#0 Introduction-Review

A review of what you should have

learned in the pre-required courses
Basics of biology
Basics of Cells
Basic chemistry

1. Three domains of life

eukaryotes

prokaryotes

2. Review of the cell

Cellthe minimum self-replicating unit of life

Prokaryote

Eukaryote

Prokaryotes vs eukaryotes
Common to both:
Plasma membrane, DNA, RNA, protein, genetic code
Mechanisms of metabolism, energy production,
protein synthesis, modification, and transportation.

Only in Eukaryotes:
Multicellular
Extensive internal membrane systems
Nucleus, other organelles, and cytoskeleton
DNA is packed into multiple chromosomes
Sexual reproduction

Eukaryotic cell
is a membrane
system
Plasma membrane
is a single
membrane. The
nuclear envelope,
mitochondrial
membrane and
chloroplast
membrane are all
double membranes
(with two lipid
bilayers).

Cell is surrounded by a plasma membrane

-Plasma
membrane is a
single lipidbilayer composed
of phospholipids
and proteins.

Nucleus is the largest organelle of eukaryotic cells

A rat hormone secretion cell

A typical animal cell

Eukaryotic cells have other organelles

A plant leaf cell

A typical plant cell

Mitochondrion and chloroplast are

energy (ATP) producing organelles

mitochondrion

chloroplast

Mitochondrion and chloroplast have their

own genomes encoding limited numbers of
their own proteins
Where are mitochondrion/chloroplast from?
- endosymbiosis

From
prokaryote to eukaryote
Approx. timeline
Earth
Prokaryote

~4.5 BYA
~3.8 BYA

Eukaryote
Multicellular

~2.0 BYA
~1.0 BYA

The oldest fossil:

cyanobacteria
3.8 BYA

Present day
cyanobacteria

3. Review of molecules
Review of Chemistry
atom and molecule
radioactive isotopes
acid vs base
quantify molecules
chemical bonds
Biomolecules
small molecules
large molecules (polymers)

Atoms

molecule
Particle

Mass

protons
~1 amu
neutrons
~1 amu
electrons 1/1800 amu

Charge
+1
0
-1

amu: atomic mass unit, also called

dalton. One amu (or dalton) is
approximately 1.7 X 10-24 g.

(methane)

Radioisotopes
Isotopes:
Atoms that contain the same number of
protons and electrons but different
number of neutrons
Radioisotopes:
with unstable atomic nuclei that loss energy
by decaying, or emitting electromagnetic
radiation (ionizing particles), which can
damage DNA/protein, and can be detected
by X-ray film or other methods

Three isotopes of hydrogen:

Hydrogen

Deuterium

Tritium

1H

2H

3H

radioactive

Radioisotopes often used in molecule biology:

31P/32P

(radioactive)

32S/35S

(radioactive)

12C/14C

(radioactive)

Different isotopes have different half-life that is

the time required for half of the atoms to undergo
radioactive decay

Radioactive isotopes (radioisotope) are widely

used in molecular biology studies

because they are physically distinguishable

but chemically identical from each other.

Presence of various particles emitted during decay

of a radioisotope can be detected by:
-Geiger counter (monitor)
-Autoradiography (exposure to X-ray film)
-Liquid Scintillation Counting

Acid and base

Acid molecules that donate proton H+
e.g. COOH/-COOpH< 7.0 is called acidic

Base (alkaline) molecules taking up protons

e.g. -NH2/-NH3+
pH > 7.0 is called basic

Quantify molecules
1. Atomic weight = #proton + #neutron,
e.g. H=1, C=12, N=14, O=16 (Dalton)
2. Molecular weight (MW) = atomic weight
3. Avogadros number: 6.02x1023
-number of H atoms per one gram of hydrogen
-one mole of any substance contains 6.02x1023 molecules
4. mole = g / MW

(g =gram, MW=Dalton)

5. M = mole / L

(L=liter)

Chemical bonds
interaction between atoms
Covalent bonds
------

Two atoms interact by sharing electrons

Strong, hold atoms in a molecule together (intra-molecular bonding)
Bond strength is ~110 kcal / mol (the energy needed to break a bond)
Single bond: two atoms sharing 1 pairs of electrons, free rotate
Double bonds: two atoms sharing 2 pairs of electrons, can not rotate

Noncovalent bonds
-- Interactions between atoms not involved with electron sharing
-- Weak for individual bond, but many weak bonds can work together to
stabilize 3D structure of a large molecule (intra-molecular bonding).
-- help molecules bind to other molecules (inter-molecule interactions).
-- particularly important for DNA, RNA, and proteins

Covalent bond vs noncovalent bond

strong

weak

Four types of noncovalent Interactions (bonds)

(Ionic bonds, Hydrogen bonds, Hydrophobic interactions, and
Van der Waal Forces)

(1) Ionic Interactions

Ionic interaction

- -

- attractive force
between positively and
negatively charged
atoms
- in ionic bonds, atoms
gain or lose electrons
completely to its partner
-strongest noncovalent
bond

(2) Hydrogen bonds

Hydrogen bond

- H bond is the electrical

attraction between a hydrogen atom
of one molecule and highly
electronegative atom in another
molecule. It forms when a
hydrogen atom is sandwiched
between two electron-attracting
atoms such as O and N. e.g. OH.O, N-HO,
-H bond is particularly important
for the high-order structures of
polymers such as the secondary
structure of protein and RNA and
the double-strand structure of
DNA.
- H2O molecules (in water) stick to
each other and others by H bonds.

Hydrophobic interactions

(3) Hydrophobic interactions

-The force that causes
nonpolar portions of molecules
to stay away from water
molecules
-In contrast to other bonds
that form because the two
parties love each other,
the hydrophobic interaction
form because all parties
involved hate water that
pushes them together.

(4) Van der Waal Forces

Van der Waals force

-Weak attractive forces

between anything.
-Occur because
momentary random
fluctuations in
distribution of electrons
in nearby covalent
bonds
-Attraction decreases
rapidly with increasing
distance. If atoms too
close repulsive force
occurs

non-covalent bonds are critical for

inter-molecule interactions

Biomolecules
Small molecules
- base:adenine (A), guanine (G),cytosine (C), thymine (T), uracil (U)
- Sugar:
glucose, ribose, etc
- fatty acid: oleic acid (C18), etc
- Amino acids: glycine, methione,
etc

Large molecules

Also called
macromolecules or
polymers:
DNA, RNA, protein, lipid

Pentoses

Amino acids

Bases

Four most important polymers of the cell

Polymer--Macromolecules composed of many copies of small
molecules (monomer) linked covalently , The size is presented in
kD (103 Dalton) or mD (106 Dalton).
DNA/RNApolymers of deoxyribonucleotides/ribonucleotides
Measured by length: bp (base pairs) for DNA, and nt (nucleotides)
for RNA (1 nt approx. 330 Da). DNA/RNA are genetic materials
of the cell.
Proteins polymers of amino acids, measured by length (number of
amino acids) or kilodalton (kD) (1 aa approx. 110 Da). Proteins are
the workforce of the cell.
Polysaccharide polymers of sugars
Polysaccharides are structure and energy materials of the cell.
lipidtriacylglyerol, which is a glycerol linked to three fatty acid
molecules, phospolipids contains 2 fatty acid plus a phosphate linked
to another molecule, phospolipids make up the cell membranes.

Formation and breakdown of polymers

condensation

H 2O

hydrolysis

Formation of polymers by condensation

Where are
different
biomolecules
found in the
cell

Biomolecules, cells, and organisms

4. What are genes?

Gene is the basic physical unit of heredity; it is a segment of
DNA that can be transcribed into RNA, which, may or may not
be translated into a protein, leads to the expression of
hereditary character. Genes usually exist as pairs.

Transmission genetics, founded by Gregor Mendel, deals with

the transmission of traits (phenotypes) from one generation
to the next (1865-)

Genotypes and phenotypes

Genotype is the combination of alleles found in an
organism
Phenotype is the visible expression of the
genotype
Wild-type the individual with the genotype and
phenotype that are most common or generally
accepted standard
Mutant the individual with the genotype and
phenotypethat are different from the wild
type

Mendels Laws of Inheritance

A gene can exist in different forms, referred to as
alleles. Agene has its defined place, or locus, on a
chromosome. A gene can also be called an allele or a
locus. One gene may exist as different alleles.
An allele can be dominant (one copy can determines
phenotype) or recessive (need two identical copies to
show the phenotype) with respect to the phenotype it
determines
An individual (diploid) carries two copies (or alleles) of a
gene, but a gamete (haploid) carries only one
Law of Segregation: the two alleles of the gene
segregate during sex reproduction
Law of Independent Assortment: alleles of different
genes assort independently during sex reproduction

Mendels Gene Transmission Theory

Somatic cells are diploid
Sex cells, or gametes, are haploid
Heterozygote is an individual that has
one copy of each of the two different
alleles (of a gene), producing different
gametes that have different alleles
Homozygote is an individual that has
two copies of the same allele, producing
the same type of gametes all with the
same allele

The Chromosome Theory of Inheritance

Chromosomes are discrete physical
entities that carry the genes (1910-)
Thomas Hunt Morgan used the fruit fly,
Drosophila melanogaster, to study
genetics, who combined Mendels law
with the chromosome theory, which
became the core of classical genetics
Autosomes occur in pairs in a given
individual
Sex chromosomes are identified as X
and Y (in human)
Female has two X chromosomes
Male has one X and one Y chromosome