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8/8/2019 Genetic Information New

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From Human to DNAFrom Human to DNA

GenesGenes

....TTGGAATTTTCCGGGGTT

AAAATTGGAACCAAGGTT....

CellsCells

ChromosomChromosom

eses

DNADNA

HumaHuma

nn


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1 2 3 45 UTR 3 UTR

From ChromosomeFrom Chromosome

to Geneto Gene


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NUCLEOTIDES are the subunits of nucleic acid,

Including DNA. Each of these subunits is made up of:

AN ORGANIC BASE

A PENTOSE SUGAR

Note that the phosphate group

is bonded to the C-5 atom of the

pentose sugar

NH2

C H

N C

C C

O N H

O-

-O P O CH2 O

O- C C

H HH H

C C

OH H

1

23

4

5


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STRUCTURE OF THE NUCLEIC ACIDSSTRUCTURE OF THE NUCLEIC ACIDSSTRUCTURE OF THE NUCLEIC ACIDSSTRUCTURE OF THE NUCLEIC ACIDS

NUCLEIC ACIDS ARE POLYMERS OF NUCLEOTIDES

- Deoxyribonucleic acid (DNA)

- Ribonucleic acid (RNA)

NUCLEOTIDE STRUCTURE

DNA and RNA, are polymers of nucleoside

monophosphates (nucleotides) group.

Each nucleotide consists of :

1. A Pentose sugar :

a. Ribose sugar RNAb. Deox ribose su ar DNA


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2. A Nitrogenous base :2. A Nitrogenous base :

a. Purines : adenine (A) and guanine (G) found in DNAor

RNA

b. Pyrimidins : Cytosine (C), thymine (T), and uracil (U)

Thymines are found only in DNA

Uracils are found only in RNA

3. Phosphate


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The normal base-pairing arrangement found in DNA.The normal base-pairing arrangement found in DNA.(The dashed lines indicate hydrogen bonds)(The dashed lines indicate hydrogen bonds)


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THE SECONDARY STRUCTURE OF DNATHE SECONDARY STRUCTURE OF DNATHE SECONDARY STRUCTURE OF DNATHE SECONDARY STRUCTURE OF DNA

THE DOUBLE HELIX

1. Two antiparallel strands form a right-handed helix

2. Complementary base pairing

a b


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TranscriptionTranscription

Transcription

1 2 3 4

Start (ATG) Stop (TGA, TAA, TAG)

Genomic DNA

5 UTR 3 UTR

1 2 3 4

Start (AUG) Stop (UGA, UAA, UAG)

Primary RNA

5 UTR 3 UTR

2 copies

many

copies


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(1) Multiple factor and RNA polymerase II are needed to initiate

transcription from TATA box promoters. Including RNA polymeraseII, more than 40 different polypeptides are needed to initiate

transcription

(a) Transcription factor IID (TFIID) recognizes and binds to the

TATA box sequences independently of RNA polymerase II

(i) The TATA box-biding protein (TBP) is the subunit of

TFIID that binds to the TATA-box DNA sequence

(ii) TFIID is made of eight other subunits called TBP-asso ciated

factros (TAF)

(b) Five other transcription factors are required for the proper initation

of transcription by RNA polymerase II (TFIIA, TFIIB, TFIIF,

TFIIE AND TFIIH)


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There is no poly (T) sequence

in the DNA template that

corresponds to this tail


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SplicingSplicing

Primary RNA

1 2 3 4


5 UTR 3 UTR

2 315 UTR 4 3 UTRmRNA

Start Stop

splicing2 3

2 3

GT AGIntron 2

exons

introns


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Primary RNA

1 2 3 4


5 UTR 3 UTR


315 UTR 4 3 UTRmRNA

215 UTR 4 3 UTRmRNA

15 UTR 4 3 UTRmRNA

Splicing:Splicing:

FlexibilityFlexibility


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TranslationTranslation


Start Stop

NC

Nucleus

Cytoplasm2 315 UTR 4 3 UTR


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FORMATION OF AMINO ACYL-tRNA

- AMINO ACYL-tRNA SYNTHETASES :

* ENZYMES THAT ACTIVATE AMINO ACID

ATTACH THEM TO THE 3 TERMINAL ADENOSINE* PROOFREADING CAPABILITY

- HYDRALYZE THE AMINO ACID FROM THE tRNA

- THE AMYNO ACYLATION REACTION

AMINO ACID + ATP + tRNA AMINO ACYL- tRNA +P i + AMP


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Removal of introns from pre-tRNA.

The intron, located at the 3 end

of the antocordon, is removed.

Ligation produces the mature

tRNA.


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Nuclear ribonucleoproteins (snRNPs U1 to U6) bind to the intron causing it toform a loop.

Cleavage at the left splice sites releases exon 1, which remains attached tothe complex (the sliceosome). A 5-2 bond forms between the indicated Gand A residues.

A second cleavage releases exon 2, which is spliced to exon 1. The lariat-shaped intron is released.


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The mature, intronless mRNA, capped at the 5-end and equiped with a poly (A) tail,

complexes with proteins and travels through pores in the nuclear envelope into the

cytoplasm.

Overview of mRNA synthesis.

Transcription produces hnRNA from the DNA template.

hnRNA processing involves addition of a 5-cap and a poly (A) tail and splicing to join

exon and remove introns.

The product, mRNA, migrates to the cytoplasm.


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Start Stop

CCGGAUGCACUUGAAAUAAGCUA

GUG

H

UUU

K


L

AAC

UAC

M

UAC

M


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UACGUGAAC

GUG

MHL

K

GUG UAC

M

GUG

H

AAC

LK

CCGGAUGCACUUGAAAUAAGCUAGUG

H

UUU

K


L

AAC

UAC

M

UAC

M


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Bonecell

Livercell

Neuron

Cell-typeCell-typespecificspecific

expressionexpression


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Cell-type specific expression

Temporal regulation

Coexpression with other genes

The transcription translation system allows

the formation of a complex life form such asa human being out of 30.000 genes

If everything goes fine


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Mutations

Abberant expression

Genetic disease

If something goes wrong


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Size of DNA molecules

- Human = 3.0 x 109 base pairs / haploid cell

= 6.0 x 109 base pairs / diploid cell- 1 chromosome ~ 7 cm in length- 46 chromosome 2 m- < 10% of DNA codes for a product

Packing of DNA in cells- DNA interacts with basic proteins known as histones

- Histones arginine and lysine- Five classes of histones : H1, H2A, H2B, H3 and H4

H2A

H2B EllipsoidH3

H4

- Other types of proteins are also associated with DNA

- Nucleosomes : * bead-like structures of DNA

* DNA coils around the surface of the ellipsoid

* Complex of histones plus DNA


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Multiple DNA polymerases with multiple enzymatic activities

(1). DNA polymerase I (pol I)

a. Function. Pol I functions in the replication of DNA and in the repair ofdamaged DNA

b. Other enzymatic activities. Pol I has two enzymatic activities -

besides DNA polymerase activity (1) Proofreading (Figure 1)

Figure 1. 3 to 5 Exonuclease (proofreading) activity

(2) Excision-repair (Figure 2). Pol I has a 5 to 3 exonuclease activity,

called excision-repair activity, that can hydrolytically remove a

segment of DNA from the 5 end of a strand of duplex DNA

(a) One to ten nucleotide segments of DNA can be removedat onetime

3 to 5

5 - G T C A T G G 5 - G T C A T G G .. .. .. ... .. .. .. ...3 - C A G T A C C G C T T A G - 5 3 - C A G T A C C G C T T A G - 5 + dTMP

exonuclease

3

-T-OH


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Figure 2. 5 to 3 exonuclease (excision-repair) activity.

3 to 5

G A A T G- 3 5 - T C -3 .. .. .. .. 3 - C A G T A C C G C T T A G - 5 3 - C A G T A C C G C T T A G - 5

+5 - T G A A - 3

exonuclease5-T-


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- Unwinds the supercoil DNA by cutting bothstrands of DNA

- Followed by the helicase activity

6. Single-strand binding protein ( SSBP )

it binds to single-stranded DNA (ssDNA)Function : - to protect ssDNA from nucleases

7. DNA Polymerases


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* Helicases unwind the parental DNA

* Single-strand binding proteins ( SSB )

prevent from reassociating

protection

- Action of DNA Polymerase

E.Coli has three DNA polymerase

Pol I

Pol IIPol III

- DNA gyrase uncoils DNA


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1. Unwind the helix by helicases

- With the aid of the DNA gyrase

- Dna B protein

- SSBP

2. DNA is replicated by DNA polymerase III.

The detail of the process :

- Primase ( a special RNA) a short RNA primer (10

nucleotides and compelemtary to the DNA)

- DNA polymerase III synthesizes complementary DNA

beginning at the 3 end of the RNA primer

- Leading and lagging strand are performed

- Lagging strand replcation is discontinous and the

fragments is called Okazaki fragments


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2. DNA polymerase also is essential for replication. It is

required for both leading and lagging strand synthesis

a. Pol associated with proliferating cell nuclear antigen(PCNA)

b. After pol has initiated replication, a protein calledreplication

factor C (RF-C) facilitates the inhibition an replacement

of pol with both PCNA and pol in an ATP-

dependent manner.


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3. DNA polymerase plays no role in replication and acts

only in DNA repair synthesis

4. DNA polymerase also is essential for replication,

although its exact role is not clearly defined. It behavessimilarly to pol and may support some component oflagging strand synthesis.

5. DNA polymerase replicates mitochondrial DNA


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1. 5 to 3 exonucleases. One is known to be associated with

DNA polymerase .

2. 3 to 5 exonucleases activity. DNA polymerase , , and have proofreading capability.

3. Ligase. Unlike prokaryotic ligase that use nicotinamideadenine dinucleotide (NAD) as an energy source,

eukaryotic ligases use

ATP

4. Helicase


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5. An SSBP called replication protein A (RP-A) has beenisolated from mammalian cells

6. Topoisomerases. These enzymes build up in advance

of replication forks.

Two basic types of eukaryotic topoisomerases.

a. Topoisomerase I is the major topoisomerase used to

relieve supercoils

b. Topoisomerase II also is required during replication.


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Model of the mechanism of replication of human telomeras


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MUTATIONS

Mutations permanent changes in the DNA

sequence.

Causes :

1. Errors in replication. If a base that noncomplementry tothe template base is added during replication, then the

error is not repaired mutation

2. Errors that accur during recombination events.

The DNA of living cells is surprisingly mobile and often isrearranged or recombined.

3. Chemical mutagens

4 Irradition


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4. Irradition

a. Ultraviolet ( UV ) light (200-400 nm) induces

dimerization of adjacent pyrimidines, particularly

adjacent thymines.B. Ionizing radiation, such as roentgen rays (x-rays) and

gamma rays ( -rays)5. Spontaneous changes. They lead to mutations if they

are not repaired before a round of replication.

a. Deamination of cytosine (C) to form uracil (U) occurs

spon-

taneously.

b. Spontaneous depurination. Purines are less stable

under normalcellular conditions than pyrimidines. The glycosidic

bond that

links purines to the sugar-phosphate backbone of

DNA oftenis broken


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1. Base substitution

- Base substitution are the most common type of

mutation, and they can be classified into twosubtypes :

(1). Transitions, in which one purine is replaced by

another purine or one pyrimidine is replaced by

another pyrimmidine

(2). Transversions, in which a purine is replaced by a

pyrimidiner a pyrimidine is replaced by a purine

2. Deletion of one or more base pairs

3. Insertion of one or more base pairs. Insertions of base

pairs intogenes can lead to severe frameshift mutation

(e.g., thalassemias)


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There are 2 types of changes:1. Point mutation gene mutation

mutation

2. Gross mutation chromosomeaberration aberration


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Abnormal structure or number ofchromosomes; includes deficiency,duplication, inversion, translocation,aneuploid, polyploid, or any changefrom normal


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A mutation caused by the altera- tion of asingle base in DNA:

Substitution of one base-pair for another

Duplication of single base-pairs

Deletion of single base-pairs


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a. MUTATION ACCORDING TO CHANGELOCATION

1. Mutation on nucleotides: deletion,

substitution, insertion, anddimerization

2. Mutation on splicing


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b. MUTATION IN ACCORDANCE WITH THEFORM OF CHANGES

1. Mis-sense mutation2. Non-sense mutation

3. Silence mutation

4. Frame-shift mutation

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1 Codon Deletion1 Codon Deletion


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1 Codon Deletion1 Codon DeletionCodogenCodogen ::TTATTATAGTAGTATAGG GAGAAA CCACCA CAACAA

CodonCodon :: AAU AUCAAU AUC AUCAUC CUUCUU GGUGGU GUUGUU

Amino acid: asn - ile - ile - leu - gly - valAmino acid: asn - ile - ile - leu - gly - val

Mutation on base sequence GGAMutation on base sequence GGA

CodogenCodogen ::TTATTATAGTAGTATACodonCodon :: AAU AUCAAU AUCAUAU

Amino acid: asn - ile -Amino acid: asn - ile -

AA CCACCA CAACAAUU GGUGGUGUUGUU

ile - gly - valile - gly - val

Frame-shift are occurred here, and proteiFrame-shift are occurred here, and proteiformed are distinctly different from theformed are distinctly different from the

originaloriginal


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1. A single-base substitution

Original

codon

Original

am. acid

New

codon

New

am. acid

UUA

GAU

Leu

Asp

UUG

GAA

Leu

Glu

SILENT MUTATION

MIS-SENSE MUTATION

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