1

Introduction to Biochemistry
and Molecular Biology
Instructor: Rob McKenna, Ph.D.
Email: rmckenna@ufl.edu

Office hours: Th 3:00 5:00 pm
(Start of course through 1
st
Exam)

Office: MBI LG-179

Lecture notes at UF e-Learning
http://lss.at.ufl.edu

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Lecture 1: Biological Organization
Reading Assignment:
Lehninger, Principles of Biochemistry, 5
th
Edition
Chapter 1 pp. 1 - 36
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Features of Living Organisms
Possess chemical complexity and microscopic
organization
Ability to extract, transform, and use energy from the
environment
Defined functions for each biological component and
regulation of interactions between components
Ability to sense and respond to the environment
Ability to self-replicate
As a species, ability to evolve and adapt to environment
4
Phylogeny of the Three Domains of Life
5
Major Features of Prokaryotic Cells
Cell size: 1 10 m
Typically single-cell microorganisms (Bacteria and
Archaea)
Flagella for mobility and pili for adhesion
Cell envelope plasma membrane and layers
surrounding the plasma membrane.
Outer layers differ for different organisms
Can be formed from membranes and peptidoglycans
Cytoplasm enclosed by plasma membrane
Cytosol aqueous solution containing biomolecules
Nucleoid genetic material, no membrane
Cytoskeleton made of protein, provides structure and
organization to cytoplasm, is dynamic
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Structural Features of Bacterial Cells
E. coli is the most studied
bacterium
Size 2 m long x 1 m in
diameter
Contains 15,000
ribosomes
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Major Features of Eukaryotic Cells
Size: 5 100 m
Mostly multicellular organisms (protists, fungi, plants,
animals)
Outer membrane dynamic structure of lipids and
proteins
Nucleus contains genetic material and enclosed by a
membrane
Cytoplasm enclosed by the outermembrane
Cytosol aqueous solution of biomolecules
Organelles enclosed by inner membranes (illustrated on next
slide)
Cytoskeleton - made of protein, provides structure and
organization to cytoplasm, is dynamic
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Structural Features of Animal Cells
Organelles underlined
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Structural Features of Plant Cells
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Cytoskeleton
Protein filaments forming a meshwork
Dynamic
3 types
Actin filaments 6 nm width, made from G-actin
Microtubules 23 nm width, made from tubulin
Intermediate filaments 10 nm width, made from a-
keratin
Each filament is composed of protein monomers bound
noncovalently to form a long polymer
Provide shape and organization, as well as help cells
and organelles move
e.g. cell division - cytoskeleton reorganizes cellular
components to be divided between daughters
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Cytoskeleton Images
Endothelial Cells Mitotic Cells
Close-up View
of Cytoplasm
Microtubules (green)
Intermediate
filaments (red)
Chromosomes (blue)
Microtubules (largest)
Intermediate filaments
(knobby)
Actin filaments (small
twisted)
Microtubules (green)
Actin filaments (red)
Chromosomes (blue)
http://mgl.scripps.edu/people/
goodsell/illustration/cell
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Molecular View of Cellular Structures
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Origin of Life on Earth?
Miller-Urey experiment*
* Miller, Stanley L. (May 1953) Production of Amino Acids
Under Possible Primitive Earth Conditions. Science 117;528
Sparking a mixture CH
4
, NH
3
, H
2
O and
H
2
yielded:

Glycine
Glycolic acid
Sarcosine
Alanine
Lactic acid
N-Methylanaline
a-Amino-n-butyric acid
a-Aminoisobutyric acid
a-Hydroxybutyric acid
b-Alanine
However, probably no H
2
on primitive
earth, but other experiments using
HCN have produced amino acids
Succinic acid
Aspartic acid
Glutamic acid
Iminodiacetic acid
Iminoaceticpropionic
acid
Formic acid
Acetic acid
Propionic acid
Urea
N-Methyl urea

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Elemental Composition of Animal Cells
99% hydrogen (H), carbon (C), nitrogen (N), and oxygen (O)
Most oxygen and hydrogen in water
Carbon ~ half the dry weight of cells
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Elemental Composition of Human Cells
Element* Mass % Atomic %
Oxygen 65 25.6
Carbon 18 9.5
Hydrogen 10 63
Nitrogen 3 1.3
Calcium 1.5 0.24
Phosphorus 1.2 0.24
* Chang, Raymond, Chemistry, 9th Edition, McGraw-Hill, 2007
Element* Mass % Atomic %
Potassium 0.2 0.03
Sulfur 0.2 0.04
Chlorine 0.2 0.04
Sodium 0.1 0.03
Magnesium 0.05 0.01
Iron
3.8 g, men
2.3 g, women
Cobalt,
Copper, Zinc,
Iodine
< 0.05 each
Selenium,
Fluorine
< 0.01 each
99% hydrogen (H), carbon (C), nitrogen (N), and oxygen (O)
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Molecular Composition of Human Cells (20 m)
Molecule Mass % MW
(daltons)
# Molecules Molecule
%
# Types
Water 65% 18 1.74 x 10
14
98.73 1
Protein 20% 50,000 1.9 x 10
10
0.011 ~5,000
Lipid 12% 700 8.4 x 10
11
0.475 50
Other Organic 0.4% 250 7.7 x 10
10
0.044 ~200
RNA 1.0% 1 x 10
6
5 x 10
7
3 x 10
-5
----
DNA 0.1% 1 x 10
11
46 3 x 10
-11
----
TOTALS 100% ---- 1.76 x 10
14
100% ----
Limits on cell size: Lower limit determined by the size of required
biomolecules, while the upper size is determined by the rate of
solute molecular diffusion in an aqueous environment.
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Four Major Classes of Biological Macromolecules
A. Nucleic Acids, e.g. DNA
Store & transmit
information
B. Proteins, e.g.
hemoglobin
Structure & catalysis
C. Lipids, e.g.
phosphatidylcholine
Membranes & energy
storage
D. Polysaccharides, e.g.
bacterial surface
Energy storage, structure,
surface recognition
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Carbon-based Life
Generally, the lightest elements
form the strongest bonds
Carbon can form covalent bonds
with up to four other carbons to
build complex molecules with linear
and branched chain
Carbon can form single bonds with
hydrogen, sulfur, and phosphorus,
and form single and double bonds
with oxygen and nitrogen
Covalent
Bond
E (kJ/mol) r (pm)
O-H 459 96
C-H 411 109
N-H 386 101
S-H 363 134
C-O 358 143
C-C 346 154
C-N 305 147
C-S 272 182
C-P 264 184
S-S 226 205
P-O 335 163
P-P 201 221
C=O 799 120
C=N 615 129
C=C 602 134
Huheey, pps. A-21 to A-34; T.L. Cottrell, "The Strengths of Chemical Bonds," 2nd ed., Butterworths, London, 1958;
B. deB. Darwent, "National Standard Reference Data Series," National Bureau of Standards, No. 31, Washington, DC, 1970;
S.W. Benson, J. Chem. Educ., 42, 502 (1965).
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Important Functional Groups
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Bioenergetics, Thermodynamics & Metabolism
Gibbs Free Energy, G: amount of energy in a reaction at
constant temperature and pressure
Enthalpy, H: heat of a reaction reflecting the number and
kind of chemical bonds in reactants and products
Entropy, S: quantitative expression of randomness or
disorder in a system.
DG: the change in free energy as a result of a chemical
reaction, can be expressed in terms of the change in enthapy
and change in entropy
DG = DH-TDS
Anabolism: the set of metabolic pathways, requiring energy,
that construct molecules from smaller units (e.g. protein
synthesis)
Catabolism: the set of metabolic pathways that breakdown
molecules into smaller units and release energy (e.g. ATP to
ADP plus P
i
)
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Self-Replication: RNA World Hypothesis
Creation of prebiotic soup, including nucleotides, in Earths primitive atmosphere


Production of short RNA molecules with random sequences


Selective replication of self-duplicating catalytic RNA segments


Synthesis of specific peptides catalyzed by RNA


Increased role of peptides in RNA replication; coevolution of RNA and protein


Primitive translation system develops, with RNA genome and RNA-protein catalysts


Genomic RNA begins to be copied into DNA


DNA genome translated on RNA-protein complex (ribosome) with protein catalysts
Adapted from Figure 1-34
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From DNA to Enzymes
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Evolution of Mitochondria in Eukaryotes
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Genomics