From DNA to Protein

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From DNA to Protein

• Chapter 14

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Impacts, IssuesRicin and your Ribosomes

• Ricin is toxic because it inactivates ribosomes,
  the organelles which assemble amino acids into
  proteins, critical to life processes

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14.1 DNA, RNA, and Gene Expression

• What is genetic information and how does a cell
  use it?

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The Nature of Genetic Information

• Each strand of DNA consists of a chain of four
  kinds of nucleotides A, T, G and C
• The sequence of the four bases in the strand is
  the genetic information

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Converting a Gene to an RNA

• Transcription
• Enzymes use the nucleotide sequence of a gene to
  synthesize a complementary strand of RNA
• DNA is transcribed to RNA
• Most RNA is single stranded
• RNA uses uracil in place of thymine
• RNA uses ribose in place of deoxyribose

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Ribonucleotides and Nucleotides
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Ribonucleotides and Nucleotides
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base (guanine)
3 phosphate groups
sugar (ribose)
guanine G (RNA) guanosine triphosphate
A Guanine, one of the four nucleotides in RNA.
The others (adenine, uracil, and cytosine) differ
only in their component bases. Three of the four
bases in RNA nucleotides are identical to the
bases in DNA nucleotides.
Fig. 14-2a, p. 216
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base (guanine)
3 phosphate groups
sugar (deoxyribose)
guanine G (DNA) deoxyguanosine triphosphate
B Compare the DNA nucleotide guanine. The only
structural difference between the RNA and DNA
versions of guanine (or adenine, or cytosine) is
the functional group on the 2 carbon of the
sugar.
Fig. 14-2b, p. 216
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DNA and RNA
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adenine A
adenine A
DNA
RNA
deoxyribonucleic acid
ribonucleic acid
NH 2
NH 2
N
N
C
C
C
C
N
N
nucleotide base
HC
HC
CH
N
CH
C
C
N
N
N
sugar phosphate backbone
guanine G
guanine G
O
O
N
C
C
N
C
C
NH
NH
HC
HC
N
N
C
C
C
C
N
N
NH 2
NH 2
cytosine C
cytosine C
NH 2
NH 2
C
C
HC
HC
N
N
C
O
O
HC
C
HC
N
N
thymine T
base pair
uracil U
O
O
C
C
CH 3
C
NH
HC
NH
O
C
O
C
HC
HC
N
N
DNA has one function It permanently stores a
cells genetic information, which is passed to
offspring.
RNAs have various functions. Some serve as
disposable copies of DNAs genetic message
others are catalytic.
Nucleotide bases of DNA
Nucleotide bases of RNA
Fig. 14-3, p. 217
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RNA in Protein Synthesis

• Messenger RNA (mRNA)
• Contains information transcribed from DNA
• Ribosomal RNA (rRNA)
• Main component of ribosomes, where polypeptide
  chains are built
• Transfer RNA (tRNA)
• Delivers amino acids to ribosomes

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Converting mRNA to Protein

• Translation
• The information carried by mRNA is decoded into
  a sequence of amino acids, resulting in a
  polypeptide chain that folds into a protein
• mRNA is translated to protein
• rRNA and tRNA translate the sequence of base
  triplets in mRNA into a sequence of amino acids

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Gene Expression

• A cells DNA sequence (genes) contains all the
  information needed to make the molecules of life
• Gene expression
• A multistep process including transcription and
  translation, by which genetic information encoded
  by a gene is converted into a structural or
  functional part of a cell or body

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14.1 Key Concepts DNA to RNA to Protein

• Proteins consist of polypeptide chains
• The chains are sequences of amino acids that
  correspond to sequences of nucleotide bases in
  DNA called genes
• The path leading from genes to proteins has two
  steps transcription and translation

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14.2 Transcription DNA to RNA

• RNA polymerase assembles RNA by linking RNA
  nucleotides into a chain, in the order dictated
  by the base sequence of a gene
• A new RNA strand is complementary in sequence to
  the DNA strand from which it was transcribed

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DNA Replication and Transcription

• DNA replication and transcription both synthesize
  new molecules by base-pairing
• In transcription, a strand of mRNA is assembled
  on a DNA template using RNA nucleotides
• Uracil (U) nucleotides pair with A nucleotides
• RNA polymerase adds nucleotides to the transcript

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Base-Pairing in DNA Synthesis and Transcription
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Stepped Art
Fig. 14-4, p. 218
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The Process of Transcription

• RNA polymerase and regulatory proteins attach to
  a promoter (a specific binding site in DNA close
  to the start of a gene)
• RNA polymerase moves over the gene in a 5' to 3'
  direction, unwinds the DNA helix, reads the base
  sequence, and joins free RNA nucleotides into a
  complementary strand of mRNA

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Transcription
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newly forming RNA transcript
gene region
RNA polymerase, the enzyme that catalyzes
transcription
DNA template winding up
DNA template unwinding
A RNA polymerase binds to a promoter in the DNA,
along with regulatory proteins. The binding
positions the polymerase near a gene in the DNA.
B The polymerase begins to move along the DNA and
unwind it. As it does, it links RNA nucleotides
into a strand of RNA in the order specified by
the base sequence of the DNA.
In most cases, the nucleotide sequence of the
gene occurs on only one of the two strands of
DNA. Only the complementary strand will be
translated into RNA.
The DNA double helix winds up again after the
polymerase passes. The structure of the opened
DNA molecule at the transcription site is called
a transcription bubble, after its appearance.
Fig. 14-5a, p. 218
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Fig. 14-5b, p. 219
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transcription site
5
3
growing RNA transcript
C What happened in the gene region? RNA
polymerase catalyzed the covalent bonding of many
nucleotides to one another to form an RNA strand.
The base sequence of the new RNA strand is
complementary to the base sequence of its DNA
templatea copy of the gene.
Fig. 14-5b, p. 219
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Animation Gene transcription details
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Transcription

• Many RNA polymerases can transcribe a gene at the
  same time

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RNA transcripts
DNA molecule
Fig. 14-6, p. 219
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14.2 Key Concepts DNA to RNA Transcription

• During transcription, one strand of a DNA double
  helix is a template for assembling a single,
  complementary strand of RNA (a transcript)
• Each transcript is an RNA copy of a gene

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14.3 RNA and the Genetic Code

• Base triplets in an mRNA are words in a
  protein-building message
• Two other classes of RNA (rRNA and tRNA)
  translate those words into a polypeptide chain

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Post-Transcriptional Modifications

• In eukaryotes, RNA is modified before it leaves
  the nucleus as a mature mRNA
• Introns
• Nucleotide sequences that are removed from a new
  RNA
• Exons
• Sequences that stay in the RNA

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Alternative Splicing

• Alternative splicing
• Allows one gene to encode different proteins
• Some exons are removed from RNA and others are
  spliced together in various combinations
• After splicing, transcripts are finished with a
  modified guanine cap at the 5' end and a poly-A
  tail at the 3' end

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Post-Transcriptional Modifications
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gene
exon
intron
exon
intron
exon
DNA
transcription into RNA
cap
poly-A tail
5
3
RNA
snipped out
snipped out
mRNA
Fig. 14-7, p. 220
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Stepped Art
Fig. 14-7, p. 220
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Animation Pre-mRNA transcript processing
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mRNA The Messenger

• mRNA carries protein-building information to
  ribosomes and tRNA for translation
• Codon
• A sequence of three mRNA nucleotides that codes
  for a specific amino acid
• The order of codons in mRNA determines the order
  of amino acids in a polypeptide chain

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Genetic Information

• From DNA to mRNA to amino acid sequence

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DNA
mRNA
mRNA
glutamic acid
amino acids
proline
threonine
lysine
Fig. 14-8, p. 220
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Genetic Code

• Genetic code
• Consists of 64 mRNA codons (triplets)
• Some amino acids can be coded by more than one
  codon
• Some codons signal the start or end of a gene
• AUG (methionine) is a start codon
• UAA, UAG, and UGA are stop codons

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Codons of the Genetic Code
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Animation Genetic code
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rRNA and tRNA The Translators

• tRNAs deliver amino acids to ribosomes
• tRNA has an anticodon complementary to an mRNA
  codon, and a binding site for the amino acid
  specified by that codon
• Ribosomes, which link amino acids into
  polypeptide chains, consist of two subunits of
  rRNA and proteins

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Ribosomes
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tunnel
large subunit
small subunit
intact ribosome
Fig. 14-10, p. 221
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tRNA
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Fig. 14-11a, p. 221
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anticodon
trp
amino acid attachment site
Fig. 14-11a, p. 221
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Fig. 14-11b, p. 221
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14.3 Key ConceptsRNA

• Messenger RNA carries DNAs protein-building
  instructions
• Its nucleotide sequence is read three bases at a
  time
• Sixty-four mRNA base tripletscodonsrepresent
  the genetic code
• Two other types of RNA interact with mRNA during
  translation of that code

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14.4 Translation RNA to Protein

• Translation converts genetic information carried
  by an mRNA into a new polypeptide chain
• The order of the codons in the mRNA determines
  the order of the amino acids in the polypeptide
  chain

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Translation

• Translation occurs in the cytoplasm of cells
• Translation occurs in three stages
• Initiation
• Elongation
• Termination

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Initiation

• An initiation complex is formed
• A small ribosomal subunit binds to mRNA
• The anticodon of initiator tRNA base-pairs with
  the start codon (AUG) of mRNA
• A large ribosomal subunit joins the small
  ribosomal subunit

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Elongation

• The ribosome assembles a polypeptide chain as it
  moves along the mRNA
• Initiator tRNA carries methionine, the first
  amino acid of the chain
• The ribosome joins each amino acid to the
  polypeptide chain with a peptide bond

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Termination

• When the ribosome encounters a stop codon,
  polypeptide synthesis ends
• Release factors bind to the ribosome
• Enzymes detach the mRNA and polypeptide chain
  from the ribosome

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Polysomes

• Many ribosomes may simultaneously translate the
  same mRNA, forming polysomes

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polysome
p. 222
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Translation in Eukaryotes
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Stepped Art
Fig. 14-12 (a-b), p. 222
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Translation in Eukaryotes
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Fig. 14-12c, p. 223
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Elongation
C An initiator tRNA carries the amino acid
methionine, so the first amino acid of the new
polypeptide chain will be methionine. A second
tRNA binds the second codon of the mRNA (here,
that codon is GUG, so the tRNA that binds carries
the amino acid valine).
A peptide bond forms between the first two
amino acids (here, methionine and valine).
Fig. 14-12c, p. 223
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Fig. 14-12d, p. 223
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D The first tRNA is released and the ribosome
moves to the next codon in the mRNA. A third tRNA
binds to the third codon of the mRNA (here, that
codon is UUA, so the tRNA carries the amino acid
leucine).
A peptide bond forms between the second and third
amino acids (here, valine and leucine).
Fig. 14-12d, p. 223
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Fig. 14-12e, p. 223
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E The second tRNA is released and the ribosome
moves to the next codon. A fourth tRNA binds the
fourth mRNA codon (here, that codon is GGG, so
the tRNA carries the amino acid glycine).
A peptide bond forms between the third and fourth
amino acids (here, leucine and glycine).
Fig. 14-12e, p. 223
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Fig. 14-12f, p. 223
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Termination
F Steps d and e are repeated over and over
until the ribosome encounters a stop codon in the
mRNA. The mRNA transcript and the new polypeptide
chain are released from the ribosome. The two
ribosomal subunits separate from each other.
Translation is now complete. Either the chain
will join the pool of proteins in the cytoplasm
or it will enter rough ER of the endomembrane
system (Section 4.9).
Fig. 14-12f, p. 223
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Animation Translation
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14.4 Key Concepts RNA to Protein Translation

• 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

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14.5 Mutated Genes and Their Protein Products

• If the nucleotide sequence of a gene changes, it
  may result in an altered gene product, with
  harmful effects
• Mutations
• Small-scale changes in the nucleotide sequence of
  a cells DNA that alter the genetic code

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Common Mutations

• Base-pair-substitution
• May result in a premature stop codon or a
  different amino acid in a protein product
• Example sickle-cell anemia
• Deletion or insertion
• Can cause the reading frame of mRNA codons to
  shift, changing the genetic message
• Example Huntingtons disease

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Common Mutations
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A Part of the DNA, mRNA, and amino acid sequence
of the beta chain of a normal hemoglobin molecule.
part of DNA
B A base-pair substitution in DNA replaces a
thymine with an adenine. When the altered mRNA
is translated, valine replaces glutamate as the
sixth amino acid of the new polypeptide chain.
Hemoglobin with this chain is HbSsickle
hemoglobin (Section 3.6).
mRNA transcribed from DNA
resulting amino acid sequence
THREONINE
PROLINE
GLUTAMATE
GLUTAMATE
LYSINE
base substitution in DNA
altered mRNA
altered amino acid sequence
THREONINE
PROLINE
VALINE
GLUTAMATE
LYSINE
C Deletion of the same thymine causes a
frameshift. The reading frame for the rest of the
mRNA shifts, and a different protein product
forms. This mutation results in a defective
hemoglobin molecule. The outcome is thalassemia,
a type of anemia.
deletion in DNA
altered mRNA
altered amino acid sequence
THREONINE
PROLINE
GLYCINE
ARGININE
Fig. 14-13, p. 224
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Stepped Art
Fig. 14-13, p. 224
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Animation Base-pair substitution
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Animation Frameshift mutation
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What Causes Mutations?

• Transposable elements
• Segments of DNA that can insert themselves
  anywhere in a chromosomes
• Spontaneous mutations
• Uncorrected errors in DNA replication
• Harmful environmental agents
• Ionizing radiation, UV radiation, chemicals

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McClintocks Transposable Elements
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Mutations Caused by Radiation

• Ionizing radiation damages chromosomes,
  nonionizing (UV) radiation forms thymine dimers

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Inherited Mutations

• Mutations in somatic cells of sexually
  reproducing species are not inherited
• Mutations in a germ cell or gamete may be
  inherited, with evolutionary consequences

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14.5 Key Concepts Mutations

• Small-scale, permanent changes in the nucleotide
  sequence of DNA may result from replication
  errors, the activity of transposable elements, or
  exposure to environmental hazards
• Such mutation can change a genes product

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Summary Protein Synthesis in Eukaryotic Cells
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Assembly of RNA on unwound regions of DNA molecule
Transcription
mRNA
rRNA
tRNA
mRNA processing
proteins
mature tRNA
mature mRNA transcripts
ribosomal subunits
Convergence of RNAs
Translation
cytoplasmic pools of amino acids, ribosomal
subunits, and tRNAs
At an intact ribosome, synthesis of a polypeptide
chain at the binding sites for mRNA and tRNAs
Protein
Fig. 14-16, p. 226
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Animation Protein synthesis summary
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Animation Structure of a ribosome
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Animation Structure of a tRNA
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Animation The major differences between
prokaryotic and eukaryotic protein synthesis
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Animation Transcription
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Animation Uracil-thymine comparison
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Video Ricin and your ribosomes