Lecture 9b (2/18/13) "How to Make Proteins"

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Announcements
• Quiz today over Chpt 2 of Phillips et al.
• Written HW due Wednesday
• Example of your 12 minute Lectures
Proteins (quick review)
RNA Proteins (The Ribosome, tRNA)
Next time: the midterm, how to choose
paper for research project
Quiz
1. The Cell Interior is a crowded place.
This means that the average spacing between molecules is:
a. Much less than the dimensions of the average molecule.
b. About equal to the dimensions of the average molecule.
c. Much greater than the dimensions of the average molecule.
2. Membrane-bound organelles, are defining features
of eukaryotic cells that differentiate these cells from bacteria
and archea. Among the roles of such membranes are to:
a. Genome management Nucleus
b. Energy Generation
Mitochondria, Cell membrane
c. Protein synthesis.
E.R. and/or Golgi Apparatus
What are the organelles associated with a, b, and c?
3. Amino acids have a side chain, sometime
called “R” (see picture). The side chains are
often grouped according to their physical
properties.
a) How are they classified? (I’m looking for
three words) Hydrophobic, Polar (Hydrophilic),
Charged
As an example: Lysine has a CH-NH3+;
Phenylalanine has a CH2-Benzene-ring.
L-Charged, Outside
A)Which tend to be inside a protein?
P-Hydrophobic, Inside
B)Which tend to be on the outside of proteins?
Quick Review
Linear sequence of ~ 20 amino acids
Can get enormous diversity and
function with Proteins
Figure 5.UN01
Amino Acid Structure
Side chain (R group)
(110 g/mole)
Amino
group
 carbon
Carboxyl
group
20 different R groups
Hydrophobic (non-polar; greasy)
Hydrophilic (polar; non-greasy)
Charge: positive, neutral, negatively
Determines where they go: inside vs. outside
Figure 5.16
Amino Acid Structure—20 Diff. R
Nonpolar side chains; hydrophobic
Side chain
(R group)
Glycine
(Gly or G)
Methionine
(Met or M)
Alanine
(Ala or A)
Valine
(Val or V)
Phenylalanine
(Phe or F)
Leucine
(Leu or L)
Tryptophan
(Trp or W)
Isoleucine
(Ile or I)
Proline
(Pro or P)
Polar side chains; hydrophilic
Serine
(Ser or S)
Threonine
(Thr or T)
Cysteine
(Cys or C)
Tyrosine
(Tyr or Y)
Asparagine
(Asn or N)
Glutamine
(Gln or Q)
Electrically charged side chains; hydrophilic
Basic (positively charged)
Acidic (negatively charged)
Aspartic acidGlutamic acid
(Asp or D) (Glu or E)
Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)
Secondary Structure
-helix, b-sheets
-helix, b-sheets depends on specific amino acids
• Tertiary structure is determined
by interactions between R groups,
rather than interactions between
backbone constituents
• These interactions between R
groups include hydrogen bonds,
ionic bonds, hydrophobic
interactions, and van der Waals
interactions
• Strong covalent bonds called
disulfide bridges may reinforce
the protein’s structure
© 2011 Pearson
Education, Inc.
Figure 5.20f
Hydrogen
bond
Hydrophobic
interactions and
van der Waals
interactions
Disulfide
bridge
(Covalent
bond)
Ionic bond
Polypeptide
backbone
(Not gone over in lecture but presented here.)
Figure 5.20b
4 layers of Protein Structure
Tertiary
structure
Secondary
structure
Quaternary
structure
 helix
Hydrogen bond
b pleated sheet
(b arrow toward
b strand
carboxyl end)
Hydrogen
bond
Transthyretin
polypeptide
Transthyretin
protein
Size of proteins
10kD to 100kD to over a million
Recall aa = 110 D…say 100D
10kD=100aa
Figure 5.18
Alternative Representations
Groove
Groove
(a) A ribbon model
(b) A space-filling model
• The sequence of amino acids
determines a protein’s threedimensional structure
• A protein’s structure determines its
function
© 2011 Pearson
Education, Inc.
Protein Structure and Function
• A functional protein consists of
one or more polypeptides
precisely twisted, folded, and
coiled into a unique shape
© 2011 Pearson
Education, Inc.
Figure 5.19
Antibody protein
Protein from flu virus
Figure 5.20d
Sickle-Cell Disease: A Change
in Primary Structure
• A slight change in primary
structure can affect a protein’s
structure and ability to function
• Sickle-cell disease, an inherited
blood disorder, results from a
single amino acid substitution in
the protein hemoglobin
© 2011 Pearson
Education, Inc.
Figure 5.21
Sickle Cell Anemia
Sickle-cell hemoglobin
Normal hemoglobin
Primary Secondary Quaternary
Structure and Tertiary Structure
Structures
1
2
3
4
5
6
7
Function
Red Blood
Cell Shape
Molecules do not
Normal
hemoglobin associate with one
another; each
carries oxygen.
b subunit

b
10 m

b
1
2
3
4
5
6
7
Exposed
Sickle-cell Molecules crystallize
hydrophobic hemoglobin into a fiber; capacity
region
to carry oxygen is
reduced.

b subunit
b
b

10 m
Why does sickle cell anemia
still exist?
It is clearly disadvantageous to have
disease; make probability of
reproducing less likely.
Recall you’re diploid—have two copies of
each gene.
If have both SS, then you have anemia.
If both genes unmutated: “normal”.
If heterozygote, (one “good”, one “bad”)
then have certain advantages.
If mother/father have SS and NN,
probability of kid having SS? NN? SN?
Advantage: More resistant to
malaria.
How Proteins are made
DNA RNA Proteins
Central Dogma of Molecular Biology
DNA: linear series of 4 nucleotides (bases): A,T,G,C

Double-stranded
Transcription [DNA & RNA similar]
RNA: linear series of 4 nucleotides (bases): A,U,G,C

Mostly single-stranded
Translation [RNA & Proteins different]
Proteins: linear series of 20 amino acids: Met-Ala-Val-…
each coded by 3 bases  amino acid
AUG Methionine; GCU  Alanine; GUU Valine
Proteins are 3-D strings of linear amino acids
Do everything: structure, enzymes…
http://learn.genetics.utah.edu/units/basics/transcribe/
RNA has 3 different uses
3 different names, (mRNA, tRNA,
rRNA)
A key element of the central dogma of molecular
biology:
that DNA makes RNA makes protein
1. Messenger RNA (mRNA)
[~copy of DNA]
2. transfer RNA (tRNA)
[binds to amino acid and
codon for mRNA]
3. ribosomal RNA (rRNA)
[Makes up Ribosome, along
with protein. Has catalytic
activity– can form peptide
bond. RNA is catalytic!]
Focus on RNA Proteins
http://en.wikipedia.org/wiki/Messenger_RNA
Ribosome
A key element of the central dogma of molecular
biology:
that DNA makes RNA makes protein
5’
3’
Takes the sequence in mRNA
and produces a polypeptide (protein)
Stages in translation:
Initiation, Elongation, Termination, Recycling
We’ll learn how to measure these things–
nanometer scale, sub-second time resolution
E.M. and x-ray crystallography, Fluorescence
Ribosome is made of two
subunits
30S and 50S sub-units
The smaller subunit binds to the mRNA, while
the larger subunit binds to the tRNA and the
amino acids. When a ribosome finishes reading
a mRNA, these two subunits split apart.
20 nm
20 nm
The assembly process involves the coordinated
function of over 200 proteins in the synthesis and
processing of the four rRNAs, as well as assembly of
those rRNAs with the ribosomal proteins.
Transfer RNA (tRNA)
CCA tail binds
to amino acid
AminoacylationtRNA synthetase
(depends on ATP)
Tertiary structure of tRNA
ds RNA
Anticodon
in black
1st base often
modified-allow
wobble
Its primary structure (including bases which
have been methylated), its secondary structure
(usually visualized as the cloverleaf structure),
and its tertiary structure (all tRNAs have a
similar L-shaped 3D structure that allows them
to fit into the P and A sites of the ribosome).
http://en.wikipedia.org/wik
i/Transfer_RNA
Translation (RNA Protein)
http://www.youtube.com/watch?fea
ture=endscreen&NR=1&v=Ikq9Ac
BcohA
Slight more detailed view of
Protein Synthesis
http://www.youtube.com/watch?v=1PSwhTGFMxs
&feature=endscreen&NR=1
Class evaluation
1. What was the most interesting thing you
learned in class today?
2. What are you confused about?
3. Related to today’s subject, what would you like
to know more about?
4. Any helpful comments.
Answer, and turn in at the end of class.

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