Today…
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Turn in Bozeman homework
Complete DNA modeling activity
Lecture notes on Transcription & Translation
POGIL
Homework assigned: read article from website
(your choice) and post a short summary. Respond
to 1 other person’s post with a comment or
question. Due Sunday by 11:59pm.
From Gene
to Protein
Chapter 17 Campbell
What do genes code for?

How does DNA code for cells & bodies?

DNA
how are cells and bodies made from the
instructions in DNA
proteins
All the traits
of the body
The “Central Dogma”
• Flow of genetic information in a cell
– How do we move information from DNA to proteins?
DNA
replication
RNA
protein
trait
RNA
•
•
•
•
Monomers = nucleotides
Phosphate
Ribose sugar
Nitrogen Bases
– uracil instead of thymine
• U bonds with A
• C bonds with G
• single stranded
DNA
transcription
RNA
Compare DNA and RNA
DNA
RNA
Shape
Double helix
2 strands
Single strand
Sugar
Deoxyribose
Ribose
Bases
A, T, C, and G
A, U, C and G
Location
Only in the
nucleus
Allowed to travel
from nucleus to
cytoplasm
Types of RNA
• Ribosomal RNA (rRNA)
– Major component of ribosomes
• Transfer RNA (tRNA)
– Folded upon itself
– Carries the amino acids to the mRNA
• Messenger RNA (mRNA)
– Sequence of nucleotides that determines the primary sequence
of the polypeptide
– Made in the nucleus from the DNA: transcription
• snRNA (small-nuclear “snurps”)
– Forms the “spliceosomes” which are used to cut out introns
from pre-mRNA
• siRNA (small-interfering)
– targets specific mRNA and prohibits it from being expressed
Protein Synthesis: From gene to protein
nucleus
a
a
a
cytoplasm
a
a
transcription
DNA
a
a
translation
mRNA
a
a
a
protein
a
a
a
a
a
a
ribosome
trait
Which gene is read on the DNA?
• Promoter region
– binding site before beginning of gene
– Generally referred to as a TATA box because it is a
repeating sequence of T and A
– binding site for RNA polymerase
& transcription
factors
• Enhancer region
– binding site far
upstream of gene
• Speeds up process
Transcription Factors
– transcription factors bind to promoter region of DNA
• proteins
• can be activated by hormones (cell signaling)
• turn on or off transcription
– triggers the binding of RNA polymerase to DNA
Transcription: DNA to mRNA
• Takes place in the nucleus
• A section of DNA is unzipped
• RNA polymerase lays down
nucleotides 5’ to 3’
direction. (Does this sound
familiar??)
• The mRNA then leaves the
nucleus through the nuclear
pores and enters the
cytoplasm
Coding strand = “sense strand”. This strand will have the same
sequence as the mRNA, and there for the codons
Template strand = “anti-sense strand” This is the strand that RNA
Polymerase II uses to generate the mRNA. It contains the anti-codons.
Eukaryotic Genes Have Untranscribed Regions
• mRNA must be modified before it leaves the nucleus
– exons = the real gene
• expressed / coding DNA
introns
– introns = non-coded section
come out!
• in-between sequence
• Spliceosomes cut out introns with ribozymes (or are they
ribozymes?!) In any case, they are super cool & super
complex! 150+ proteins, 5 snRNAs)
intron = noncoding (inbetween) sequence
eukaryotic DNA
exon = coding (expressed) sequence
Alternative splicing
• A single gene can code for multiple proteins.
• Particular exons of a gene may be included within or
excluded from the final, processed messenger RNA
(mRNA) produced from that gene.
• Intron presence can determine which exons stay or go
• Increases efficiency and flexibility of cell
• snRNA’s have big role in alternative splicing
Starting to get
hard to
define a gene!
Final mRNA processing…
• Need to protect mRNA on its trip from nucleus
to cytoplasm (enzymes in cytoplasm attack mRNA)
• protect the ends of the molecule
• add 5 GTP cap
• add poly-A tail
–longer tail, mRNA lasts longer
3'
mRNA
5'
G P
P P
A
The Transcriptional unit
enhancer
1000+b
20-30b
3'
RNA
TATA
polymerase
translation
start
TAC
translation
stop
exons
transcriptional unit (gene)
5'
DNA
ACT
DNA
introns
promoter
transcription
start
transcription
stop
5'
pre-mRNA
5'
GTP mature mRNA
3'
3'
AAAAAAAA
Genetic Code
• Genetic code is based on sets of 3 nucleotides …called
CODONS!
– Read from the mRNA
– 64 different possible combinations exist
• Only 20 amino acids commonly exist in the human body
– Some codons code for the same amino acids
(degenerate or redundant)
• Sequence of codons determines the sequence of the
polypeptide
• Code is “almost” universal…same for all organisms
(evolutionary heritage)
The Code
• You don’t need to
memorize the
codons
(except for AUG)

Start codon



AUG
methionine
Stop codons

UGA, UAA, UAG
mRNA codes for proteins in triplets
DNA
TACGCACATTTACGTACGCGG
codon
mRNA
AUGCGUGUAAAUGCAUGCGCC
?
protein
MetArgValAsnAlaCysAla
How is the code “translated?”
Process of reading mRNA and
creating a protein chain from the
code.
Ribosomes: Site of Protein
Synthesis
• Facilitate coupling of
tRNA anticodon to mRNA codon
• Structure
– ribosomal RNA (rRNA) & proteins
– 2 subunits
• large
• small
E P A
Ribosomes: 3 binding sites
• A site (aminoacyl-tRNA site)
– holds tRNA carrying next amino acid to be
added to chain
• P site (peptidyl-tRNA site)
– holds tRNA carrying growing polypeptide chain
• E site (exit site)
Met
– Empty tRNA
leaves ribosome
from exit site
5'
U A C
A U G
Transfer RNA
•
•
•
•
•
Found in cytoplasm
Carries amino acids to ribosome
Contains an “anticodon” of nitrogen bases
Anticodons use complementary bond with codons
Less tRNA’s than codons, so one tRNA may bind
with more than one codon.
• Supports the degenerate code
• “Wobble” hypothesis: anticodon with U in third
position can bind to A or G
Translation: mRNA to Protein
• In the cytoplasm ribosomes attach to the mRNA
– Ribosome covers 3 codons at a time
• Initiation - The tRNA carrying an amino acid comes into
P-site and bonds by base pairing its anti-codon with the
mRNA start codon (what is the start codon?)
• Elongation – The second tRNA then comes into A-site
and bonds to codon of mRNA
– The two amino acids joined with peptide bond
• Termination – ribosome continues reading mRNA until
a STOP codon is reached (doesn’t code for anything)
McGraw Hill Animations
Building a polypeptide
• Initiation
– mRNA, ribosome subunits,
initiator tRNA come together
• Elongation
– adding amino acids based on
codons
Good Overview
animation
• Termination
3 2 1
– STOP codon = Release factor
Leu
Val
Met
Met
Met
Met Leu
Ala
Leu
Leu
release
factor
Ser
Trp
tRNA
U AC
5'
C UGAA U
mRNA A U G
3'
E P A
5'
UAC GAC
A U G C U GAA U
5'
3'
U A C GA C
A U G C U G AAU
5'
3'
U AC G A C
AA U
AU G C U G
3'
A CC
U GG U A A
3'
RNA polymerase
DNA
Can you tell
the story?
amino
acids
exon
intron
tRNA
pre-mRNA
5' GTP cap
mature mRNA
poly-A tail
large ribosomal subunit
polypeptide
5'
small ribosomal subunit
tRNA
E P A
ribosome
3'
Prokaryote vs. Eukaryote
Differences
• Prokaryotes
– DNA in cytoplasm
– circular chromosome
– naked DNA
– no introns
– No splicing
– Promoter &
terminator sequence
– Smaller ribosomes
• Eukaryotes
– DNA in nucleus
– linear chromosomes
– DNA wound on
histone proteins
– introns and exons
– TATA box promoter
– Transcription factors
present
Protein Synthesis in Prokaryotes
• Transcription & translation are simultaneous in
bacteria
– Both occur in
cytoplasm
– no mRNA
editing
– ribosomes
read mRNA
as it is being
transcribed