Lecture 5

PROTEINS AND
PROTEIN SYNTHESIS (2)

Physics in
Life Sciences

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 Q&A
Bond
V φ: Bond energy
{ Molecular
Interactions in Bio-
molecular Structures
- Dipole-dipole
interactions. You ro ro: length of bond
mentioned something r
about having 0
φ
negative sign on the
formula which I didn't
catch what you
mean.

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Q&A
{ I don't
understand how
to differentiate
between
hydrogen-bond
acceptor
Hydrogen Hydrogen
and hydrogen- bond donor bond donor
bond donor?

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Lecture 2

Biologically important “molecules”-ions

Some common ions:

z Sodium Na+ (Cation),
z Potassium K+ (Cation),
z Chlorine Cl- (Anion),
z Calcium Ca2+ (Cation)

z NH4+
z CH3COO-

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Lecture 2
Biologically important molecules-water,
dipole-dipole interaction and hydrogen bond

{ In H2: H-H are equal.

The covalent bond is
non-polar.
{ In H2O, O takes more of δ-
H than it gives.
{ So H is dependent on
this “partnership”. δ+ δ+
{ In O-H, O δ-, H δ+. -
Polar covalent bond.
{ Dipole moment μ = δr
δ+ δ-

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Scalars and Vectors
{ A scalar quantity is one that can be
described by a single number:
temperature, speed, mass
{ A vector quantity deals inherently
with both magnitude and direction:
velocity, force, displacement

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Scalars and Vectors
{ Arrows are used to represent
vectors. The direction of the arrow
gives the direction of the vector.
By convention, the length of a vector
arrow is proportional to the
magnitude
of the vector.
4 lb 8 lb

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Scalars and Vectors

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Lecture 2
Molecular Interactions in Bio-molecular
Structures- Dipole-Dipole Interactions

General Formula for Dipole-

Dipole Interactions

r = distance between the dipoles rather

than the charge-charge distance within
a dipole

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 Q&A

{ If I didn't hear wrongly, you

mentioned that the order of
secondary structure allows us to
predict the next amino acids. I
don't understand how this is so? Is
it got to do with the charge of the
amino acids which may interfere
how the structure will fold?

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11
 Q&A
{ Another thing that you mentioned about to
measure the protein structure. What do you
mean by that? ( Sorry, I am not sure if I have
heard it wrongly.)

Protein 3D
structure

The 3D structure of protein is directly

associated with its biofunctions.

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Translation is a process where proteins are synthesized!

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Overview of Gene Expression

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 Translation
{ In translation, you are
going into a whole new
language: from the
language of nucleotides to
the language of amino
acids.
{ In order to make protein
from DNA, that DNA starts
to make messenger RNA;
{ the mRNA is then the new
template which codes
directly to protein.

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Biologically important molecules-
RNA
{ mRNA is a single
strand of
nucleotides, which
are A,U,G,C.
{ One section of
mRNA

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Biologically important molecules-
RNA
{ There are 20
amino acids.
{ In order to have
enough info in the
RNA to refer to all
20 amino acids,
what are we going
to
do???????????????
?????????????????
????????????

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 tem
n s ys
d o
Co

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The Genetic Code
{ In order to have
enough codes in
the RNA to refer to
20 amino acids, a
triple codon
system is utilized:
{ Each codon (3
nucleotides) in the
row to represent
one amino acid!

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The Genetic Code
{ In other words, each
amino acid is
represented by 3 of
these magic letters:
A,U,G & C!
{ A codon is a 3
nucleotide sequence in
mRNA that specifies a
particular amino acid,
and 1 starting and 3
termination signals,
and functions as a
basic generic unit of
the code.

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 The Genetic Code

For example:

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Is the codon system sufficient?
{ How many combinations do we
have? (how many codons do we
have?)
z The positioning of the 3 letters
should be taken into account (ie.
AUC ≠ UAC ≠ UCA…).

z64

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Is the codon system sufficient?

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The Genetic Code (Codon System)

+ start and
termination

zDegeneracy (redundancy)

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The Genetic Code (Codon System)

Degeneracy
{ Degeneracy means
there are more
codons than amino
acids.
{ Each amino acid
has more than one
code assigned to
it.

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Biologically important molecules-
RNA

{ Some important codons:

Go…
{ AUG, used as “START” in telling
ribosome to start making
polypeptide.

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Biologically important molecules-
RNA

STOP!
{ 3 codons, UAA,
UAG, UGA, are
used as
termination
codons in telling
ribosome to stop
making
polypeptide when
the job is done.

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 Biologically important molecules-
RNA

{ mRNA makes
polypeptide by way
of degenerate code
system.

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The Genetic Code
{ 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
z 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)
z Codons in the genetic code are all three bases
(symbols) long
{ Function as “words” of genetic information
{ Permutations:
z There are 64 possible arrangements of four symbols
taken three at a time
z Often referred to as triplets
{ Genetic language only has 64 “words”

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 The Genetic Code
{ Properties of the genetic code:
z Universal
{ With few exceptions, all organisms use
the code the same way
{ Encode the same 20 amino acids with the
same 64 triplets
z Degenerate (redundant)
{ There are 64 codons available for 20
amino acids
{ Most amino acids encoded by two or more
codons

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The Genetic Code
z 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
z 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

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The Genetic
Code (mRNA)

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tRNA
{ tRNA molecules come in 64 different
kinds
{ All very similar except that
z One end bears a specific triplet (of the 64
possible) called the anticodon
z Other end binds with a specific amino acid type
z 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

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Structure of tRNA

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 Ribosomes
{ Ribosomal RNA
(rRNA):
z Produced from a DNA
template in the
nucleolus
z Combined with
proteins into large and
small ribosomal
subunits

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 Ribosomes
{ A completed ribosome
has three binding sites
to facilitate pairing
between tRNA and
mRNA
z The E (for exit) site
z The P (for peptide) site,
and
z The A (for amino acid)
site

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Ribosomal Structure and Function

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Steps in Translation: #1 - Initiation

{ Components necessary for initiation are:

z Small ribosomal subunit
z mRNA transcript
z Initiator tRNA, and
z Large ribosomal subunit
z Initiation factors (special proteins that bring
the above together)
{ Initiator tRNA:
z Always has the UAC anticodon
z Always carries the amino acid methionine
z Capable of binding to the P site

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Steps in Translation: #1 - Initiation
{ Small ribosomal subunit attaches to
mRNA transcript

z Beginning of transcript always has the START

codon (AUG)

{ Initiator tRNA (UAC) attaches to P site

{ Large ribosomal subunit joins the small

subunit

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Steps in Translation: #1 - Initiation

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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
z 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
z Methionine of initiator is connected to
amino acid of 2nd tRNA by peptide bond

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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
z 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

z Dipeptide on 2nd amino acid is connected to

amino acid of 3nd tRNA by peptide bond

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Steps in Translation: #2 - Elongation

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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
z UAA, UAG, or UGA
z 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

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Steps in Translation: #3 - Termination

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Summary of Gene Expression (Eukaryotes)

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Review
{ Genetic Code
{ Translation
z Transfer RNA
z Ribosomal RNA

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 Main Related Chapters in the
textbooks:

- Chapters 3, 13,14 in biology

- Chapter 1 in Physics, CUTNELL

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