Lecture 4
Proteins and
Protein Synthesis:
Physics in
Life
Outline
Proteins and Protein Structure
RNA and Protein Synthesis
Genetic Code
Transcription
Processing Messenger RNA
Translation
Transfer RNA
Ribosomal RNA
Proteins
Bio-functionalities of protein- S3CDET
Protein Subunits: The Amino Acids
Proteins are just
a bunch of amino
acids which are
linked together.
20 important
amino acids all
have the same
core structure.
Protein Subunits: The Amino Acids
Each amino acid has a
central carbon atom
(the alpha carbon) to
which are attached
Amino Carboxylic
group acid
Allof them have
basically the same
structure except for
Variable side chain R what occurs at the
defining different placeholder R
amino acids.
Protein Subunits: The Amino Acids
Structural
Formulas for the
20 Amino Acids
Proteins:
The Polypeptide Backbone
Amino acids joined together end-to-end
COOH of one AA covalently bonds to the NH2 of
the next AA
Special name for this bond - Peptide Bond
Two AAs bonded together – Dipeptide
Three AAs bonded together – Tripeptide
Many AAs bonded together – Polypeptide
Proteins:
The Polypeptide Backbone
A protein is made of adding amino acids
together in a chain.
Virtually unlimited number of
“proteins”
So…
the sequence of amino acids is the key to
the 3 dimensional structure of protein…
the 3 dimensional structure of protein is
the key to the biological function.
Protein Molecules: 4 Levels of
Structure
Primary:
Literally, the sequence of amino acids
A string of beads (up to 20 different colors)
Secondary:
The way the amino acid chain coils or folds
Describing the way a knot is tied
Tertiary:
Overall three-dimensional shape of a polypeptide
Describing what a knot looks like from the outside
Quaternary:
Consists of more than one polypeptide
Like several completed knots glued together
4 Levels of Protein Organization
Protein: some key points
Peptide = a chain of amino acids
Amino acids are chained together to
form proteins.
Polypeptide Amino acid chain
Protein
Protein means function
Protein Synthesis:
From DNA to RNA to Protein
The mechanism of gene expression
DNA in genes specify information, but
information is not structure and function
Genetic info is expressed into structure &
function through protein synthesis
The expression of genetic info into
structure & function:
DNA in gene controls the sequence of
nucleotides in an RNA molecule
RNA controls the primary structure of a protein
RNA
RNA is a polymer of RNA nucleotides
RNA Nucleotides are of four types: Uracil,
Adenine, Cytosine, and Guanine
Uracil (U) replaces thymine (T) of DNA
Types of RNA
Messenger (mRNA) - Takes genetic message
from DNA in nucleus to ribosomes in
cytoplasm
Ribosomal (rRNA) - Makes up ribosomes
which read the message in mRNA
Transfer (tRNA) - Transfers appropriate amino
acid to ribosome when “instructed”
RNA Structure
Comparison of DNA & RNA
Feature DNA RNA
Sugar Deoxyribose Ribose
Cytosine, guanine; Cytosine, guanine;
Bases
adenine, thymine adenine, uracil
Double-stranded;
Strands Mostly single stranded
Pairing across strands
Helix Yes No
Heredity; cellular Interprets genetic info;
Function
control center protein synthesis
Chromosomes of cell Cellnucleus and
Where
nucleus cytoplasm
Overview of Gene Expression
Steps in Gene Expression:
Transcription
Transcription
Gene unzips and exposes unpaired bases
Serves as template for mRNA formation
Loose RNA nucleotides bind to exposed
DNA bases using the C=G & A=U rule
When entire gene is transcribed into mRNA,
result is an mRNA transcript of the gene
The base sequence in the mRNA is
complementary to the base sequence in
DNA
Steps in Gene Expression: Translation
tRNA molecules have two binding sites
One associates with the mRNA transcript
The other associates with a specific amino acid
Each of the 20 amino acids in proteins associates with one or more
of 64 species of tRNA
Translation
An mRNA transcript migrates to rough endoplasmic reticulum
Associates with the rRNA of a ribosome
The ribosome “reads” the information in the transcript
Ribosome directs various species of tRNA to bring in their specific
amino acid “fares”
tRNA specified is determined by the code being translated in the
mRNA transcript
The Genetic Code (Codons System)
The unit of a code consists of codons, each of
which is a unique arrangement of symbols
Each of the 20 amino acids found in proteins is
uniquely specified by one or more codons
The symbols used by the genetic code are the mRNA
bases
Function as “letters” of the genetic alphabet
Genetic alphabet has only four “letters” (U, A, C, G)
Codons in the genetic code are all three bases
(symbols) long
Function as “words” of genetic information
Permutations:
There are 64 possible arrangements of four symbols
taken three at a time
Often referred to as triplets
Genetic language only has 64 “words”
The Genetic Code (Codons System)
Properties of the genetic code:
Universal
With few exceptions, all organisms use the
code the same way
Encode the same 20 amino acids with the
same 64 triplets
Degenerate (redundant)
There are 64 codons available for 20 amino
acids
Most amino acids encoded by two or more
codons
The Genetic Code (Codons System)
Unambiguous (codons are exclusive)
None of the codons code for two or
more amino acids
Each codon specifies only one of the
20 amino acids
Contains start and stop signals
Punctuation codons
Like the capital letter we use to signify
the beginning of a sentence, and the
period to signify the end
The Genetic
Code (mRNA)
Transcription of mRNA
A single chromosomes consists of one
very long molecule encoding hundreds or
thousands of genes
The genetic information in a gene
describes the amino acid sequence of a
protein
The information is in the base sequence of one
side (the “sense” strand) of the DNA molecule
The gene is the functional equivalent of a
“sentence”
Transcription of mRNA
The segment of DNA corresponding to a
gene is unzipped to expose the bases of
the sense strand
The genetic information in the gene is
transcribed (rewritten) into an mRNA molecule
The exposed bases in the DNA determine the
sequence in which the RNA bases will be
connected together
RNA polymerase connects the loose RNA
nucleotides together
The completed transcript contains the
information from the gene, but in a mirror
image, or complementary form
Transcription
RNA Polymerase
Processing Messenger RNA
Primary mRNA transcript is modified before it leaves
the eukaryotic nucleus
RNA splicing:
Primary transcript consists of:
Some segments that will not be expressed (introns)
Segments that will be expressed (exons)
Performed by spliceosome complexes in nucleoplasm
Introns are excised
Remaining exons are spliced back together
Modifications to ends of primary transcript:
Cap of modified guanine on 5′ end
Poly-A tail of 150+ adenines on 3′ end
Result is mature mRNA transcript
mRNA Processing in Eukaryotes
Functions of Introns
As organismal complexity increases;
Number of protein-coding genes does not keep pace
But the proportion of the genome that is introns increases
Humans:
Genome has only about 25,000 coding genes
Up to 95% of this DNA genes is introns
Possible functions of introns:
More bang for buck
Exons might combine in various combinations
Would allow different mRNAs to result from one segment of
DNA
Introns might regulate gene expression
Exciting new picture of the genome is emerging
tRNA
tRNA molecules come in 64 different kinds
All very similar except that
One end bears a specific triplet (of the 64
possible) called the anticodon
Other end binds with a specific amino acid type
tRNA synthetases attach correct amino acid to
the correct tRNA molecule
All tRNA molecules with a specific
anticodon will always bind with the same
amino acid
Structure of tRNA
Ribosomes
Ribosomal RNA
(rRNA):
Produced from a DNA
template in the
nucleolus
Combined with
proteins into large and
small ribosomal
subunits
Ribosomes
A completed ribosome
has three binding sites
to facilitate pairing
between tRNA and
mRNA
The E (for exit) site
The P (for peptide) site,
and
The A (for amino acid)
site
Ribosomal Structure and Function
Steps in Translation: #1 - Initiation
Components necessary for initiation are:
Small ribosomal subunit
mRNA transcript
Initiator tRNA, and
Large ribosomal subunit
Initiation factors (special proteins that bring
the above together)
Initiator tRNA:
Always has the UAC anticodon
Always carries the amino acid methionine
Capable of binding to the P site
Steps in Translation: #1 - Initiation
Small ribosomal subunit attaches to
mRNA transcript
Beginning of transcript always has the START
codon (AUG)
Initiator tRNA (UAC) attaches to P site
Large ribosomal subunit joins the small
subunit
Steps in Translation: #1 - Initiation
Steps in Translation: #2 - Elongation
“Elongation” refers to the growth in
length of the polypeptide
RNA molecules bring their amino
acid fares to the ribosome
Ribosome reads a codon in the mRNA
Allows only one type of tRNA to bring its
amino acid
Must have the anticodon complementary
to the mRNA codon being read
Joins the ribosome at it’s A site
Methionine of initiator is connected to
amino acid of 2nd tRNA by peptide bond
Steps in Translation: #2 – Elongation
(cont.)
Second tRNA moves to P site (translocation)
Spent initiator moves to E site and exits
Ribosome reads the next codon in the mRNA
Allows only one type of tRNA to bring its amino
acid
Must have the anticodon complementary to the
mRNA codon being read
Joins the ribosome at it’s A site
Dipeptide on 2nd amino acid is connected to amino
acid of 3nd tRNA by peptide bond
Steps in Translation: #2 - Elongation
Steps in Translation: #3 – Termination
Previous tRNA moves to P site
Spent tRNA moves to E site and exits
Ribosome reads the STOP codon at the end of
the mRNA
UAA, UAG, or UGA
Does not code for an amino acid
Polypeptide is released from last tRNA by
release factor
Ribosome releases mRNA and dissociates into
subunits
mRNA read by another ribosome
Steps in Translation: #3 - Termination
Summary of Gene Expression (Eukaryotes)
Review
Macromolecules
Proteins
Nucleic Acids
Genetic Code
Transcription
Processing Messenger RNA
Translation
Transfer RNA
Ribosomal RNA
Main Related Chapters in the
textbook:
-Chapters 3, 13,14 in biology
