AJI SUTRISNO

FOOD SCIENCE AND TECHNOLOGY

UNIVERSITAS BRAWIJAYA (UB)

genome sum total of genetic material of

an organism (chromosomes +
mitochondria/chloroplasts and/or plasmids)
genome of cells DNA
genome of viruses DNA or RNA
chromosome length of DNA containing
genes
gene-fundamental unit of heredity
responsible for a given trait
site on the chromosome that provides
information for a certain cell function
segment of DNA that contains the
necessary code to make a protein or RNA
3
molecule

Two Types
1.

DNA
Deoxyribonucleic
acid

2.

RNA
Ribonucleic acid

Defines the relationships between DNA,

RNA, and protein in the transmission of
genetic information into functional units of
biological activity.
DNA

RNA

Protein

 Nucleic

acids are made of nucleotides

similar to how proteins are made of
amino acids

each

nucleotide consists of 3 parts

a 5 carbon sugar (deoxyribose or
ribose)
a phosphate group
a nitrogenous base (adenine, thymine,
cytosine, guanine, and uracil)
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Nucleotide
RNA

DNA

Nucleotides are the building blocks of nucleic acids

Nucleotides also play other important roles in the cell

Building blocks of nucleic acids (RNA,

DNA)
Analogous to amino acid role in proteins

Energy currency in cellular metabolism

(ATP: adenosine triphosphate)

Structural components of many enzyme

cofactors (NAD: nicotinamide adenine
dinucleotide)

Adenosinetriphosphate

triphosphate

Base (adenine)
Ribose

G = -50 kJ/mol

nicotinamide

NADH is a hydride transfer agent,

or a reducing agent.
Derived from Niacin

Nucleotides have three characteristic components:

A phosphate group

A nitrogenous base
(pyrimidines or purine)

A pentose sugar
4

Remove the phosphate group, and you have a nucleoside.

DNA contains genes, the information needed to

synthesize functional proteins and RNAs
DNA contains segments that play a role in
regulation of gene expression (promoters)
Ribosomal RNAs (rRNAs) are components of
ribosomes, playing a role in protein synthesis
Messenger RNAs (mRNAs) carry genetic
information from a gene to the ribosome
Transfer RNAs (tRNAs) translate information in
mRNA into an amino acid sequence

Below is the general structure of a nucleotide. The

pentose sugar, the base, and the phosphate moieties
all show variations among nucleotides.

 Ribose (-D-furanose) is
a pentose sugar (5membered ring).

 An important derivative of ribose is 2'-deoxyribose, or just

deoxyribose, in which the 2' OH is replaced with H.
Deoxyribose is in DNA (deoxyribonucleic acid)
Ribose is in RNA (ribonucleic acid).

Both retain a 3 hydroxyl group

Nucleotide bases in nucleic acids are pyrimidines or purines.

Nucleotide bases in nucleic acids are pyrimidines or purines.

 The bases are

abbreviated by their first
letters (A, G, C, T, U).
The purines (A, G) occur
in both RNA and DNA

Among the pyrimidines, C

occurs in both RNA and
DNA, but
T occurs in DNA, and
U occurs in RNA

Nucleotides in nucleic acids

Bases attach to the C-1' of ribose or deoxyribose
The pyrimidines attach to the pentose via the N-1 position of
the pyrimidine ring
The purines attach through the N-9 position
Some minor bases may have different attachments.

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Deoxyribonucleotides
2'-deoxyribose sugar
with a base (here, a purine,
adenine or guanine)
attached to the C-1'
position is a
deoxyribonucleoside
(here deoxyadenosine and
deoxyguanosine).
Phosphorylate the 5' position
and you have a nucleotide(here,
deoxyadenylate or
deoxyguanylate)

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Fig. 8-4

Deoxyribonucleotides are abbreviated (for example) A, or

dA (deoxyA), or dAMP (deoxyadenosine monophosphate)

The major deoxyribonucleotides

Fig. 8-4
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Ribonucleotides
The ribose sugar with a
base (here, a pyrimidine,
uracil or cytosine) attached
to the ribose C-1' position
is a ribonucleoside (here,
uridine or cytidine).
Phosphorylate the 5'
position and you have a
ribonucleotide (here,
uridylate or cytidylate)

Ribonucleotides are abbreviated (for example) U, or UMP

(uridine monophosphate)
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Fig. 8-4

The major ribonucleotides

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Fig. 8-4

Nucleotide nomenclature

25
10/10/05

Nucleotide nomenclature

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Fig. 8-39

10/10/05

Nucleic acids
Nucleotide monomers
can be linked together via a
phosphodiester linkage
formed between the 3' -OH
of a nucleotide
and the phosphate of the
next nucleotide.
Two ends of the resulting polyor oligonucleotide are defined:
The 5' end lacks a nucleotide at
the 5' position,

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and the 3' end lacks a nucleotide

at the 3' end position.
Fig. 8-7

10/10/05

Sugar-phosphate backbone

The polynucleotide or nucleic acid backbone thus consists of

alternating phosphate and pentose residues.
The bases are analogous to side chains of amino acids; they vary
without changing the covalent backbone structure.
Sequence is written from the 5' to 3' end: 5'-ATGCTAGC-3'
Note that the backbone is polyanionic. Phosphate groups pKa ~ 0.
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Berg Fig. 1.1

10/10/05

Compare polynucleotides and polypeptides

As in proteins, the sequence of side chains
(bases in nucleic acids) plays an important
role in function.
Nucleic acid structure depends on the
sequence of bases and on the type of ribose
sugar (ribose, or 2'-deoxyribose).
Hydrogen bonding interactions are
especially important in nucleic acids.

31
10/10/05

Interstrand H-bonding between DNA bases

Watson-Crick base pairing

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Fig. 8-11

lompat

DNA structure determination

Franklin collected x-ray

diffraction data (early 1950s)
that indicated 2 periodicities
for DNA: 3.4 and 34 .
Watson and Crick proposed a 3D model accounting for the data.
33

10/10/05

DNA structure
2 strands twisted into a helix
sugar -phosphate backbone
nitrogenous bases form steps in ladder
constancy of base pairing
A binds to T with 2 hydrogen bonds
G binds to C with 3 hydrogen bonds

antiparallel strands 3to 5 and 5to 3

each strand provides a template for the exact
copying of a new strand
order of bases constitutes the DNA code
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39

40

41

SignificanceofDNAstructure
1. Maintenanceofcodeduringreproduction.
Constancyofbasepairingguaranteesthat
thecodewillberetained.
2. Providingvariety.Orderofbases
responsibleforuniquequalitiesofeach
organism.

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DNAreplication

Beginsatanoriginofreplication
HelicaseunwindsandunzipstheDNAdoublehelix
AnRNAprimerissynthesized
DNApolymeraseIIIaddsnucleotidesina5to3
direction
LeadingstrandsynthesizedbyDNApolymerase
continuouslyin5to3direction
Laggingstrandsynthesized5to3inshortsegments;
overalldirectionis3to5
DNAisreadinthe3to5direction;Nucleotidesare
addedinthe5to3direction.

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ManyProteinCollaborateat
ReplicationFork

Flowofgeneticinformation

46

Geneexpression
TranscriptionDNAisusedtosynthesize
RNA
RNApolymeraseistheenzymeresponsible

Translationmakingaproteinusingthe
informationprovidedbymessengerRNA
occursonribosomes

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 Whataretheproductsthatgenesencode?
RNAsandproteins

Howaregenesexpressed?
transcriptionandtranslation

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 Genotypegenesencodingallthepotential
characteristicsofanindividual
Phenotypeactualexpressedgenesofan
individual(itscollectionofproteins)

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DNAproteinrelationship
1. Eachtripletofnucleotides(codon)specifies
aparticularaminoacid.
2. Aproteinsprimarystructuredeterminesits
shape&function.
3. Proteinsdeterminephenotype.Livingthings
arewhattheirproteinsmakethem.
4. DNAismainlyablueprintthattellsthecell
whichkindsofproteinstomakeandhowto
makethem.
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DNAproteinrelationship

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3typesofRNA

messengerRNA(mRNA)
transferRNA(tRNA)
ribosomalRNA(rRNA)

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53

DNA
Transcription
RNApolymerase

RNA
Translation
ribosomes

PROTEINS
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Transcription
1. RNApolymerasebindstopromoterregion
upstreamofthegene
2. RNApolymeraseaddsnucleotides
complementarytothetemplatestrandofa
segmentofDNAinthe5to3direction
3. Uracilisplacedasadeninescomplement
4. Attermination,RNApolymeraserecognizes
signalsandreleasesthetranscript
1001,200baseslong
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Transcription

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Translation
Ribosomesassembleonthe5endofa
mRNAtranscript
RibosomescansthemRNAuntilitreaches
thestartcodon,usuallyAUG
AtRNAmoleculewiththecomplementary
anticodonandmethionineaminoacidenters
thePsiteoftheribosome&bindstothe
mRNA
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Translation

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59

Using this
chart, you can
determine
which amino
acid the codon
codes for!
Which amino
acid is
encoded in the
codon CAC?

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Find the
second
letter of
the codon
CAC

Find the
first letter
of the
codon
CAC

Find the
third letter
of the
codon
CAC
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CAC codes
for the
amino acid
histidine
(his).

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What does
the mRNA
codon
UAC code
for?
Tyr or tyrosine

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InterpretingtheDNAcode

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Translationelongation
AsecondtRNAwiththecomplementary
anticodonfillstheAsite
Apeptidebondisformed
ThefirsttRNAisreleasedandtheribosomeslides
downtothenextcodon.
AnothertRNAfillstheAsite&apeptidebondis
formed.
Thisprocesscontinuesuntilastopcodonis
encountered.
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66

Translationtermination
TerminationcodonsUAA,UAG,and
UGAarecodonsforwhichthereisno
correspondingtRNA.
Whenthiscodonisreached,theribosome
fallsoffandthelasttRNAisremovedfrom
thepolypeptide.

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Polyribosomalcomplex

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Eucaryotictranscription&translationdiffers
fromprocaryotic
1. Donotoccursimultaneously.Transcriptionoccurs
inthenucleusandtranslationoccursinthe
cytoplasm.
2. EucaryoticstartcodonisAUG,butitdoesnotuse
formylmethionine.
3. EucaryoticmRNAencodesasingleprotein,unlike
bacterialmRNAwhichencodesmany.
4. EucaryoticDNAcontainsintronsintervening
sequencesofnoncodingDNAwhichhavetobe
splicedoutofthefinalmRNAtranscript.
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Splitgeneofeucaryotes

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MultiplicationofdsDNAviruses

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Multiplicationof+ssRNA

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Regulationofproteinsynthesis&
metabolism

Operons
acoordinatedsetofgenes,allofwhichare
regulatedasasingleunit.
2types
inducibleoperonisturnedONbysubstrate:
catabolicoperonsenzymesneededtometabolize
anutrientareproducedwhenneeded
repressiblegenesinaseriesareturnedOFFby
theproductsynthesized;anabolicoperon
enzymesusedtosynthesizeanaminoacidstop
beingproducedwhentheyarenotneeded
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Lactoseoperon:inducibleoperon
Madeof3segments:
1. Regulatorgenethatcodesforrepressor
2. Controllocuscomposedofpromoterand
operator
3. Structurallocusmadeof3geneseachcoding
foranenzymeneededtocatabolizelactose
galactosidasehydolyzeslactose
permeasebringslactoseacrosscellmembrane
galactosidasetransacetylaseuncertainfunction
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Lacoperon
Normallyoff
Intheabsenceoflactosetherepressorbinds
withtheoperatorlocusandblockstranscription
ofdownstreamstructuralgenes

Lactoseturnstheoperonon
Bindingoflactosetotherepressorprotein
changesitsshapeandcausesittofalloffthe
operator.RNApolymerasecanbindtothe
promoter.Structuralgenesaretranscribed.
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Lactoseoperon

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Arginineoperon:repressible
Normallyonandwillbeturnedoffwhen
nutrientisnolongerneeded.
Whenexcessarginineispresent,itbindsto
therepressorandchangesit.Thenthe
repressorbindstotheoperatorandblocks
argininesynthesis.

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Repressibleoperon

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Antibioticsthataffectgene
expression
RifamycinbindstoRNApolymerase
ActinomycinDbindstoDNA&haltsmRNA
chainelongation
Erythromycin&spectinomycininterferewith
attachmentofmRNAtoribosomes
Chloramphenicol,linomycin&tetracyclinebind
toribosomeandblockelongation
Streptomycininhibitspeptideinitiation&
elongation
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MutationschangesintheDNA
Pointmutationaddition,deletionor
substitutionofafewbases
Missensemutationcauseschangeina
singleaminoacid
Nonsensemutationchangesanormal
codonintoastopcodon
Silentmutationaltersabasebutdoesnot
changetheaminoacid
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