Biochemistry: A Short Course

1
Biochemical Unity of Life
Mass difference is 100,000,000 X but at a
molecular level remarkable similar.
In what ways are bacteria, plants, elephants
similar?
2
Of the 90 naturally occurring elements, only
threeoxygen, hydrogen, and carbonmake up 98 of
the atoms in any organism.
Hydrogen and oxygen are so prevalent because of
the ubiquity of water.
Carbon is uniquely suited to be a key atom of
biomolecules.
What might serve as a carbon substitute?
3
Elements of Life and their Availability
Miss selection for carbon and silicon?
Consider 1 Bond strength in catabolism/
anabolism 2 Combustion products
4
Proteins play many roles, such as signal
molecules, receptors for signal molecules and
enzymes, and biological catalysts.
5
Biomolecules Four Major Classes
I. Proteins Catalysis, Structure and energy
Directional convention
6
Amino Acid Chemical Structure Representations
Name the structure and color types? Why have
these different representations?
7
Biochemical Polymers

• Finite common monomer motif generates a huge
  polymer variety
• Specific residue linkage
• Polymer directionality

Synthetic or natural monomer/polymer pairs?
8
Dipeptide
9
The Protein Cytoskeleton Provides Cell Shape and
Movement
Are protein-rich components present that involve
catalysis?
10
Human Endothelin Polypeptide Structure
A signaling protein that constrict blood vessels
and raise blood pressure Twenty one amino acid
residues Shaded blue to red (N?C)
11
Biomolecules Four Major Classes
II. Nucleotides Information catalysis and
structure
Adenosine Triphosphate building block/energy
storage
What is the difference between a nucleotide, a
nucleoside, and a nucleic acid?
12
Nucleotides Sugars and Bases
Compare and Contrast Deoxyribonucleic acid
(DNA) versus Ribonucleic Acid (RNA)
13
H2O

Phosphodiester bond
14
Nucleic Acid Sequence Structural Representations
How can you ascertain if this is an RNA or DNA
sequence? What is the color coding in this
structure?
CGUACG
15
Biomolecules Four Major Classes
III. Lipids Energy Storage and Barrier
Common structural features for lipids?
16
Biomolecules Four Major Classes
IV. Carbohydrates Fuel, Structure and
Information
How many chiral centers in glucose? In what form
do humans store sugars?
17

H2O
Glycosidic bond
18
Glucose and its Polymers Starch and Cellulose
Humans are excellent at distinguishing metabolite
stereochemistry
Match terms with cellulose or starch Edible/Ined
ible Helical/Linear Alpha/Beta-Linked
19
Biological Functions for Biopolymers
What is an example of polysaccharides encoding
for information?
20
Biochemical Functional Groups
21
Biochemical Functional Groups
22
The Central Dogma states that information flows
from DNA to RNA to protein. Moreover, DNA is
replicated.
23
DNA Replication
Proteins catalyzed i unwinding of the super
helix DNA helicases ii unwinding of the
double helix DNA helicases iii replicate the
master template DNA polymerases
24
DNA Transcription
RNA polymerase and transcription factors catalyze
messenger RNA (mRNA) formation from DNA sections
In eukaryotes the primary transcript (pre-mRNA)
is processed via alternative splicing
25
RNA to Protein Conversion Translation
Mature mRNAs attach to ribosomes where it is read
as a triplet codon Initiation and elongation
factors bring aminoacylated transfer RNAs (tRNAs)
into the ribosome-mRNA complex
26
A membrane is a lipid bilayer.
Eukaryotes contain membrane-enclosed compartments
inside the cell.
Prokaryotes lack intracellular membranes.
27
Membrane Bilayer Structure
Two layers or sheet with the hydrophobic regions
interacting
28
The plasma membrane of a plant cell is surrounded
by a cell wall composed largely of cellulose, a
linear polymer of glucose.
Cell wall
Nucleus
29
Prokaryotic Versus Eukaryotic Cells Internal
Structure
30
Energy Exchange in Biological Systems
What makes for potent biological fuels? What
defines energy in a chemical system?
31
Carbon Oxidation and Reduction Lifes Energy
Exchange
Where would sugars, lipids, gasoline, carbon
dioxide and methane gas be placed on an poor/rich
energy scale?
32
Carbon Oxidation Ranking from Most Oxidized to
Most Reduced
How does acetyl-aldehyde versus ethanol rank in
terms of energy content?
33
Gibbs Free Energy Indicates Reaction Spontaneity
?G ?H - T?S
?G' ?H' - T?S'
?G ?G' RTlnKeq
What determines if a reaction is spontaneous in
the forward direction reverse direction or at
equilibrium?
34
Entropy (?S) is a measure of Disorder
Lower Entropy
Higher Entropy
Enthalpy (?H) is a measure of Heat Content
Negative ?H ? Exothermic reaction Positive ?H ?
Endothermic reaction
What is ?G, ?H and ?S for Burning paper?
Dissolving (NH4)2SO4 in H2O?
35
Text Chapter 1, 1-10 Workbook Section 1,
Critical thinking questions 1-10 (due 1/29/13)