A review of what you should have learned in the pre-required courses

Basics of biology Basics of Cells Basic chemistry

#0 Introduction-Review

1. Three domains of life

prokaryotes

eukaryotes

Prokaryote

2. Review of the cellCellthe minimum self-replicating unit of life

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 lipid- bilayer composed of phospholipids and proteins.

Nucleus is the largest organelle of eukaryotic cells

A typical animal cell A rat hormone secretion cell

A typical plant cell A plant leaf cell

Eukaryotic cells have other organelles

Mitochondrion and chloroplast are energy (ATP) producing organelles

mitochondrion chloroplast

Where are mitochondrion/chloroplast from? - endosymbiosis

Mitochondrion and chloroplast have their own genomes encoding limited numbers of

their own proteins

From prokaryote to eukaryote

Approx. timeline Earth ~4.5 BYA Prokaryote ~3.8 BYA Eukaryote ~2.0 BYA Multicellular ~1.0 BYA

The oldest fossil: cyanobacteria

3.8 BYA

Present day cyanobacteria

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

3. Review of molecules

Atoms

molecule (methane) Particle Mass Charge protons ~1 amu +1neutrons ~1 amu 0electrons 1/1800 amu -1

amu: atomic mass unit, also called dalton. One amu (or dalton) is approximately 1.7 X 10-24 g.

Radioisotopes

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

Isotopes: Atoms that contain the same number of protons and electrons but different number of neutrons

Three isotopes of hydrogen:

Radioisotopes often used in molecule biology:

radioactive

1H1 3H1DeuteriumHydrogen Tritium

2H1

31P/32P 32S/35S 12C/14C (radioactive) (radioactive) (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 molecules that donate proton H+

e.g. COOH/-COO- pH< 7.0 is called acidic

Base (alkaline) molecules taking up protons

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

Acid and base

1. Atomic weight = #proton + #neutron, e.g. H=1, C=12, N=14, O=16 (Dalton)

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)

Quantify molecules

2. Molecular weight (MW) = atomic weight

Chemical bonds interaction between atoms

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 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

Covalent bond vs noncovalent bond

strong weak

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

Ionic interaction

- --

Four types of noncovalent Interactions (bonds) (Ionic bonds, Hydrogen bonds, Hydrophobic interactions, and

Van der Waal Forces)

(2) Hydrogen bonds - 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. O-H.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.

Hydrogen bond

(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.

Hydrophobic interactions

(4) Van der Waal Forces -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

Van der Waals force

non-covalent bonds are critical for inter-molecule interactions

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

Biomolecules

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

Pentoses

Amino acids

Bases

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.

Polysaccharide polymers of sugars Polysaccharides are structure and energy materials of the cell.

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.

Polymer--Macromolecules composed of many copies of small molecules (monomer) linked covalently , The size is presented in kD (103 Dalton) or mD (106 Dalton).

Four most important polymers of the cell

Formation and breakdown of polymers

hydrolysis

H2O

condensation

KKSticky Notewill definitley be on test!!!

hydrolysis is chem reaction that breaks down polymers by adding h20 u break covalent bond

Formation of polymers by condensation

Where are different

biomolecules found in the

cell

Biomolecules, cells, and organisms

Transmission genetics, founded by Gregor Mendel, deals with the transmission of traits (phenotypes) from one generation to the next (1865-)

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.

4. What are genes?

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