Download From DNA to Protein

Protein Synthesis
and Structure
Section 2-4
Protein Functions: General
Information
• Proteins account for almost 50% of the dry mass of most cells
• Proteins are the most structurally sophisticated molecules
known
• Each protein has a specific 3-diminsional shape, or
“confirmation” that is vital to its function
Protein Functions
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Enzymatic
Structural
Storage
Transport
Hormonal
Receptor
Contractile and motor
Defensive
Four Levels of Protein
Structure
Primary Structure
• The unique sequence of amino acids
that make up a polypeptide
• Amino acids:
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An asymmetrical carbon
An amino group (contains Nitrogen)
A carboxyl group
A side chain (R group) which makes each
amino acid unique
Primary Structure
• Amino acids are linked together with
dehydration reactions
• Peptide bonds- the bonds between
amino acids
Primary Structure
• The chain will have two ends:
• An amino end- known as the Nterminus
• A carboxyl end- known as the Cterminus
• Primary structure is achieved through
the processes of transcription and
translation
Secondary Structure
• Refers to the coils and folds in the polypeptide chain due to
hydrogen bonds between repeating areas on the polypeptide
backbone
Secondary Structure
• Alpha helix (α helix)- a delicate coil held together by hydrogen
bonding between every fourth amino acid
• Beta pleated sheet (β pleated sheet)- two or more regions of a
polypeptide chain lying side by side and connected by hydrogen
bonds between the two parallel polypeptide back bones
Tertiary Structure
• Folding due to interactions
between the amino acid side
chains
• Main causes of tertiary
structure
• Hydrogen bonds between polar
R-groups
• Hydrophobic interactions
between nonpolar R groups
causes them to clump together
and form Van der Wall’s
interactions
• Dislufide bridges between two
sulfhydryl groups
Tertiary Structure: Main
Causes
• Hydrogen bonds between polar
R-groups
• Hydrophobic interactions
between nonpolar R groups
causes them to clump together
and form Van der Wall’s
interactions
• Dislufide bridges between two
sulfhydryl groups
Quaternary Structure
• Overall shape of the protein caused by the association of two
or more polypeptide chains
• NOT ALL PROTEINS HAVE QUATERNARY STRUCTURE
Protein Synthesis
General Information
• Also called gene
expression
• DNA provides the
blueprints for the building
of proteins
General Information
• Involves two processes:
• Transcription- copying DNA
into mRNA
• Translation- translates the
code from nucleic acid into
amino acid at the
ribosome
Evolutionary Advantage of
Transcription and Translation
• DNA is protected inside the nucleus
• Using an RNA intermediate allows multiple copies of a protein
to be made at once because many mRNA molecules can be
made from one gene, then translated repeatedly
Prokaryotes vs. Eukaryotes
Prokaryotes
• Only one compartment
(no nucleus)
• Transcription and
Translation occur
simultaneously
Prokaryotes vs. Eukaryotes
Eukaryotes
• Transcription occurs in the
nucleus
• The primary transcript is
then modified (RNA
processing) before leaving
the nucleus
• Translation occurs in the
cytoplasm at the ribosome
The Genetic Code
• Triplet Code- the flow if information from gene (DNA) to
protein is written in the DNA as non-overlapping, threenucleotide segments
• Template Strand:
• The mRNA is complimentary to the template strand
• The DNA is read in the 3’ to 5’
• The mRNA is synthesized and read from 5’ to 3’
The Genetic Code
• Codons- each three base sequence on the mRNA strand
• Each codon codes for a specific amino acid
Redundant but not Ambiguous
• Redundant- multiple
codons can code for
the same amino acid
• Not Ambiguous- no
codon codes for
more than one
amino acid
Special Codons
• AUG= start
• UAA, UAG, UGA=
stop
Transcription
Initiation
• RNA polymerase binds to the promoter
• The promoter is a specific sequence that tells the RNA
polymerase where to bind and determines what DNA strand
will serve as the template
• In eukaryotes, specific proteins called transcription factors
assist the RNA polymerase in binding and forming the
transcription initiation complex
Initiation
Elongation
• RNA polymerase adds
nucleotides to the 3’
end of the growing
RNA molecule
• Complimentary base
pairing occurs
• The new RNA molecule
peals away from the
DNA template and the
DNA reforms
Termination
• In prokaryotes, the RNA polymerase detaches after the
termination signal is transcribed
• In eukaryotes, the RNA polymerase transcribes the
polyadenylation signal sequence then the mRNA is cut off of
the RNA polymerase
RNA Processing
EUKARYOTIC
CELLS ONLY
Altering of the Ends of the
mRNA
• 5’ cap- modified guanine molecule added on the 5’ end
• Poly-A-tail- 50-250 adenine nucleotides are added to the 3’
end
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Functions:
Facilitate export from the nucleus
Protect the mRNA from degradation by enzymes
Assist the ribosomes in attaching in the cytoplasm
RNA Processing
RNA Splicing
• Removal of large portions of the mRNA
• snRNPs (“snurps”) recognize and cut out areas of the mRNA
• Introns- the portions of the mRNA that are removed
• Exons- the portions of the mRNA that exit the nucleus
Translation
Transfer RNA, tRNA
• Translates nucleotides
into amino acids
• One end has an
anticodon,
complementary to the
mRNA codon
• The other end is bound
to an amino acid
• Excellent example of
how structure fits
function
Ribosomes
• Contain three sites for holding tRNA:
• P site- holds the growing polypeptide
chain
• A site- holds the tRNA that is carrying
the next amino acid in the chain
• E site- where the tRNA leaves the
ribosome
• Exit Tunnel= where the polypeptide
leaves the ribosome
Translation- The Process
Initiation
• Small ribosomal subunit binds the mRNA and the initiator
tRNA
• Subunit scans the mRNA until it reaches the start codon,
establishing the correct reading frame as the tRNA hydrogen
bonds to the start codon
Initiation
• Translation initiation complex forms- the large ribosomal
subunit attaches with the assistance of initiation factors and
an expenditure of energy
Elongation
Elongation
• The ribosome reads the mRNA in the 5’ to 3’ direction
• Anticodon of the incoming tRNA hydrogen bonds to the mRNA
codon in the A site
• The peptide bond forms between the amino acid on the tRNA of
the A site and the growing polypeptide chain in the P site
• Translocation of the tRNA shifts the A site tRNA to the P site and
the P site tRNA to the E site so it can exit
Termination
• Release factor:
• Added when stop codon is reached
• Causes the addition of a water molecule to the end of the
polypeptide
• The polypeptide is released
Forming a Functional Protein
Protein Folding
• Folding occurs as the protein is being synthesized
• Folding is dependent on
• The properties of the peptide chain
• The physical and chemical properties of the environment
WHY MIGHT THIS BE A PROBLEM???
Chaperonins
• Proteins that assist in the proper folding of other proteins by
shielding them form the cell environment
Post-Translational
Modification
• Chemical modification by the attachment of sugars, lipids,
phosphate groups, or other components
• Enzymes may remove one or more amino acids from the Nterminus
• Single polypeptides may by cut into two or more smaller
pieces
Denaturation
• The changes in a protein’s native conformation that renders it
biologically inactive
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Factors that cause denaturation:
Change in the environment
Change in temperature
Change in pH
Changes in Environment
• If moved from an aqueous environment to a nonpolar organic
solvent, the protein will turn inside out
• Chemicals can disrupt disulfide and hydrogen bonds that
stabilize secondary and tertiary structure
Changes in Temperature
• Excessive heat can cause movement to overpower sensitive
hydrogen bonds
• Excessive cold will slow the protein down substantially
Changes in pH
• All proteins have an optimal pH at which they function
• Optimal pH is not necessarily 7