Chapter 16 From gene to protein

1
Chapter 16From gene to protein
2
The Central Dogma of Molecular
Biology
DNA------gtRNA------gtprotein The central dogma
concerns the flow of biological information DNA
is a self-replicating molecule containing genetic
information that can be transcribed into an RNA
message that can be translated into a polypeptide
(protein).
3
Reverse Transcription

• Most importantly, some RNA viruses, called
  retroviruses make a DNA copy of themselves
  using the enzyme reverse transcriptase. The DNA
  copy incorporates into one of the chromosomes and
  becomes a permanent feature of the genome. This
  represents a flow of information from RNA to DNA.

4
The Central Dogma of molecular biology
Synthesis of three types of informational
molecules DNA, RNA and Protein. Note that only
one strand of the DNA is transcribed into RNA.
5
Genome size 3.2 billion base pairs sufficient
for 103,480,000,000 combinations 2 m of it
squeezed into every cell. "If our strands of DNA
were stretched out in a line, the 46 chromosomes
making up the human genome would extend more than
six feet close to two metres. If the ... length
of the 100 trillion cells could be stretched out,
it would be ... over 113 billion miles 182
billion kilometres. That is enough material to
reach to the sun and back 610 times." Source
Centre for Integrated Genomics
6
RNA

• RNA plays a central role in the life of the cell.
  We are mostly going to look at its role in
  protein synthesis, but RNA does many other things
  as well.
• RNA can both store information (like DNA) and
  catalyze chemical reactions (like proteins).
• RNA/protein hybrid structures are involved in
  protein synthesis (ribosome), splicing of
  messenger RNA, telomere maintenance, guiding
  ribosomes to the endoplasmic reticulum, and other
  tasks.
• Recently it has been found that very small RNA
  molecules are involved in gene regulation.

7
RNA Used in Protein Synthesis

• messenger RNA (mRNA). A copy of the gene that is
  being expressed. Groups of 3 bases in mRNA,
  called codons code for each individual amino
  acid in the protein made by that gene.
• ribosomal RNA (rRNA). Make up part of the
  structure of the ribosome. They perform the
  actual catalysis of adding an amino acid to a
  growing peptide chain.
• transfer RNA (tRNA). Transfer amino acids to the
  correct codon to make a specific protein

8
RNA vs. DNA

• RNA contains the sugar ribose DNA contains
  deoxyribose.
• RNA contains the base uracil DNA contains
  thymine instead.
• RNA is usually single stranded DNA is usually
  double stranded.
• RNA is short one gene long at most DNA is long,
  containing many genes.

9
The Structure of DNA
Four nucleic acid bases are found in DNA,
adenine (A), guanine (G), cytosine (C) and
thymine (T)
10
The Structure of DNA
The double helix of DNA has a complementary and
antiparallel structure. One chain ends in a 5'-
phosphate and the opposite chain ends in a
3'-hydroxyl.
11
The Structure of DNA
12
DNA replication is semiconservative
13
DNA replication Is bidirectional
14
(No Transcript)
15
Proteins

• Proteins are composed of one or more
  polypeptides, plus (in some cases) additional
  small molecules (co-factors).
• Polypeptides are linear chains of amino acids.
  After synthesis, the new polypeptide folds
  spontaneously into its active configuration and
  combines with the other necessary subunits to
  form an active protein. All the information
  necessary to produce the protein is contained in
  the DNA base sequence that codes for the
  polypeptides.
• The sequence of amino acids in a polypeptide is
  known as its primary structure.

16
Amino Acids and Peptide Bonds

• There are 20 different amino acids coded in DNA.
• They all have an amino group (-NH2) group on one
  end, and an acid group (-COOH) on the other end.
  Attached to the central carbon is an R group,
  which differs for each of the different amino
  acids.
• When polypeptides are synthesized, the acid group
  of one amino acid is attached to the amino group
  of the next amino acid, forming a peptide bond.

17
(No Transcript)
18
Transcription and translation in a prokaryote
A single mRNA often contains more than one coding
region, separated during translation into
distinct polypeptides. Also, in prokaryotes
transcription and translation are
coupled, meaning that they occur simultaneously.
19
(No Transcript)
20
A gene is a segment of DNA that encodes for a
protein A genome refers to the total complement
of DNA in a cell.
21
Transcription has to be cell type-specific
developmental stage-specific cell cycle
stage-specific responsive to external signals

• Transcription is the process of making an RNA
  copy of a single gene
• The enzyme used in transcription is RNA
  polymerase.
• The raw materials for the new RNA are the 4
  ribonucleoside triphosphates ATP, CTP, GTP, and
  UTP. Its the same ATP as is used for energy in
  the cell.
• As with DNA replication, transcription proceeds
  5- to 3 new bases are added to the free 3 OH
  group.
• Unlike replication, transcription does not need
  to build on a primer. Instead, transcription
  starts at a region of DNA called a promoter.
  For protein-coding genes, the promoter is located
  a few bases 5 to (upstream from) the first base
  that is transcribed into RNA.
• Promoter sequences are very similar to each
  other, but not identical.

22
Flow of Genetic information Transcription Transf
er of the information to RNA is called
transcription, and the molecule that encodes for
one or more polypeptides (proteins) is called
messenger RNA (mRNA).
23
Flow of Genetic information Translation During
translation, this genetic code in mRNA is read
and converted into protein by means of the
protein synthesizing machinery, which consists of
ribosomes, tRNA, amino acids, and a number of
enzymes.
24
Transcription is the process by which nucleotide
sequences in DNA are copied to a complementary
copy of messenger RNA
25

• Transcription starts with RNA polymerase binding
  to the promoter.
• RNA polymerase is the enzyme that unwinds a small
  section of DNA and copies it into a
  complementary copy of RNA.
• The DNA strand used as a template is the coding
  strand the other strand is the non-coding
  strand. Notice that the RNA is made from 5 end
  to 3 end, so the coding strand is actually read
  from 3 to 5.
• In prokaryotes, each RNA ends at a specific
  terminator sequence. In eukaryotes transcription
  doesnt have a definite end point the RNA is
  given a definitive termination point during RNA
  processing.

26
Promoters Promoters are specific sites on DNA
that RNA polymerase first binds to to initiate
the transcription of a gene.
27
Sigma factors Sigma factors are one component of
the multicomponent RNA polymerase enzyme that
allow the RNA polymerase to recognize the
initiation (promoter) site.
28
Transcription Terminators Transcription
terminators are sequences of nucleotide bases at
the end of the gene that signal termination of
transcription.
29
(No Transcript)
30
After Transcription

• In prokaryotes, the RNA copy of a gene is
  messenger RNA, ready to be translated into
  protein. In fact, translation starts even before
  transcription is finished.
• In eukaryotes, the primary RNA transcript of a
  gene needs further processing before it can be
  translated. This step is called RNA
  processing. Also, it needs to be transported out
  of the nucleus into the cytoplasm.
• Steps in RNA processing
• 1. Add a cap to the 5 end
• 2. Add a poly-A tail to the 3 end
• 3. splice out introns.

31
Introns

• Introns are regions within a gene that dont code
  for protein and dont appear in the final mRNA
  molecule. Protein-coding sections of a gene
  (called exons) are interrupted by introns.
• The function of introns remains unclear. They
  may help is RNA transport or in control of gene
  expression in some cases, and they may make it
  easier for sections of genes to be shuffled in
  evolution. But , no generally accepted reason
  for the existence of introns exists.
• There are a few prokaryotic examples, but most
  introns are found in eukaryotes.

32
During translation, the genetic code in mRNA is
read and converted into protein by means of the
protein synthesizing machinery, which consists of
ribosomes, tRNA, amino acids, and a number of
enzymes.
33
Translation

• Translation of mRNA into protein is accomplished
  by the ribosome, an RNA/protein hybrid.
  Ribosomes are composed of 2 subunits, large and
  small.
• Ribosomes bind to the translation initiation
  sequence on the mRNA, then move down the RNA in a
  5 to 3 direction, creating a new polypeptide.
• Each group of 3 nucleotides in the mRNA is a
  codon, which codes for 1 amino acids. Transfer
  RNA is the adapter between the 3 bases of the
  codon and the corresponding amino acid.

34
The Genetic Code allows for correspondence
between triplets of bases in DNA and the amino
acid sequence of a polypeptide (protein) written
or expressed in terms of RNA triplets as compared
to DNA triplets because it is with messenger RNA
that the translation process occurs
35
The Genetic Code Codons Triplets of three
bases in RNA that encode an amino acid. There are
64 possible codons (4 bases taken 3 at a time
43) Stop and start codons Start AUG (codes
for methionine) - site where translation
begins Stop UAA, UAG and UGA - sites where
translation ends Degeneracy Most amino acids
have more than one codon. For example, glycine is
encoded by GGU GGC GGA and GGG.
36
The structure of transfer RNA (tRNA)
37

• Steps in Protein Synthesis
• 1. initiation
• begins with an initiation complex made up
  ribosomes, initiation factors, mRNA and formyl
  methionine tRNA.
• In eukaryotes, ribosomes bind to the 5 cap, then
  move down the mRNA until they reach the first
  AUG, the codon for methionine. Translation
  starts from this point. Eukaryotic mRNAs code
  for only a single gene. (Although there are a
  few exceptions, mainly among the eukaryotic
  viruses).
• Note that translation does not start at the first
  base of the mRNA. There is an untranslated
  region at the beginning of the mRNA, the 5
  untranslated region (5 UTR).

38
Steps in Protein Synthesis 2a. elongation The
mRNA is threaded through the ribosome which
contains other sites where tRNAs interact. The
acceptor (A) site is the site where the new
charged tRNA first attaches. The peptide (P)
site is the site where a growing peptide is held
by a tRNA and where peptide bond formation takes
place between the incoming amino acid (at the A
site) and the amino acid at the P site. the
ribosome advances by three nucleotides exposing a
new codon at the A site and pushing the now empty
tRNA to the exit (E) site where it is released
from the ribosome.
39
Steps in Protein Synthesis 3. termination occurs
when a nonsense (stop) codon is encountered. No
tRNA binds to a stop codon. Instead, specific
proteins called release factors recognize this
chain terminating signal and cleave the completed
polypeptide from the terminal tRNA.
40
Post-Translational Modification

• New polypeptides usually fold themselves
  spontaneously into their active conformation.
  However, some proteins are helped and guided in
  the folding process by chaperone proteins
• Many proteins have sugars, phosphate groups,
  fatty acids, and other molecules covalently
  attached to certain amino acids. Most of this is
  done in the endoplasmic reticulum.
• Many proteins are targeted to specific organelles
  within the cell. Targeting is accomplished
  through signal sequences on the polypeptide.
  In the case of proteins that go into the
  endoplasmic reticulum, the signal seqeunce is a
  group of amino acids at the N terminal of the
  polypeptide, which are removed from the final
  protein after translation.

41
Overview of Translation
42
(No Transcript)