Prof. Dr. Samih Tamimi

Biology 1 Al-Ahlya Amman University

Prof. Dr. Samih Tamimi

Chapter 16 and 17 Notes


Chapter 16 People:

1. Griffith - studied bacteria- heat killed cells (bacteria) were able to take in material from living cells that were not harmful (bacteria)- mixture would kill the mice- bacteria cells were transformed

2. Avery - announced transformation agent was DNA

4. Chargaff - identified 4 nitrogen bases: adenine, thymine, guanine, cytosine- base pairing rules: A-T, C-G- % of A = % of T, % of C = % of G

6. Watson and Crick – model for DNA molecule


Sugar–phosphate backbone

5 end

Nitrogenous bases

Thymine (T)

Adenine (A)

Cytosine (C)

Guanine (G)

DNA nucleotide

Sugar (deoxyribose)

3 end

Phosphate

one side of DNA withbases

5’ carbon attachedto phosphategroup

3’ carbon attachedto hydroxyl group

Structure of the double helix


The double helixMonomer of nucleic acid:

3 parts to a nucleotide:

1.

2.

3.

nucleotide

phosphate

sugar-DNA (deoxyribose)

base - purines - pyrimidines


Purines -

-

-

Pyrimidines -

-

-

Bonds that connect bases:

double ringed bases

adenine

guanine

single ringed bases

cytosine

thymine

hydrogen bonds


A T

GC

T A

TA

G C

(a) Parent molecule

A T

GC

T A

TA

G C

(c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand

(b) Separation of strands

A T

GC

T A

TA

G C

A T

GC

T A

TA

G C

complementary base pairing

A - T C - G


Parent cellFirst replication

Second replication

(a) Conservative model

(b) Semiconserva- tive

model

(c) Dispersive model

Semiconservative model:

the old strand makes a new strand


Origin of replication Parental (template) strand

Daughter (new) strand

Replication fork

Replication bubble

Two daughter DNA molecules

(a) Origins of replication in E. coli

Origin of replication Double-stranded DNA molecule

Parental (template) strandDaughter (new) strand

Bubble Replication fork

Two daughter DNA molecules

(b) Origins of replication in eukaryotes

0.5 µm

0.25 µm

Double-strandedDNA molecule

bacterial DNA


A

C

T

G

G

G

GC

C C

C

C

A

A

AT

T

T

New strand 5 end

Template strand 3 end 5 end 3 end

3 end

5 end5 end

3 end

Base

Sugar

Phosphate

Nucleoside triphosphate

Pyrophosphate

DNA polymerase

Antiparallel - side chains of DNA run in DNA elongates only in the5’ 3’3’ 5’ 5’ 3’ direction

oppositedirections


OverviewOrigin of replication

Leading strand

Leading strand

Lagging strand

Lagging strandOverall directions

of replication

Leading strand

Lagging strand

Helicase

Parental DNA

DNA pol III

Primer Primase

DNA ligase

DNA pol III

DNA pol I

Single-strand binding protein

5

3

5

5

5

5

3

3

3

313 2

4

helicase - unwinds double helix

ssbp’s – stabilize unwound DNA

primase – synthesizes RNA primer

DNA polymerase III – synthesizes new DNA on 3’ endDNA polymerase I – removes primers and brings in DNA nucleotides

ligase – covalently connectsDNA nucleotides



TRANSCRIPTION

TRANSLATION

DNA

mRNARibosome

Polypeptide

DNA

Pre-mRNA

Prokaryotic cell

Nuclearenvelope

mRNA

TRANSLATION

TRANSCRIPTION

RNA PROCESSING

Ribosome

Polypeptide

Eukaryotic cell

Transcription – synthesis of

makes

Translation – synthesis of a polypeptide

-

-

CHAPTER 17

RNA from DNA

mRNA (messenger)

occurs on ribosome

from mRNA

uses tRNA

Compartmentalization oftranscription and translation

-provides an opportunity to

*bacteria

-

modify mRNA beforeit leaves the nucleus

do not havethis

no nucleus


DNAmolecule

Gene 1

Gene 2

Gene 3

DNA strand(template)

3

TRANSCRIPTION

Codon

mRNA

TRANSLATION

Protein

Amino acid

35

5**

-

-codon-

-start codon:

1 gene codes for oneprotein (polypeptide)

gene/protein results inthe organisms

3 consecutive baseson mRNA

AUG (methaionine)

20 different amino acids

phenotype


Second mRNA base

Firs

t mR

NA

base

(5 e

nd o

f cod

on)

Third

mR

NA

base

(3 e

nd o

f cod

on)


Promoter Transcription unit

Start point DNA

RNA polymerase

5533

Initiation1

2

3

5533

UnwoundDNA

RNAtranscript

Template strandof DNA

Elongation

RewoundDNA

5

55

5

5

333

3

RNAtranscript

Termination

5533

35Completed RNA transcript

Newly madeRNA

Templatestrand of DNA

Direction oftranscription(“downstream”)

3 end

RNApolymerase

RNA nucleotides

Nontemplatestrand of DNA

Elongation

Promotor region: a start point for RNA polymerase

also determines which strand will be copied


Amino acidattachment site

3

5

Hydrogenbonds

Anticodon

(a) Two-dimensional structure

Amino acidattachment site

5

3

Hydrogenbonds

3 5AnticodonAnticodon

(c) Symbol used in this book(b) Three-dimensional structure

anticodon – complementary to the

tRNA – transfers amino acids

from the cytoplasms pool to

a ribosome

codon on mRNA


Amino acid Aminoacyl-tRNAsynthetase (enzyme)

ATP

AdenosineP P P

AdenosineP

PP i

PPi

i

tRNA

tRNA

Aminoacyl-tRNAsynthetase

Computer modelAMPAdenosineP

Aminoacyl-tRNA(“charged tRNA”)

connecting an aminoacid to tRNA


Polypeptide

tRNA withamino acidattached

Ribosome

tRNA

Anticodon

35

mRNA

Aminoacids

Codons

Synthesis of proteins:

A site –

P site –

E site –

incoming

growing polypeptide

exit site


Ribosome

-

-

Functional ribosome:

- small

- add

- large

Growingpolypeptide Exit tunnel

Largesubunit

Smallsubunit

tRNAmolecules

E PA

mRNA5 3

(a) Computer model of functioning ribosome

P site (Peptidyl-tRNAbinding site)

E site(Exit site)

A site (Aminoacyl-tRNA binding site)

E P A Largesubunit

mRNAbinding site Small

subunit

(b) Schematic model showing binding sites

Amino end Growing polypeptide

Next amino acidto be added topolypeptide chain

mRNAtRNAE

3

5 Codons

(c) Schematic model with mRNA and tRNA

2 subunits

rRNA and protein

ribosomal unit

mRNA and tRNA

unit binds

-uses energy


3355U

UA

ACGMet

GTP GDPInitiator

tRNA

mRNA5 3

Start codon

mRNA binding siteSmallribosomalsubunit

5

P site

Translation initiation complex

3

E A

Met

Largeribosomalsubunit

1. Initiation

3 stages for building a polypeptide:

Binding of mRNA to small subunit and initiator tRNA carrying met to P site with initiation codon (AUG)

Then large subunit attaches


Amino endof polypeptide

mRNA

5

3E

Psite

Asite

GTP

GDP

E

P A

E

P A

GDPGTP

Ribosome ready fornext aminoacyl tRNA

E

P A

2. Elongation Cycle

peptide bonds are formedbetween amino acids

Codon recognition

Peptide bond formation

Translocation


Releasefactor

3

5Stop codon(UAG, UAA, or UGA)

5

32

Freepolypeptide

2 GDP

GTP

5

3

3. Termination release factor attaches to stop codon, everythingreleases

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Prof. Dr. Samih Tamimi