Todays Plan: 3/23/16

DNA/RNA modeling (30 mins)

Pick up graded work/quest (during
DNA modeling time)
Go over replication (30 mins)
Begin Protein Synthesis activity (the
rest of class)
Todays Plan: 3/24/16
Bellwork: Talk about chromosome
packaging (10 mins)
How DNA Controls. . . activity (40
mins)
Transcription and translation with
video clips (the rest of class)
Todays Plan: 4/4/16
Bellwork: Scientists and Genetics
History Activity (15 mins)
Finish How DNA Controls. . . (45
mins)
Finish notes on post-transcriptional
modification and Mutation
Todays Plan: 4/5/16
Bellwork: Grab your answer
sheet/marker/eraser and get ready to
ask questions/quest!
DNA/Protein Synthesis Quest (as
needed)
When you finish the quest, do the
operon activity at your desk.
DNA Structure
Building block=nucleotide
Double Helix of consisting of
2 antiparallel strands-one runs 5 to 3, the other
in the opposite direction
A backbone on each strand consisting of a
repeating phosphate-deoxyribose segment
Complimentary base-paired links between the
strands using hydrogen bonds between a purine
(either A or G) and a pyrimidine (either T or C)
Figure 14-6
Structure of a deoxyribonucleotide
Phosphate group
attached to
5 carbon Could be
of the sugar 5
adenine (A),
thymine (T),
guanine (G)
3 cytosine (C)
Hydroxyl (OH)
group on 3 carbon
of the sugar

Primary structure of DNA

5 end of strand
Nitrogen-
containing bases
Sugar-phosphate
5 project from the
backbone of backbone
DNA strand

Phosphodiester
bond links
deoxyribonucleotides

3 end of strand
Figure 14-7
Complementary base pairing The double helix
3
5 5 3

Sugar-phosphate
backbone of DNA

Complementary
base pairs joined by
hydrogen bonding

5 5 3
3
Replication
DNA is copied in preparation for cell division
Involves a symphony of enzymes
Is done in a 5 to 3 direction
This means that replication is antiparallel
One strand is the leading strand and is replicated
continuously, the other is the lagging strand and is
replicated in pieces (called Okazaki fragments),
requiring linking later
Is semi-conservative
Has a single point of origin in bacteria, and multiple
points of origin in eukaryotes
Requires an RNA primer because the enzymes that
synthesize DNA cannot initiate a strand, they can only
add to an existing strand
Ends with proofreading by enzymes to make sure the
correct bases are in place.
Figure 14-10

A chromosome being replicated Bacterial chromosomes have a single point of origin.

Old DNA
3 5
New DNA
5 3

Replication
proceeds in
Origin of both directions
replication

Eukaryotic chromosomes have multiple points of origin. Replication

fork
5 5 5
3 3
Replication
3 3
5
3 bubble 3
5 5
Old DNA
New DNA
Replication proceeds in both
directions from each starting point
Figure 14-13-Table 14-1-1
Figure 14-13-Table 14-1-2
Figure 14-11

SYNTHESIS OF LEADING STRAND

Primase synthesizes RNA primer
3 5
Topoisomerase relieves twisting forces

5
3

Helicase opens double helix

5
Single-strand DNA-binding proteins (SSBP) stabilize single strands

1. DNA is opened, unwound, and primed.

Sliding clamp holds DNA polymerase in place

3 5 DNA polymerase III works in 5 3 direction, synthesizing leading strand

RNA primer
5
Leading strand
3

2. Synthesis of leading strand begins.

Figure 14-13-Table 14-1-3
Figure 14-13-1

SYNTHESIS OF LAGGING STRAND

5
3
RNA
primer 5
3
5 Topoisomerase
SSBPs Helicase
Primase

1. Primase synthesizes RNA primer.

Figure 14-13-2

SYNTHESIS OF LAGGING STRAND

5
3
Okazaki fragment
5
3
3 5
5

Sliding clamp
DNA polymerase III
2. DNA polymerase III works in 5 3 direction, synthesizing first
Okazaki
fragment of lagging stand.
5
3
Okazaki fragment
Okazaki fragment 5
5 3
3
5

3. Primase and DNA polymerase III synthesize another Okazaki fragment.

Figure 14-13-3

SYNTHESIS OF LAGGING STRAND

5
3

DNA polymerase I 5
3 5 3
5

4. DNA polymerase I removes ribonucleotides of primer, replaces them with

deoxyribonucleotides in 5 3 direction.

5
3
DNA ligase 5
5 3
3
5

5. DNA ligase closes gap in sugar-phosphate backbone.

Figure 14-15

TELOMERE REPLICATION
Missing DNA on
lagging strand 1. When the RNA primer is removed from the
5 5 end of the lagging strand (see Figure 14.14),
a strand of parent DNA remains unreplicated.

3
Telomerase with its
own RNA template
2. Telomerase binds to the overhanging section
of single-stranded DNA. Telomerase adds
5 3 5 deoxyribonucleotides to the end of the parent
DNA, extending it.

3. Telomerase moves down the DNA strand and

5 3 5 adds additional repeats.

RNA primer
4. Primase, DNA polymerase, and ligase then
5 5 synthesize the lagging strand in the 53
direction, restoring the original length of the
chromosome.
3
DNA polymerase Sliding clamp
Figure 14-16

Mismatched bases

5 OH 3

3 5

DNA polymerase III can repair mismatches.

OH

5 OH
3

3 5
Figure 14-17

UV light Kin Thymine

DNA strand k
with adjacent dimer
thymine bases
Figure 14-18
NUCLEOTIDE EXCISION REPAIR
1. Enzymes detect an
irregularity in DNA
structure and cut the
damaged strand.

Damaged bases

2. An enzyme excises
nucleotides on the
damaged strand.

3 5 3. DNA polymerase
fills in the gap in the
5 3 direction.

5 3

4. DNA ligase links the

new and old nucleotides.

Repaired damage
From DNA to Chromosomes
DNA, after replication is bound to
proteins called histones-this is
chromatin
There are 8 histones per complex, and
DNA winds around these
In preparation for cell division,
chromatin coils, then supercoils (think
of coiling a phone cord) to become
more compact
Why RNA?
RNA, like DNA is made of nucleotides,
however:
RNA nucleotides use ribose, not deoxyribose
Uracil, a base, replaces Thymine,
RNA is single-stranded
RNA contains only 1 gene
RNA is smaller, and can therefore leave the
nucleus through the nuclear pores. DNA
cant
RNA code is written as codons (3-base
segments)
Figure 15-5

Information flows from DNA to RNA to DNA sequences define the genotype; Changes in the genotype may
proteins. proteins create the phenotype. lead to changes in the phenotype.
3 3
5 5
DNA
(information
storage)

TRANSCRIPTION TRANSCRIPTION

mRNA
(information 3
3
carrier)
5 5

TRANSLATION TRANSLATION
Proteins
(active cell
machinery)
Figure 15-8

SECOND BASE

Phenylalanine (Phe) Tyrosine (Tyr) Cysteine (Cys)

Serine (Ser)
Stop codon Stop codon
Leucine (Leu)
Stop codon Tryptophan (Trp)

Histidine (His)
FIRST BASE

THIRD BASE
Leucine (Leu) Proline (Pro) Arginine (Arg)
Glutamine (Glu)

Asparagine (Asn) Serine (Ser)

Isoleucine (Ile)
Threonine (Thr)
Methionine (Met) Lysine (Lys) Arginine (Arg)
Start codon

Aspartic acid (Asp)

Valine (Val) Alanine (Ala) Glycine (Gly)
Glutamic acid (Glu)
Figure 15-9a

Using the genetic code to predict an amino acid sequence

5 3

The DNA sequence 3 5 Remember that RNA polymerase

works only in the 5 to 3 direction
and that RNA is antiparallel to DNA
would be transcribed as 5 3

Also remember that RNA contains

and translated as the base uracil (U) instead of
thymine (T), and that uracil forms
a complementary base pair with
adenine (A)
Transcription
This is the 1st step of protein synthesis, but
also makes any RNA molecule (mRNA,
tRNA, rRNA)
Begins at the promoter and ends at the
terminator
Involves:
Making an RNA copy of a gene from DNA
Another symphony of enzymes
Opening DNA at one place only, and when
complete, the DNA closes again
Making an RNA molecule from 5 to 3
Figure 16-1

Non-template
(coding) strand DNA

5 3
5 RNA 3 Phosphodiester bond is
formed by RNA polymerase
3 5
after base pairing occurs
Template strand 3 5

RNA 5 3

Hydrogen bonds form between

complementary base pairs

DNA template 3 5
Figure 16-3-Table 16-1
Figure 16-3

HOW TRANSCRIPTION BEGINS

Promoter (on non-template strand)
35 box 10 box
Upstream
Template strand DNA
Upstream +1 site RNA
DNA Sigma
Non-template
strand
RNA
+1 site exit
Zipper
site
Active Downstream Rudder
site DNA RNA

RNA polymerase NTPs Downstream

DNA
1. Initiation begins 2. Initiation continues 3. Initiation is complete
Sigma binds to promoter Sigma opens the DNA helix; Sigma releases; mRNA
region of DNA. transcription begins. synthesis continues.
Figure 16-4

HOW TRANSCRIPTION ENDS

Upstream DNA

Hairpin loop RNA

RNA
polymerase

RNA

Downstream DNA
Transcription DNA
termination
signal

1. RNA polymerase reaches a transcription 2. The RNA hairpin causes the RNA strand
termination signal, which codes for RNA to separate from the RNA polymerase,
that forms a hairpin. terminating transcription.
Post-transcription RNA modification
After transcription, the new RNA molecules is called pre-
RNA because its not yet translation-ready
End-modification
5 end receives a cap with modified Guanine when
transcription has gone about 20-40 nucleotides
3 end receives a poly-A tail (30-250 Adenines) that help the
RNA leave the nucleus and attach to the ribosome for
translation
RNA splicing
Often, RNA has large, noncoding sections tha must be
removed
Introns are noncoding regions between coding regions
Exons are regions that actually get translated (the exit the
nucleus)
Small nuclear ribonucleoproteins (snRNPs-snurps) join with
other proteins to form a spliceosome.
Spliceosomes cut out the introns and join their flanking exons
together
Figure 16-8

5 cap Poly(A) tail

5 3

5 untranslated Coding region 3 untranslated

region region
Figure 16-7a

Introns must be removed from RNA transcripts.

Intron 1 Intron 2
DNA 3 5
Promoter Exon 1 Exon 2 Exon 3
Primary RNA transcript 5 3

Spliced transcript 5 3
Figure 16-7b snRNPs ARE THE EDITORS.

Primary snRNPs
RNA

5 A 3
Exon 1 Intron Exon 2

1. Several snRNPs and

proteins assemble to
A form a spliceosome.
5 The 2 hydroxyl group
3 on an adenine
nucleotide (A) reacts
Spliceosome with the 5 end of the
intron, breaking RNA.

2. The 5 end of the

intron becomes attached
5 to the A nucleotide,
A forming a loop of RNA.
3 5 The free 3 end of one
5 3
exon reacts with the 5
end of the other.

Excised 3. The 3 and 5 ends

intron of adjacent exons bond
covalently, releasing the
A intron (which is then
degraded).

5 3 Mature mRNA
Exon 1 Exon 2
Other transcripts
A spliceosome is not always used for other transcripts
(rRNA, tRNA)
Ribozymes are RNA molecules that act as enzymes
and actually catalyze their own splicing reactions
For example: the intron can splice itself from a
protozoan, Tetrahymena
Why introns?
Some introns may actually help regulate the cell
Proteins are actually synthesized in Domains
(segments). Each exon codes for a different domain,
and if each domain was continuously coded, there is
a smaller chance that a crossover could alter a
domain. Introns elongate the gene, allowing for a
greater chance of crossovers, and possibly more
evolutionary variety in proteins
Translation
mRNA goes to the ribosome to be read 5 to 3
tRNA carries amino acids to the ribosome to be
assembled when its anticodon matches with the
mRNA codon thats in place in the ribosome
Aminoacyl-tRNA Synthase ensures that tRNA picks up
an amino acid
Ribosomes have 2 parts and are made of rRna and
protein
Small subunit of the ribosome clamps onto the mRNA
Initiators help this process by attaching at the start
codon sequence (Met)
Large subunit of the ribosome:
E site-exit site holds the tRNA thats about to leave
P site-pepdityl-tRNA site holds the growing
polypeptide
A site-aminoacyl-tRNA binding site is where the new
tRNA and amino acid enter the ribosome
Figure 16-12
HOW AMINO ACIDS ARE LOADED ONTO tRNAs
ATP 1. Active site on aminoacyl
tRNA synthetase binds ATP
and amino acid. Each
aminoacyl tRNA synthetase
is specific to one amino acid.
Aminoacyl tRNA
synthetase specific
to leucine

2. Reaction leaves AMP and

amino acid bound to enzyme;
Activated two phosphate groups
enzyme released. Activated amino
complex acid has high potential energy.

tRNA
specific to
leucine
3. The activated amino acid is
transferred from tRNA
synthetase to the tRNA
specific to that amino acid;
AMP leaves.
AM
P

4. The finished aminoacyl

tRNA is ready to participate
in translation.
Aminoacyl tRNA
Figure 16-14

Secondary structure of tRNA Early model of aminoacyl tRNA function

3
Amino acid
3 Binding site
5 for
5 amino acid

Binding site
Serine anticodon for
5 mRNA codon 3
mRNA
Serine codon

Revised model incorporating tertiary structure of tRNA

5
3

3
Anticodon

Codon
5 mRNA
Figure 16-15

Ribbon model of ribosome during translation Diagram of ribosome during translation

Polypeptide grows in amino
to carboxyl direction Peptide bond
(amino acids in green) formation occurs
here

Large
subunit Aminoacyl
Large
tRNA
subunit

mRNA Anticodon
5 3
Small Codon
Small
subunit subunit

The E site The P site holds The A site

holds a tRNA the tRNA with holds an
tRNA in E site tRNA in P site tRNA in A site that will exit growing polypeptide aminoacyl
(blue) (green) (red) attached tRNA
Figure 16-17l

ELONGATION OF POLYPEPTIDES DURING TRANSLATION

Ribosome

Peptidyl site tRNA

Exit site Aminoacyl site

mRNA
5 3 5 3 5 3
Start
codon

1. Incoming aminoacyl tRNA 2. Peptide bond formation 3. Translocation

New tRNA moves into A site, where The amino acid attached to the tRNA Ribosome moves down mRNA. The
its anticodon base pairs with the in the P site is transferred to the tRNA attached to polypeptide chain
mRNA codon. tRNA in the A site. moves into P site. The A site is empty.
Figure 16-17r

ELONGATION OF POLYPEPTIDES DURING TRANSLATION

Exit tunnel Elongation cycle
continues

5 3 5 3 5 3

4. Incoming aminoacyl tRNA 5. Peptide bond formation 6. Translocation

New tRNA moves into A site, where
its anticodon base pairs with the
mRNA codon.
The polypeptide chain attached to
the tRNA in the P site is transferred
to the aminoacyl tRNA in the A site.
Ribosome moves down mRNA. The
tRNA attached to polypeptide chain
moves into P site. Empty tRNA from
P site moves to E site, where tRNA is
ejected. The A site is empty again.
Figure 16-19

TERMINATION OF TRANSLATION
Large
subunit

Hydrolysis of
bond linking
tRNA and
polypeptide

5
tRNA Release
factor
mRNA 3
mRNA mRNA
5 3 5 3
STOP
codon Small
subunit

1. When translocation opens the A site
and exposes one of the stop codons, a
protein called a release factor fills the A
site. The release factor catalyzes the
hydrolysis of the bond linking the tRNA
in the P site with the polypeptide chain.
2. The hydrolysis reaction frees the
polypeptide, which is released from the
ribosome. The empty tRNAs are released
either along with the polypeptide or
3. when the ribosome separates from the
mRNA, and the two ribosomal subunits
dissociate. The subunits are ready to
attach to the start codon of another
message and start translation anew.
What about prokaryotes?
In bacteria, transcription and
translation are closely coupled
processes, since mRNA doesnt need
to leave a nucleus to occur.
Transcription and translation are
simultaneous
Mutations
Point Mutations are changes to the
sequence of DNA that occur at one point
Substitutions-one base pair is substituted with
another
Cause missense mutations-the new base pair
codes for an amino acid, but the amino acid is
not the correct one
Insertions and deletions-also called frameshift
Mutagens are physical or chemical agents
that cause mutations by interacting with
the DNA molecule
Ex: UV radiation
Base analogues are similar to the DNA bases,
but pair incorrectly during replication
Figure 16-21-Table 16-3
Figure 16-21

DNA point mutation can lead to a different amino acid sequence. Phenotype
DNA sequence 5 3
of non-template
(coding) strand

Amino acid
sequence
Normal
Normal red blood cells

DNA sequence 5 3
of non-template
(coding) strand

Amino acid
sequence
Mutant
Sickled red blood cells
Figure 16-21-Table 16-4