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From Gene To Protein

Ch. 17 -- Prezi skeleton by David Knuffke

Miss Schwinge

on 24 November 2015

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Transcript of From Gene To Protein

Universal across all domains of life.
The Central Dogma
Once the structure of DNA was determined, it was time to figure out how it worked

Central Dogma
: Term coined by Francis Crick to explain how information flows in cells.
The process by which the instructions in DNA are converted into a functional product

Allows for Gene Expression
Allows for Heritability
The Three Stages of Transcription
1. Initiation
RNA polymerase attaches to a "promoter" region in front ("upstream") of a gene
Prokaryotes: RNA polymerase binds directly to the promoter.
Eukaryotes: RNA polymerase requires an assemblage of
transcription factor proteins
to be able to bind to the promoter.

Promoters have characteristic DNA sequences. A TATA Box in eukaryotes, for example
2. Elongation
A gene can be transcribed simultaneously by several RNA polymerases.
Similar to DNA replication, RNA production occurs in a 5' to 3' direction.

template strand
of DNA is the one that the RNA transcript is being produced off of (its sequence is opposite to the transcript)

nontemplate strand
coding strand
) of the DNA will have
the same sequence
as the RNA transcript (with thymines replaced by uracils in the transcript)
3. Termination
Transcript production continues until the end of the transcription unit is reached.

The mechanisms of termination are different in bacteria and eukaryotes:
, the polymerase continues transcription after the pre-mRNA is cleaved from the growing RNA chain; the polymerase eventually falls off the DNA
, the polymerase stops transcription at the end of the terminator

: the transcript bases hydrogen bond with themselves, fold back and pull the transcript out of RNA polymerase.

: The Rho protein destabilizes the RNA-DNA hydrogen bonding at RNA polymerase and ceases transcription
What Happens Next?
Many Kinds of RNA
Unlike DNA, RNA plays many roles in the cell
There are ~10 described types of RNA, each with different functions, but there are
three major types of RNA

Messenger RNA (mRNA)
: Carries DNA sequence information to the ribosome
Transfer RNA (tRNA)
: Carries specific amino acids to the ribosome
Ribosomal RNA (rRNA)
: Major structural building block of ribosomes
Post-Transcriptional mRNA Processing
(Eukaryotes ONLY!)
5'Cap and poly-A tail
Split Genes and RNA Splicing
To produce a functional protein, RNA splicing must occur. This means the introns are removed and the exons must be spliced togetherto create an mRNA molecule with a continuous coding sequence.
This occurs
to the movement of the mRNA transcript out of the nucleus.

This process is accomplished by a
; a type of enzymatic RNA molecule
The Genetic Code:
The Ribosome
- A cell translates an mRNA message into protein with the help of
transfer RNA (tRNA)

- tRNA are responsible for bringing amino acids to the ribosome. A tRNA with an amino acid attached is said to be

- Molecules of tRNA are not identical:
Each carries a specific amino acid on one end
Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA

Triplet code
: mRNA is read in units of three bases (

There are
possible codons (61 code for amino acids; 3 triplets are “stop” signals to end translation) for
possible amino acids

The code is redundant and unambiguous.

The code has "
" and "
" punctuation.
Pig with GFP from a jellyfish
Tobacco plant with luciferase from a firefly
The Three Stages of Translation
1. Initiation
mRNA attaches to the small ribosomal subunit, and the subunit moves along the mRNA until it reaches the
start codon
, methionine (

Methionine is brought to the start codon by the methionine tRNA.

The ribosome assembles so that the start codon (AUG) is in the P-site.

This is called the
translation initiation complex
2. Elongation
The next codon determines the next amino acid to be brought to the ribosome. The incoming charged tRNA enters at the
The growing polypeptide is transferred to the new tRNA molecule. A peptide bond is formed.
The ribosome shifts
). The tRNA with the polypeptide is now in the
. The uncharged amino acid is now in the
The next codon is now available in the
for the next incoming charged tRNA
3. Termination
tRNA binding at the ribosome is mediated by an
loop in the tRNA molecule
tRNA "anti-codon"
Protein Synthesis in Total
Prokaryote & Eukaryote
Translation Specifics
Since prokaryotes do not have a nucleus, transcription and translation can be coupled. This means they can simultaneously transcribe and translate the same gene
In eukarya, transcription and translation are separated by the nuclear envelope. Once they have been modified after translation, eukaryotes need to target different polypeptides to different areas of the cell
Problems with the process: Mutations
Changes in DNA can cause changes in protein structure and function. There are 2 major types of DNA-level mutations:

Point mutations
: One DNA base is replaced by another DNA base.
Frame-shift mutation
s: DNA bases are inserted or deleted ("in/dels").

Each type of mutation can have different effects, depending on the situation
Point Mutations
The substitution changes a codon to another codon, but for the same amino acid so nothing is affected
The substitution changes a codon to a codon for a different amino acid (which may be the wrong one)
The substitution changes a codon to a stop codon, almost always leading to a nonfunctional protein
Frameshift Mutations
Extensive missense
The reading frame of the ribosome is altered so that all amino acids downstream from the insertion or deletion are altered
Immediate nonsense
The reading frame of the ribosome is altered so that a stop codon is introduced prematurely
Limited Effect
The reading frame is restored when insertions or deletions occur in multiples of three.
Big Questions
Make Sure You Can
Polypeptide synthesis always begins in the cytosol, and finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER. Polypeptides destined for the ER or for secretion are marked by a
signal peptide
; a small sequence on polypeptides that need to be made at the endoplasmic reticulum. They recruit a
signal-recognition particle (SRP),
which brings the signal peptide and its ribosome to the ER
An RNA "
" loop, similar to what happens in Rho-independent termination
Sickle Cell Anemia is due to a point mutation.
How is the structure of DNA related to its function?

How does DNA allow for heritability?

How does DNA allow for traits in an organism?

How do mutations affect DNA structure and function?
Explain all steps of replication, transcription and translation, the enzymes required for each and the flow of information from DNA to RNA to protein.

Compare replication, transcription and translation in prokaryotic and eukaryotic biological systems.

Interpret the genetic code and use it to determine the amino acid sequence of a polypeptide if given the DNA sequence.

Explain the relationship between DNA sequence, protein sequence, and phenotype of an organism.

Describe the possible effects of DNA-level mutations on protein structure and organismal phenotype.
Blame it on the DNA
Sickle Cell Again!
The Genetic Code
Actual Gene Expression
is the synthesis of RNA under the direction of DNA

RNA is the intermediate between genes and the proteins for which they code

In transcription we use
messenger RNA (mRNA)
to make a copy of DNA that can leave the nucleus
During transcription, one of the two DNA strands called the
template strand
provides a template for ordering the sequence of nucleotides in an RNA transcript

During translation, the mRNA base triplets, called
, are read in the 5' to 3' direction. Each codon specifies the amino acid to be placed at the corresponding position along a polypeptide
This is how
genes can be transcribed and translated after being transplanted from one species to another
RNA synthesis is catalyzed by
RNA polymerase
, which pries the DNA strands apart and hooks together the RNA nucleotides

RNA synthesis follows the same base-pairing rules as DNA, except
uracil (U)
substitutes for
thymine (T)

are DNA sequences that signal the initiation of RNA synthesis
(where RNA polymerase first attaches)
; in bacteria, the sequence signaling the end of transcription is called the

The stretch of DNA that is transcribed is called a
transcription unit

Molecular Components of Transcription
Enzymes in the eukaryotic nucleus modify pre-mRNA before the genetic messages are dispatched to the cytoplasm
During RNA processing,
both ends of the primary transcript are usually altered
usually some interior parts of the molecule are cut out, and the other parts spliced together
Each end of a pre-mRNA molecule is modified in a particular way:
The 5' end receives a modified nucleotide 5' cap
The 3' end gets a poly-A tail (made of several hundred adenine residues)
These modifications share several functions:
They seem to facilitate the export of mRNA
They protect mRNA from hydrolytic enzymes
They help ribosomes attach to the 5' end

Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions. These
noncoding regions of nucleotides are called intervening sequences, or

The other regions are called
because they are eventually expressed, usually translated into amino acid sequences
are catalytic RNA molecules that function as enzymes and can splice RNA.
Their discovery rendered obsolete the belief that all biological catalysts were proteins

Three properties of RNA enable it to function as an enzyme
1.) It can form a three-dimensional structure because of its ability to base pair with itself
2.) Some bases in RNA contain functional groups
3.) RNA may hydrogen-bond with other nucleic acid molecules
The Importance of Introns
Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing. These variations are called
alternative RNA splicing

Because of alternative splicing, the number of different proteins an organism can produce is much greater than its number of genes
(in other words, eukaryotes can make multiple functional proteins from one gene)
In many cases, different exons code for the different domains (architecture) in a protein. Exon shuffling may result in the evolution of new proteins
Accurate translation requires two steps:
1.) A correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase
2.) A correct match between the tRNA anticodon and an mRNA codon
Flexible pairing at the third base of a codon is called
and allows some tRNAs to bind to more than one codon
Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis
(the "site" of protein synthesis"

The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA)
A ribosome has 3 binding sites for tRNA:
A site:
"Aminoacyl"- where amino acids enter the ribosome. It holds the tRNA that carries the next amino acid to be added to the chain
P site:
"Peptidyl"- where the growing polypeptide is kept. Holds the tRNA that carries the growing polypeptide chain
E site:
"Exit"- where empty tRNA molecules leave the ribosome
During the elongation stage, amino acids are added one by one to the preceding amino acid
Termination occurs when a stop codon (UAG, UAA, UGA) in the mRNA reaches the A-site of the ribosome. The A-site accepts a protein called a release factor.

The release factor causes the addition of a water molecule instead of an amino acid, which causes the polypeptide to be released. The translation assembly then comes apart, and the ribosome is disassembled
Completing and Targeting the Functional Proteins
Typically, multiple ribosomes translate an mRNA at the same time (in other words, a single mRNA is used to make many copies of a polypeptide simultaneously). This string of ribosomes are known as
(or polysomes)
During and after synthesis, a polypeptide chain spontaneously coils and folds into its three-dimensional shape.
Proteins may also require
post-translational modifications
before doing their job

Some polypeptides are activated by enzymes that cleave them, whereas other polypeptides come together to form the subunits of a protein
Two populations of ribosomes are evident in cells:
free ribsomes
(in the cytosol) and
bound ribosomes
(attached to the ER)

Free ribosomes mostly synthesize proteins that function in the cytosol, and bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell

Ribosomes are identical and can switch from free to bound
Can be divided into two general categories:
Base-pair substitutions
Base-pair insertions or deletions

Have a disastrous effect on the resulting protein more often than substitutions do, because they are complete additions (insertions) or losses (deletions) of nucleotide pairs in a gene. Insertion or deletion of nucleotides may alter the reading frame
(hence the term "frameshift")
Spontaneous mutations
can occur during DNA replication, recombination, or repair

are physical or chemical agents that can cause mutations
Full transcript