorTypewritten TextAbsence

AdministratorTypewritten TextSignificant

AdministratorTypewritten TextAging

AdministratorTypewritten TextCarcinogenesis (cancer causing)

AdministratorTypewritten TextStrands

AdministratorTypewritten TextTranscription

AdministratorTypewritten TextTechnology




___________ DNA solutions at physiological pH and_____ is very viscous

Double stranded DNA and RNA can become denaturedby raising the temperature to above ____C or alter thepH to extreme acid or base there is a physical change tothe DNA

Denaturation or ___________ of the double-helical DNA

_______ temperatures and ____ influence the H-bondsbetween bases on the two complimentary strands andon the _______ stacking on one strand of DNA

AdministratorTypewritten TextNative

AdministratorTypewritten TextRT

AdministratorTypewritten TextCarefully prepaired


AdministratorTypewritten TextMelting


AdministratorTypewritten TextPH

AdministratorTypewritten TextBase


DNA can __________ or ________________ unwind

No ____________ backbone bonds are _________

during the unwinding

DNA can undergo renaturation if _______ of the double

strands (minimum _____ bases) are still ________

When pH and/or temperature are _________ to

physiological conditions, DNA will reanneal (or rewind)

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If the DNA is __________ denatured into two separatestrands, then renaturation requires ____ steps

Strands will attempt to find each other through________ collisions and start to form short segments of______________ DNA

If the complimentary section is appropriate and longenough then the _________ of the strand will ________to form the double-helix __________

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Annealing and Denaturation of

double stranded DNA

Fig 8.26

UV Absorbance of DNA

________ bases in nucleic acids decrease the absorbance

of UV light relative to ______ nucleotides in solution

Presence of double stranded DNA ________ the

absorbance of UV light even more known as

__________________ effect

Denatured single stranded DNA __________ the

absorbance of light known as _____________ effect

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tm - melt temperature

Viral and bacterial DNA _________ slowly in solution if________

tm is species _________ and is the point at which ______the DNA is single stranded

Higher ______ content the higher the melt temperature

tm influenced by the _________ interactions ofneighbouring bases and by H-bond ___________

tm can be determined under fixed ____ and ________strength conditions (concentration of Na+)

Under carefully controlled conditions, only ____ richregions will _____ and the G/C conditions will remain_________

AdministratorTypewritten TextDenature

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AdministratorTypewritten TextInteractions

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Denatured regions are called bubbles

In vivo, strand separation is initiated at A/T rich areas forreplication and transcription

regions will melt and the G/C conditions will remainintact

Fig 8.27


Denatured regions are called bubbles

In vivo, strand separation is initiated at A/T rich areas forreplication and transcription

regions will melt and the G/C conditions will remainintact

Partial denatured DNAand then fixed for viewing

Red arrows point to somebubbles

Electron micrograph with5-fold enhancement ofDNA

RNA and RNA/DNA hybrids

RNA can form ________ and they are ______ stable toheat denaturation than _____ duplexes

So require _______ temperatures for denaturation(about 20C than for comparable DNA duplex sequences)

RNA and DNA can form _______ and denature at_____________ temperatures between pure RNAduplexes and DNA duplexes

Using the complimentary nature of DNA, complimentarysequences may be found between ___________

_________ and human DNA were isolated, denaturedand then mixed and allowed to sit for many hours at25C below tm, some of the DNA will anneal

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RNA and RNA/DNA hybrids

Temperature, DNA composition (length, ___________,complexity and _____ content), ____ concentrationinfluence the ability of DNA to anneal

______ temperature results in short sequences annealingto any complimentary sequence which will prevent_________ sequences from properly annealing

Most Human DNA will anneal to form ________ DNAduplexes and same with the mouse DNA

A small portion will form a mixture of DNAhuman/mouse _______ which shows the part of the DNAthat has ______________ heritage

________ portion of human/mouse DNA will formhybrids than human/yeast DNA hybrids

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DNA from two sources and the presence of hybrids

Fig 8.29

Uses of Hybridization Procedures

evolutionary _________ between two species influencehow ______ hybridization will occur

A specific gene or sequence can be found if there is a________ complimentary sequence that is labelled(fluorescently or with chemical tags)

Complimentary ______ can be from the same species,different species or chemically __________

Slight modifications are made to find RNA sequences

This procedure can be used to ID a person from hair leftat a crime scene or to predict the onset of disease (thatmay exist in modifications within certain genes asequence of DNA)

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Nonenzymatic transformation of Nucleotides

Cells do not want ________ in their genetic material

Too many changes will lead to ________ death or species_________

Purine and pyrimidine can undergo ___________alterations on a very slow time basis.

Alterations lead to __________ (permanent changes inthe DNA)

Too many alterations / mutations leads to ________ andpossibly carcinogenesis

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Deamination

Loss of ____________ amino groups

1 cytosine will be converted to ________ in every 107

cytosine bases in ____ hours

Result is about _____ spontaneous events per day

Rate for deamination of A and G is about 1/100th ______

DNA contains ___ not ____

Presence of U appears as ______ DNA which is removedand repaired

If U was present in the DNA than it would be harder tofind the spontaneous deamination events and this wouldlead to _________ changes in the genetic material

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Deamination

C deamination leads to_____ in G/C content andwould _______ the A/Ubase pairing in DNA cells

Over a millennia, Cdeamination could lead to_______ of C/G pairingand its genetic code

Using Thymine as a _____was a important turningpoint for _____ termstorage of geneticinformation

Fig 8.30

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Depurination

Hydrolysis of N-b-_________ bond leads to the ______of a ________ from the pentose

Creates a DNA ________ called ____ site (apurinic orapyrimidinic depending on which base was lost) or________ site

Rate is faster for _________ (1 in 105 purines inmammalian cells for 24 hours) in typical cell conditionsthan in pyrimidines

Add _______ acid to purines in a test tube and the rateof reaction is faster

DNA incubated in pH __ will result in a selective removalof purine bases to yield __________ acid

Fig 8.30

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Depurination

UV-Radiation

Radiation causes condensation of 2 ethylene groups toform a ___________ ring or ______ photoproduct

X-rays and gamma rays (ionizing radiation) initiate thering opening

Yeild fragmentation of bases and breaks in covalentbackbone of nucleic acids

______ and _______

Solar spectra (200 nm to 400 nm) in near UV radiationcause pyrimidine dimer formation or other chemicalchanges in the DNA in human ______ cells and bacteria

UV and ionizing radiation make up __% DNA damage byenvironmental agents

Fig 8.30

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Fig 8.31

Radiation damage products (dimers and

photoproduct) to DNA and their result to

DNA structure (kink)

Industrial Activity

DNA can be damaged by industrial products or their sidereactions

____________ agents (nitrous acid (HNO2) orcompounds which can generate nitrous acid or nitrites)

Used as preservatives in food to prevent bacterial growth

_______ health hazard with them in food (andmodifications to DNA) than them not in food (foodspoilage)

Fig 8.32a


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Industrial Activity Alkylating agents (will alter certain bases)

Dimethylsulfate (DMSO) will methylate guanine at O6

which prevents base pairing with cytosine (if in thecorrect tautomer)

Other reactions do occur naturally in cells such as the S-adenosyl methionine

Fig 8.32b and pg 302

Oxidative species and damage to DNA Hydrogen peroxide, hydroxyl radicals and superoxide

radicals are products of irradiation or byproduct ofaerobic metabolism

Cells are able to destroy oxidative species throughcatalase or superoxide dismutase but some destruction isdone

DNA is able to self repair most of the damage before it ispermanently passed on to the next generation

Methylation of some DNA bases _________ and _______ are more often methylated then

guanine or thymine

Methylation occurs more prominently in some sequencesor sections of genes

Not all reasons for methylation are understood

DNA methylases (enzyme) use S-adenoylmethionine forthe ________ source

Ecoli uses methylation for two reasons:

To label its DNA so that _______ DNA can be moreeasily found

To label a _______ where DNA repair must be madedue to ____________ bases

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Methylation of some DNA bases Adenine and cytosine are more often methylated then

guanine or thymine

Methylation occurs more prominently in some sequencesor sections of genes

Not all reasons for methylation are understood

DNA methylases (enzyme) use S-adenoylmethionine forthe methyl source

Ecoli uses methylation for two reasons:

To label its DNA so that foreign DNA can be moreeasily found

To label a sequence where DNA repair must be madedue to mismatched bases

Sequencing DNA

Before 1970s very time consuming process

1977 two new techniques were developed (AlanMaxam and Walter Gilbert) and (Frederick Sanger)

Used improved understanding of nucleotide chemistryand DNA metabolism and electrophoresis to separateDNA strands one nucleotide at a time

Polyacrylamide gel used for shorter DNA sequences

Agarose used for longer DNA sequences

Sequencing DNA

Basic principle reduce the DNA to four sets of labelledfragments

Reaction producing each fragment is nucleobase specific

Fragments are radioactively labelled on the 5 end

Mixtures undergo electrophoresis and the fragment canbe sequenced based on where the bands appear

Sanger method: desired sequence has a primer to which the

nucleotides are added following the template strand

Sanger method: desired sequence has a primer to which the

nucleotides are added

Sanger method: dideoxynucleotides (ddNTP) are used interrupt the bonding sequence of the

addition of one ddNTP at a time to the template

Sanger method: mixture of dNTPand ddNTP are

added, the template grows a

complementary sequence which has

a labeled primer, sequence is read after mixture of templates are

passed through the electrophoresis gel

Sequencing DNA

Each nucleotide is added as dNTP and ddNTP and thefragments will stop growing with ddNTP is placed in thegrowing strand

Shorter fragments will migrate faster in the gel

Knowing the location of the nucleotide in the gel, thesequence can be read one base at a time

The sequence that is read from the gel is thecomplementary sequence to the one that was beinganalyzed

Human Genone Project (HGP)

HGP accelerated DNAsequencing methods

Each nucleotide would belabeled with a fluorescent tag toallow large sequences to beanalyzed in a few hours

Each fragment of DNA wouldhave a tag and be read by adetector as it passed throughelectrophoresis gel

Fig 8.34

Creating DNA on a solid silica support

Phosphoramidite method

Growing strand is attached to a solid support

Protecting groups prevent unwanted reactions

Polynucleotides up to 70 or 80 bases in length can beeasily made

Progress can be followed spectrophotometrically if thebase is coloured with a tag

Extra care must be taken to protect 2 OH in ribose whenRNA is being produced

Creating DNA on a solid silica support:Phosphoramidite method

Fig 8.35

Summary: Nucleic Acid Chemistry-1

DNA can melt at high temperatures or extreme pH

G/C rich areas melt at higher temperatures than A/T richareas

Single stranded DNA that is denatured can form duplexeswith a complimentary strand of DNA from the samespecies or different species (hybrid)

Hybridization concept used to isolate certain genes andRNA

Summary: Nucleic Acid Chemistry-2

DNA is fairly stable but can undergo some chemicalreactions at very slow rates but still influence stability ofgenetic material

deamination C to U (so foreign U base substitutionscan be repaired)

Hydrolysis of base sugar bonds

Radiation forming pyrimidine dimers or photoproducts

Oxidative damage

Sequence of DNA can be determined by several differentmanners

Oligonucleotides can be synthesized rapidly andaccurately

Other Functions of Nucleotides

Nucleotides have other functions besides being subunitsin nucleic acids

Energy carriers

Components of enzyme cofactors

Chemical messengers

Ribonucleotides can have 1 to 3 phosphates linked to theribose

Known as a, b or g depending

on distance from ribose

Fig 8.36

Nomenclature of Nucleotides

Fig 8.36

Other Functions of Nucleotides

Hydrolysis of phosphate groups provides chemical energyto drive other chemical reactions within the cell

_______ (adenosine 5triphosphate) is the most__________ energy form

GTP, UTP and CTP are also used as forms of energy

__________ are activated precursors of DNA and RNAsynthesis



AdministratorTypewritten TextATP



AdministratorTypewritten TextCommon


Other Functions of Nucleotides ________ linkage between a and ribose yields 14 kJ/mol

____________ linkage between a/b and b/g yields about30 kJ/mol each

Hydrolysis of ATP is often _______ to other biochemicalreactions to provide positive free-energy change and willresult in product formation

Fig 8.37

Adenosine Participates in Many Reactions

__________ is an non protein component of an enzyme(inorganic ion or co-enzyme) required for catalysis

Enzyme co-factors use _______ as part of their structure

Adenosine appears in the _________ structure but mostcofactors do not look like nucleotides

Adenosine does not participate in the ________ functionof the co-factor

_____ of adenosine reduces the activities of the co-factorby _____ amount

Loss of 3-phosphoadenosine diphosphate fromacetoacetyl-Co-A (reduces its reactivity by a factor of106

Regulatory Molecules

First _____________ are hormones or external chemicalsignals which interact with receptors on cell surfaces

First messengers can lead to formation of________messengers inside cells

Second messengers will trigger _________ changes inthe cell interior

_______ = adenosine 3,5-cyclic monophosphate

Formed from ATP in a reaction catalyzed by adenylylcyclase (enzyme located in the inner face of plasmamembrane)

cAMP has ____________ functions for every celloutside the plant kingdom

Coenzyme A (CoA) functions in acyl group transfer reactions

acyl group is attached it CoA through the thioesterlinkage of b-mercaptoethylamine

Fig 8.38

Flavin adenine dinucleotide (FAD)

active form of Vitamin B2works in electron transfers

Fig 8.38

Nicotinamideadenine dinucleotide

(NAD+) works in hydride transfers

Fig 8.38

Why use Adenosine?

Adenosine may be used due to evolutionary ________

Adenosine can _________ potential binding energy

Other nucleobases can offer ________ potential bindingenergy

Using one compound for many purposes reduces downthe need for many additional systems and is an____________ advantage

Presence of _______ amounts of adenosine led to itsincorporation into other _________

Single protein ________ that can bind adenosine can beused in many _________ enzymes

__________ binding fold present in many enzymes thatuse ATP and nucleotide cofactors


cGMP = guanosine 3,5- cyclic monophosphate

Exists in many cells and also has _________ functions

ppGpp = guanosine 5 diphosphate, 3 diphosphate

Found in ___________ cells

Produced when there is a _________ in proteinsynthesis during amino acid __________

___________ the synthesis of rRNA and tRNAmolecules ________ for protein synthesis (to preventunwanted production of nucleic acids)


Fig 8.39

Summary: Other Functions of Nucleotides

ATP is important commodity in cells for energy

Adenosine is used in many cofacotors that involve energybinding requirements

cAMP is used as a second messenger to triggered byhormones or other chemical signals

Learning Outcomes

Structure and function of nucleic acids

Draw and ID purine and pyramidine nitrogeneous bases

Draw and understand the mechanism for formation of ring inpentose ring in nuclotides

Draw the mechanism for formation and cleavage of N-glycosidic bond

ID and draw the mechanism for the formation ofphosphodiester bond which links nucleotides together in DNA

What are the major characteristics of DNA that highlight theimportant chemical interactions that impart structure andfunctionality

Can you define the terms?

Gene (pg 281)

Ribosomal RNA (rRNA) (pg 281)

Messenger RNA (mRNA) (pg 281)

Transfer RNA (rRNA) (pg 281)

Nucleotide (pg 281)

Nucleoside (pg 281)

Pyrimidine (pg 282)

Purine (pg 282)

Deoxyribonucleotides (pg 283)

Ribonucleotides (pg 283)

Phosphodiester linkage (pg 285)

5end (pg 285)

3end (pg 285)

Oligonucleotide (pg 286)

Polynucleotide (pg 286)

Base pair (pg 287)

Major groove (pg 289)

Minor groove (pg 289)

B-form DNA (pg 291)

A-form DNA (pg 291)

Z-form DNA (pg 291)

Palindrome (pg 291)

Hairpin (pg 292)

Cruciform (pg 292)

Triplex DNA (pg 292)

G tetraplex (pg 292)

Transcription (pg 294)

Monocistronic mRNA (pg 294)

Polycistronic mRNA (pg 294)

Mutation (pg 299)

Second messenger (pg 308)

Adenosine 3, 5 cyclic monophosphate (cyclic AMP, cAMP) (pg 308)

Things to ponder for next lecture

Try to determine the correct answer

Results taken up in next lecture

What other name can be given to a nucleotide?

A. Glycosylated nucleosideB. Purinated pentoseC. DeoxyribonucleotideD. Nucleoside phosphateE. Pyrimidinate

Some effort has been made to extract DNA fromfossilized dinosaur bones that have been buried formany millions of years in arid climates. In what form isthis DNA most likely to be found?

A. A

B. B

C. Z

D. Tetraplex

E. Completely denatured

What function is served by the major groove in DNA?

A. It is the binding site for ethidium bromide.

B. It is a binding site for regulatory proteins.

C. It is a region of denatured DNA to which restrictionendonucleases bind.

D. It is a region of DNA that can form a hybrid duplexwith DNA of another species.

E. It is the site of guanine tetraplex formation.

Which structure is found in RNA, but would be theresult of a mutation or faulty annealing in DNA?

A. Hairpin

B. Double-stranded helix

C. Cruciform

D. Sequence complementation

E. Bulge

Telomeres are non-coding sequences on the ends ofchromosomes. They contain a high concentration ofguanosine. Given this information, what other structuremay be in telomeres?

A. Cyclobutane dimers

B. A high concentration of triplexes

C. Cruciform

D. Tetraplexes

E. A-form DNA

biological chemistry chapter 8

Documents

acid rnas

ribose dribose

dna molecules

section of dna

deoxy d

known function of dna

acid nucleotide sequences

ribofuranose ring formation