Burr

2311

BIO

Exam Review
1. Origin of our planet, & evolution of life on it
A.

All the elements of the periodic table of the elements have been synthesized in nuclear
fusion reactions in the center of stars.
Stars begin their lives by fusing hydrogen nuclei to form helium. (All the
hydrogen in the universe was created in the big bang, 13.7 billion years ago.) Later
in their life, stars fuse helium nuclei to make carbon. When stars the size of our sun
run out of helium to burn, they go nova; in the nova explosion oxygen nuclei are
formed. (Heavier elements (up to iron) are synthesized in stars more than 10x bigger
than our sun; when such stars run out of fuel, they go super nova and create all the
rest of the elements.)
Our sun is a second generation star. It and our planetary system were formed by the
gravitational collapse of the gas and dust released from supernova explosions
elsewhere in our galaxy. Our sun was formed about 5 billion years ago. It is still
burning hydrogen and will continue to do so for another 5 billion years.

B.

Our earth was formed approximately 4.5 billion years ago.

How do we know the age of our earth?
How old is the earliest evidence of life on earth? (Answer: earliest fossil evidence:
3.5 billion years old; earliest carbon isotope evidence: 3.8 billion years ago.)

C. Chemical evolution
Oparin & Haldane proposed that the atmosphere of the early earth was composed of
hydrogen, methane, water and ammonia (H2, CH4, H2O and NH3). This is the gas
mixture that Miller & Urey used in their apparatus, in which organic material
including amino acids and nucleotides was formed.
Later research indicated that the atmosphere of the early earth would be dominated
the volcanic gases: carbon dioxide, water, and nitrogen (CO2, H2O, and N2). When
these gases were put into the Miller/Urey apparatus no biological molecules were
formed.
But then it was realized that there was in fact a significant amount of hydrogen (and
other reduced molecules) in the early earth atmosphere, and high levels of UV
radiation. When volcanic gases plus hydrogen are irradiated in the laboratory,
formaldehyde and hydrogen cyanide (H2CO, HCN) are formed. And when the mix of
irradiated gasses is put into a Miller/Urey apparatus, once again interesting biological
molecules are formed.
D. Early biological evolution
Earliest cells were prokaryotes (no nuclear membrane); RNA probably served the
roles now played by DNA and proteins (RNA world)

A crucial event in the evolution of early prokaryotic life was the appearance of
oxygen-producing photosynthetic cells, able to use the energy of sunlight to make
food.
Subsequently, certain prokaryotic cells evolved the ability to use oxygen as an
electron acceptor for energy-producing reactions (the process called oxidative
phosphorylation)
Another significant event was the evolution of a cell with a nuclear membrane- an
early eukaryotic cell.
Finally, a cell resembling modern eukaryotic cells arose out of the symbiotic
relationship of an early eukaryote plus an oxygen-utilizing prokaryote; the oxygenutilizing prokaryote became a precursor to the modern mitochondrion. In a similar
fashion, the lineage leading to modern plants arose when a eukaryote with a protomitochondrion acquired a photosynthesizing prokaryote that became a protochloroplast.
All this, and much additional cellular evolution occurred during the first 3 billion
years of the earths history, a period called the Precambrian. Throughout this
period there was little or no atmospheric oxygen. As oxygen was produced by the
early photosynthetic organisms, it reacted with Fe++ in the ocean to form insoluble
iron oxide; eventually all the Fe++ was titrated out and free oxygen could begin to
accumulate. The appearance of oxygen in the atmosphere is roughly coincident with
the end of the Precambrian and the beginning of the Cambrian period.
The subsequent 500 million years, beginning with the Cambrian and leading up to the
present, saw the development of large animals and plants in the oceans and on the
continental crust.
If the 4.5 billion years of the earths history are represented as a 12 month calendar,
the first land animals appear on December 1; homo sapiens appears at 11pm on
December 31.

E. Evolution is manifest at the molecular level

Nucleotide sequencing reveals phylogenetic relationships between currently living
individuals, and both confirms and extends the phylogenetic tree deduced by earlier
scientists from both morphology and the fossil record.
Carl Woese found by nucleotide sequencing of ribosomal RNA that there are three
domains in the tree of life: Bacteria, Archaea, and the Eukarya.
F. (Not in my lecture notes) (Page 4 in your text): Know that natural selection occurs in a
population of individuals when:
(a) individuals within the population vary in their characteristics
(b) the variable traits are heritable
(c) certain heritable traits help individuals produce more offspring
2. Basic chemistry
A. Basic concepts

At a simple level, understand the following terms and concepts: kinetic

energy vs potential energy; heat and temperature; exothermic, endothermic,
exergonic, endergonic; energy of activation (Ea); enthalpy (H), entropy S, Gibbs
Free Energy (G)

LECT 1 and 2 END

Understand what a hydrogen bond is

Understand what we mean by a covalent bond
Understand pH at an elementary level; ie, pH 1 is acid, pH 7 is neutral, etc; acids
release protons (H+) into solution; bases take up protons
Understand redox reactions; know what we mean by saying a molecule becomes
reduced or oxidized

B. Functional groups
Recognize the names and chemical structure and properties of the six functional
groups commonly found attached to carbon atoms (Table 2.3) (2.1, 3rd ed.). Know
that two sulfhydryl groups
(-SH) can react with each other to form a disulfide bond (-S-S-).
3. Biological chemistry
A. Small biological molecules
Given the structure, be able to identify a sugar, an amino acid, a nucleotide
Properties of some of the 20 amino acids-know the properties of the following 7
amino acids
(see Fig 3.3):
Lysine:
basic amino
Arginine

side chains have positively charged amino groups (these are

Glutamate:

side chain has carboxyl group that is ionized

and negatively charged at physiological pH (this is
an acidic amino acid)

Serine:

side chain has an hydroxyl group (often phosphorylated in various

proteins)

Cysteine:

side chain has a sulfhydryl group (-SH); if two cysteines are

adjacent to each other in a folded protein structure, they can react
to form a covalent disulfide bond (-S-S-). Disulfide bonds act like
molecular staples to stabilize the folded structure of a protein.

Phenylalanine:
Isoleucine:

side chain has a benzene group; is hydrophobic

side chain has an isobutyl group; hydrophobic

acids)

B. Macromolecules
i) Polysaccharides
Storage polysaccharides: (starches [plants], glycogen [animals]); (1-4) linkage
Structural polysaccharides [(1-4)
linkage]: Cellulose (plants); Chitin (insects); peptidoglycan(bacteria)
ii) Proteins
Primary, secondary, tertiary, quaternary structure
Proteins fold to their thermodynamically most stable state; primary sequence
determines how a protein folds
Proteins catalyze chemical reactions by lowering the energy of activation for the
reaction
iii) Polynucleotides
Differences between DNA and RNA
How nucleotides polymerize (3 hydroxyl attacks -phosphate of incoming
nucleotide triphosphate. (Polynucleotides are synthesized in a 5 to 3 direction.)
The two strands of DNA are antiparallel
Rosalind Franklin obtained the x-ray crystallography pictures of DNA; Watson
and Cricksolved the structure.

4. Membranes

Biological membranes are made up of lipids and proteins

The current model for the structure of biological membranes is the SingerNicholson Fluid Mosaic model

A. Lipids
3 kinds of lipids: fats, phospholipids, cholesterol
(i) Fats:
Fats are triglycerides (ester linkages between glycerol backbone and 3 fatty
acids.
Fatty acids are amphipathic (know what this means); fats however
(triglycerides) are notamphipathic.
Fatty acids are soaps; form micelles
How do soaps solubilize fat molecules?

Unsaturated fatty acids contain C=C double bonds; in cells, these are
always cis double bonds (energetically unfavorable compare to
the trans configuration)
Fats composed of saturated fatty acids are solid at room temperature; those
composed of unsaturated fatty acids are liquid. (Why?)
Understand why the process of partially hydrogenating vegetable oils creates
fats with trans fatty acids
Linoleic (omega-6) and linolenic (omega-3) acids
are essential polyunsaturated fatty acids that our bodies cannot synthesize

(ii) Phospholipids
Have a structure resembling that of fats, but only two fatty acids esterified to
glycerol; the third glycerol OH group is esterified to phosphoric acid. The
phosphoric acid is in turn also esterified to another substituent, such as choline
or the amino acid serine, etc.
Spontaneously form planar bilayers, phospholipids vesicles. (Why do
phospholipids form planar bilayers (vesicles), whereas fatty acids (soaps,
detergents) form micelles?)
Phospholipids diffuse in the plane of the bilayer (2/sec-length of bacterium),
but do not readily flip from one leaflet of the bilayer to the other leaflet.
As above with fats, membranes which have a high percentage of saturated
fatty acids in their phospholipids are solid at room temperature; those with
unsaturated fatty acids are fluid. The fluidity of the membrane is governed
by the percentage of phospholipids with unsaturated vs saturated fatty
acids. Another membrane constituent that affects membrane fluidity and
permeability is cholesterol.
(iii) Cholesterol
Cholesterol fills in the spaces between unsaturated phospholipids
Adding cholesterol to lipid bilayers with unsaturated phospholipids decreases
the permeability of the bilayer

B. Membrane Proteins
How many amino acids in the form of an alpha helix does it take to traverse the
lipid bilayer? (approximately 20) Would these amino acids have hydrophilic or
hydrophobic side chains?
What is the difference between an integral membrane protein and a peripheral
membrane protein? How would one experimentally distinguish between these two
types of membrane proteins?
How do the results of freeze-fracture experiments support the Singer-Nicholson
Fluid-Mosaic model of the arrangement of proteins in membranes?
C. Transport

Know what kinds of molecules can and cannot traverse a pure lipid bilayer.
Understand diffusion and osmosis.
What is the difference between active transport and passive
transport? the difference between simple diffusion across a membrane and
facilitated diffusion? (Do not worry about being able to reproduce the detailed
model for active transport by the sodium-potassium pump.)