NUCLEUS

Chromosome
Structure and Genes

Owl cake instruc/ons are

very easy to follow

Nucleus gives the instruc/ons

to make materials that are
needed by the cell
DNA!

 1953 Watson
and Crick
determined
structure of DNA
Double helix
Sugar and
Phosphate group
Ester bond
C,G,T,A
long

DNA Double Helix

10.4 nucleu/des/turn; 3.4 nm between nucleu/des

The Func)ons of DNA

Gene/c informa/on is carried in the linear
sequence of nucleo/des in DNA
Gene/c informa/on contains instruc/ons to
synthesize proteins
DNA forms double helix with two
complimentary strands holding together by
hydrogen bonds between A-T (2 bonds) and G-
C (3 bonds)
DNA duplica/on occurs using one strand of
parental DNA as template to form
complimentary pairs with a new DNA strand

How are DNA (gene/c material)

packed in the nucleus?
chromosomes

Humans have 23 pairs of chromosomes. Of these 23,

22 are autosomes (non sex chromosomes) and one is a
sex chromosome. Sex chromosomes determine our sex
(this is not the case for all animals). In humans, females
have XX while males have XY

Dierent bits of the

chromosomes represent
dierent genes
Dierent genes code for dierent
thing
Humans have approximately
22,000 genes

These dierent bits are

called
GENES
Gene Jury

Structural Organiza/on of the Core Histones

The bending of DNA in a nucleosome

1. Flexibility of DNAs: A-T riched minor groove inside
and G-C riched groove outside
2. DNA bound protein can also help

The func/on of Histone H1

The func/on of Histone

tails

Chroma/n Packing
Condensin plays important roles

Chromosome

The structure of a
human centromere
1. Alpha satellite DNA
sequence
2. Kinetochore inner plate
3. Kinetochore outer plate
4. Spindle microtubules

The organiza)on of genes of a human chromosome

To carry the genomic informa/on to daughter cells

DNA Duplica/on
Using itself as template

CENTRAL DOGMA
Cell Cycle and DNA
Replication
Transcription and 
RNA Processing

CENTRAL DOGMA OF MOLECULAR BIOLOGY

Central Dogma of Molecular Biology

Paderns of Base Pairing

Bases in DNA strands can pair in only one way
A always pairs with T; G always pairs with C

The sequence of bases is the genetic code

Variation in base sequences gives life diversity

Four requirements for DNA to be genetic material:

Must carry information
Cracking the genetic code
Must replicate
DNA replication
Must allow for information to change
Mutation
Must govern the expression of the
phenotype
Gene function
hdp://www.google.com.ph/url?sa=t&rct=j&q=DNA%20replica/on%20momna%20hejmadi&source=web&cd=4&ved=0CDsQFjAD&url=hdp%3A%2F%2Fwww.bath.ac.uk%2Fbio-sci%2Foer%2Fincluder.php
%3Fid%3D52%26nocache%3D1267210964&ei=XBFIULnwFcmwiQfV4IC4AQ&usg=AFQjCNHs4JKyIJUJsOAEaJL0ezkkhuycLg

DNA Replication
Process of duplication of the entire genome prior to cell
division
Biological significance
extreme accuracy of DNA replication is necessary in
order to preserve the integrity of the genome in
successive generations
In eukaryotes , replication only occurs during the S
phase of the cell cycle.
Replication rate in eukaryotes is slower resulting in a
higher fidelity/accuracy of replication in eukaryotes

The mechanism of DNA replication

Initiation
Proteins bind to DNA and open up double helix
Prepare DNA for complementary base pairing

Elongation
Proteins connect the correct sequences of
nucleotides into a continuous new strand of DNA

Termination
Proteins release the replication complex

In DNA replication:
Semi-conservative
Starts at the origin
Can be uni or bidirectional
Semi-discontinuous
Synthesis always in the 5-3 direction
RNA primers required

DNA replication
Of the 3
possible
models,
replication
is

Semi-conserva/ve

Starts at origin
Initiator proteins identify specific base
sequences on DNA called sites of origin
Prokaryotes single origin site E.g E.coli - oriC
Eukaryotes multiple sites of origin (replicator)
E.g. yeast - ARS (autonomously replicating
sequences)

Prokaryotes

Eukaryotes

Uni or bidirectional
Replica/on forks move in one or opposite direc/ons

Semi-discontinuous replication
Anti parallel strands replicated simultaneously
qLeading strand synthesis continuously in 5 3
qLagging strand synthesis in fragments in 5-3

hdps://wikispaces.psu.edu/download/adachments/54886630/DNA_structure.jpg
hdp://jan.ucc.nau.edu/lrm22/lessons/dna_notes/dna_structure.gif

Semi-discontinuous replication
New strand synthesis always in the 5-3 direction

What happens if a base

mismatch occurs?

DNA polymerase has 3 5

exonuclease ac/vity in order to
correct errors

Where does energy for addition

of nucleotide come from?

From cleavage of high energy phosphate

of incoming triphosphate

RNA primers required

DNA polymerase can only join an incoming nucleo/de to one that
is base-paired
RNA primase provides a base paired 3 end as a star/ng point for
DNA pol by synthesising ~10 nucleo/de primers

Core proteins at the replication fork

Topoisomerases - breaks, swivels and rejoins parental
DNA ahead of the replica/on fork,
relieves strain caused by unwinding
Helicases - separates 2 strands
Primase - RNA primer synthesis
Single strand - prevent reannealing of single strands
binding proteins - synthesis of new strand
DNA polymerase - stabilises polymerase
Tethering protein - seals gaps via phosphodiester linkage
DNA ligase

Core proteins at the replication fork

Nature (2003) vol 421,pp431-435

Why has DNA

evolved as the
gene/c material but
not RNA?
Because DNA is more
stable
RNA is prone to base-
catalysed hydrolysis.

hdp://serc.carleton.edu/microbelife/research_methods/genomics/replica/on.html

Recall
DNA Replica/on

hdp://ingsscience.com/Documents/DNA%20Transcrip/on%20and%20Transla/on%20GELNCOE.ppt

Replica/on Fork Overview

DNA replica/on

The parent molecule unwinds, and two new

daughter strands are built based on base-
pairing rules

T

A
G

(a) The parent molecule

has two complementary
strands of DNA. Each base
is paired by hydrogen
bonding with its specific
partner,
A with T and G with C.

(b) The first step in

replication is separation of
the two DNA strands.

(c) Each parental strand

now serves as a template
that determine as the order
of nucleotides along a new,
complementary strand.

(d) The nucleotides are

connected to form the
sugar-phosphate
backbones of the new
strands. Each daughter
DNA molecule consists of
one parental strand and one
new strand.

DNA Replica/on

The copying of DNA is remarkable in its speed and accuracy

Involves unwinding the double helix and synthesizing two
new strands.
More than a dozen enzymes and other proteins par/cipate
in DNA replica/on
The replica/on of a DNA molecule begins at special sites
called origins of replica/on, where the two strands are
separated

Enzymes in DNA replica)on

Helicase unwinds
parental double helix

DNA polymerase III

binds nucleotides
to form new strands

Binding proteins
stabilize separate
strands

Primase adds
short primer
to template strand

DNA polymerase I
(Exonuclease) removes
RNA primer and inserts
the correct bases

Ligase joins Okazaki

fragments and seals
other nicks in sugarphosphate backbone

Replica)on
3
3

5
3
5

Helicase protein binds to DNA sequences called

origins and unwinds DNA strands.
Binding proteins prevent single strands from rewinding.
Primase protein makes a short segment of RNA
complementary to the DNA, a primer.

Replica)on
Overall direction
of replication

3
3

5
3
5

3
5

DNA polymerase enzyme adds DNA nucleotides

to the RNA primer.

Replica)on
Overall direction
of replication

3
5

3
5
3
5

3
5

DNA polymerase enzyme adds DNA nucleotides

to the RNA primer.
DNA polymerase proofreads bases added and
replaces incorrect nucleotides.

Replica)on
Overall direction
of replication

3
3

5
3
5

Leading strand synthesis continues in a

5 to 3 direction.

3
5

Replica)on
Overall direction
of replication

3
3

5
Okazaki fragment

3
5

Leading strand synthesis continues in a

5 to 3 direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.

3 5

3
5

Replica)on
Overall direction
of replication

3
3

5
Okazaki fragment

3
5

Leading strand synthesis continues in a

5 to 3 direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.

35

3
5

Replica)on
3
5

3
5
3
5

3 5

35

3
5

Leading strand synthesis continues in a

5 to 3 direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.

Replica)on
3
5

3
5
3
5

35

35

3
5

Leading strand synthesis continues in a

5 to 3 direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.

Replica)on
3
5

3
5
3
5

35

35

3
5

Exonuclease activity of DNA polymerase I removes RNA primers.

Replica)on
3
3
5
3
5

35

3
5

Polymerase activity of DNA polymerase I fills the gaps.

Ligase forms bonds between sugar-phosphate backbone.

Proofreading
DNA must be replicated
but mistakes occur

DNA polymerase (DNA pol)

inserts the wrong
nucleo/de base in 1/10,000
bases
DNA pol has a proofreading
capability and can correct
errors

Mismatch repair: wrong

inserted base can be
removed
Excision repair: DNA may
be damaged by chemicals,
radia/on, etc. Mechanism
to cut out and replace with
correct bases

1 A thymine dimer
distorts the DNA molecule.
2 A nuclease enzyme cuts
the damaged DNA strand
at two points and the
damaged section is
removed.
Nuclease

DNA
polymerase

3 Repair synthesis by
a DNA polymerase
fills in the missing
nucleotides.
DNA
ligase

4 DNA ligase seals the

Free end of the new DNA
To the old DNA, making the
strand complete.

Muta/ons
A mismatching of base pairs, can occur at a
rate of 1 per 10,000 bases
DNA polymerase proofreads and repairs
accidental mismatched pairs
Chances of a muta/on occurring at any one
gene is over 1 in 100,000
Because the human genome is so large,
even at this rate, muta/ons add up. Each
of us probably inherited 3-4 muta/ons!

DNA Transcription
and Translation
hdp://ingsscience.com/Documents/DNA%20Transcrip/on%20and%20Transla/on%20GELNCOE.ppt

Gene
Segment of DNA
that codes for a
protein
DNA codes for RNA
and RNA makes
protein
Beadle and Tatum
experiment showed
one gene codes for
one enzyme

hdp://www.genomenewsnetwork.org/gnn_images/whats_a_genome/gene.gif

DNA and RNA

DNA has one func)on: It

permanently stores a cells
gene)c informa)on, which is
passed to ospring.

RNAs have various

func/ons. Some serve
as disposable copies of
DNAs gene/c message;
others are cataly/c.

Recall RNA!
RNA stands for:

Ribonucleic acid

RNA is found:

Nucleus and Cytoplasm

Structure: RNA is made up

of subunits called
nucleo)des, which are
made of three parts:
Sugar (ribose)
Phosphate
Nitrogen Base

RNA Nitrogen Bases

Adenine (A)
Cytosine (C)
Guanine (G)
Uracil (U)

Types of RNA
Messenger RNA (mRNA) carries genetic information from
DNA to direct protein synthesis in cytoplasm
Ribosomal RNA (rRNA) associates with protein to form
ribosome
Transfer RNA (tRNA) transfer amino acid to the ribosome

Transcrip)on
First step in making proteins
Process of taking one gene (DNA) and
converting into a mRNA strand
DNA -> RNA
Location:
Nucleus of the cell

Steps to Transcrip/on
1. An enzyme attaches to the promoter
(start signal region) of a gene and unwinds
the DNA

Steps to Transcrip/on
2. One strand acts as a template

Steps to Transcrip/on
3. A mRNA copy is made from the DNA
template strand by RNA polymerase

Steps to Transcrip/on
4. A mRNA copy is made until it reaches the
termination (stop signal) sequence
5. The two strands of DNA rejoin

mRNA Processing
Pre-mRNA the
original
sequence of RNA
created during
transcription
mRNA reaches
the ribosomes

Post-transcrip)onal modica)ons of RNA

accomplish two things
1) Modications help the RNA molecule to be
recognized by molecules that mediate RNA
translation into proteins;

2) During post-transcriptional processing,
portions of the RNA chain that are not
supposed to be translated into proteins are cut
out of the sequence.
Introns - non-coded sections
Exons - codes for a protein

Post-transcrip)onal processing
Helps increase the eciency of protein synthesis
allows only specic protein- coding RNA to go on to
be translated.
Without post-transcriptional processing, protein
synthesis could be signicantly slowed
since it would take longer for translation machinery to
recognize RNA molecules
signicantly more RNA would have to be
unnecessarily translated to achieve the same results

Post-transcip/onal modica/on of
pre-mRNA to mRNA

an example

Original DNA Sequence (DNA):

5 GTACTACATGCTATGCAT 3
Translate it (RNA):
3 CAUGAUGUACGAUACGUA 5

Add the 5 cap:

3 CAUGAUGUACGAUACGUA 5

cap

Finish the job!

Remove the introns UGUA and AUAC:
3 CAUGAUGUACGAUACGUA 5cap
3 CAUGACGGUA 5cap

Add a poly A tail onto the 3 end

Poly A tail

3 CAUGACGGUA 5cap

What is RNA Processing?

Before RNA leaves
the nucleus, introns
are removed and
exons are spliced
together
5cap is added
poly A tail to 3 end
mRNA leaves the
nucleus through the
nuclear pores

Proteins are made up of amino acids

Proteins are polymers of amino acids
Only 20 dierent amino acids
BUT there are hundreds of thousands of
dierent proteins

English language
How many letters are in the alphabet?
A,b,c,d,
26
How many words are there?
Miss, Ings, is, smart, ..
Almost innite!
Each word has a unique structure of letters.
Similar to proteins and amino acids

Proteins
-made of 20 different Amino Acids
- Amino Acids bond to form polypeptide
chains

Protein
Structure

http://www3.interscience.wiley.com:8100/legacy/college/boyer/0471661791/structure/HbMb/hbmb.htm

Transla)on
Production of proteins from mRNA
mRNA goes to the ribosomes in the
cytoplasm or the RER and produces
proteins

Steps to Transla/on
1. mRNA leaves the nucleus and binds to a
ribosome
2. The 5 end of mRNA binds to ribosome

Ribosome

Two subunits to the ribosome

3 grooves on the ribosome (A, P, E)
A: tRNA binding site
P: polypeptite bonding site
E: exit site

Steps to Transla/on
3. Ribosome looks for the start Codon
(AUG)
Codon: group of 3 nucleotides on the
messenger RNA that species one amino
acid (64 dierent codons)

The image cannot be displayed. Your computer may not have enough memory to open the image, or the image may have been corrupted. Restart your computer, and then open the file again. If the red x still appears, you may have to delete the image and then insert it
again.

Steps to Transla/on
4. Amino acids attached to a tRNA
molecule and are brought over to the
mRNA.
5. This tRNA has an anticodon that
matches the codon on the mRNA strand
Anticodon:
Group of 3 unpaired
nucleotides on a tRNA
strand. (binds to mRNA
codon)

Steps to Transla/on
6. tRNA binds to the mRNA sequence and
adds an amino acid
7. Each amino acid matches up with 1-6 tRNA
molecules
8. tRNA leaves and amino acids bond
together through a polypeptide bond

Steps to Transla/on
9. The mRNA sequence continues until a
stop codon is reached.
10. The amino acids disconnect from the
mRNA sequence and a protein is formed.

transcription

Assembly of RNA on unwound regions

of DNA molecule

Pre mRNA
transcript
processing

mRNA

rRNA

tRNA

protein
subunits
mature
mRNA
transcripts

translation

At an intact
ribosome,
synthesis of a
polypeptide
chain at the
binding sites for
mRNA and
tRNAs

ribosomal
subunits

Convergence
of RNAs

matur
e
tRNA

cytoplasmic
pools of
amino acids,
ribosomal
subunits and
tRNAs

final protein

For use in cell or for

transport


RNA to Protein: Transla/on
Key Concepts

Translation is an energy-intensive process

by which a sequence of codons in mRNA is
converted to a sequence of amino acids in a
polypeptide chain

Organization and
Evolution of Nuclear
Genome

Regulation of Gene
Expression

Operon Model for Gene Control

Francois Jacon and Jacques Monod 1961

Repressor Inac/ve Operon is On

Repressor Ac/ve Operon is O

How does Trp Operon works?

In the lac operon, allolactose binds to the

repressor protein, allowing gene transcrip/on,
while in the trp operon, tryptophan binds to
the repressor protein eec/vely blocking gene
transcrip/on. In both situa/ons, repression is
that of RNA polymerase transcribing the genes
in the operon.

END