Biology I

Types of Bonds present in Biological Molecules
-Covalent Bonds
-Nonpolar Covalent Bonds (dEN<0.4)
-Polar Covalent Bonds (dEN<1.7)
-Ionic Bonds (dEN>1.7)
-Weak Chemical Bonds
-Hydrogen Bonds
-Van der Waals Interactions

Electronegativity
-The attraction of a particular atom for the electrons of a particular atom

pH
-a way to express the concentraton of H+ and OH- in a solution
pH>7 = basic
pH=7 = neutral
pH<7 = acidic
-Buffers: a substance that minimizes changes in the concentrations of H+ and OH- in a solution. They do so by accepting hydrogen ions from the solution when they are in excess and donating hydrogen ions to the solution when they have been depleted.

Types of Carbon Skeletons
-Length
-Branching
-Double Bond Position
-Presence of Rings

Isomers: compounds that have the same number of atoms of the same elements but different structures and different properties
-Cis-Trans Isomers
-Cis Isomer: 2 x's on the same side
-Trans Isomer: 2 x's on opposite sides
Enantiomers: isomers that are mirror images of each other and that differ in shape due to the presence of an asymmetric carbon, one that is attached to 4 different atoms or groups of atoms.

Biologically Important Chemical Groups
-Hydrocyl: O-H
-Carbonyl: C=O
-Carboxyl: HO-C=O
-Amino: H-N-H
-Sulfhydryl: S-H
-Phosphate: PO4
-Methyl: CH3

Dehydration (Condensation) Reaction: two molecules are covalently bonded together through the loss of a water molecule
Hydrolysis Reaction: the reverse of dehydration reaction. To break using water.

Starch (2 types): enable the plant to store surplus glucose. Because glucose is a major cellular fuel, starch represents stored energy (alpha)
-Amylose: unbranched
-Amylopectin: 1-6 glycosidic linkages
Maltose: 1-4 glycosidic linkages
Glycogen: stores and releases glucose when the demand for sugar increases. More branches means more more access for enzymes to break down. Like amylopectin but more extensively branched
Cellulose: a major component of the tough walls that enclose plant cells i.e. fiber. (beta) 1-4 glycosidic linkages
Chitin: a carb used by arthropods to build their exoskeletons. Humans can;t digest chitin as we don't have the enzymes to break down the beta linkages.

Steroids: lipids cahracterized by a carbon skeleton consisting of four fused rings. Cholesterol ( a type of steroid) is a crucial molecule in animals. It is a common component in animal cell membranes.

Cell Wall: provides structural integrity to cell
Nucleoid: DNA in the bacterial cell is generally confined to this central region
Plasmid: small circular DNA fragments found in the cytoplasm that contain code responsible for antibiotic resistance and other characteristics.
Cytoplasm: internal "soup" of the bacterial cell that is bounded by the cell envelope.
Ribosomes: protein synthesis take place here
Gas Vacuole: in aquatic bacteria, gas vacuoles are protein bound structures that contain air and allow bacteria to adjust their buoyancy.
Capsule: layer of polysaccharide that protects the bacterial cell and is often associated with pathogenic bacteria.
Pili, Fimbriae: hair like structures made of protein allow bacteria to attach to other cells. A specialized pilus, the sex pilus, allows transfer of plasmid DNA.
Flagella: allows mobility
Endospore: some bacteria can survive hostile environments, often for long periods of time, by bundling their genetic material in a tough internal structure.

Models of DNA Replication:
-Conservative Model: the two parental strands re-associate after acting as templates for new strands, thus restoring the parental double helix
-Semi-Conservative Model (correct): the two strands of the parental molecule seperate, and each functions as a template for synthesis of a new complementary strand.
-Dispersive Model: each strand of both daughter molecules contains a mixture of old and newly synthesized DNA

Chemical Components of Membranes: lipids and proteins are the staple ingredients of membranes although carbs are also important. The most abundant lipids are phospholipids. Steriods act as a "fluidity buffer" in membranes.

Types of Diffusion:
-Simple: in the absence of other forces, a substance will diffuse from high concentration to low concentraion. No work has to be done.
-Facilitated: large polar molecules difffusing from high concentration to low concentration. No energy input is required.
-Channel Proteins
-Carrier Proteins
-Active Transport: to pump a solute across a membrane against its gradient. This requires energy.
-Sodium Potassium Pump

Osmosis: the diffusion of water through a membrane

Endocytosis:
-Phagocytosis: cellular eating
-Pinocytosis: cellular drinking
-Receptor Mediated Endocytosis: enables the celll to acquire bulk quantities of specific substances
Exocytosis: water and small solutes leave the cell by diffusing through the lipid bilayer of the plasma membrane

Operons:
-Constitutive: always on (negative regulation)
-Tryp Operon
-Lac Operon
-Regulated: off until needed by cell (positive regulation)
-Lac Operon

Gycolysis:
-Input: 2 ATP, Glucose, 2NAD+, 2Pi
-Net Output: 2 ATP, 2NADH, 2 Pyruvate
-Occurs in cytosol
-Substrate level phosphorylation
Krebs Cycle:
-Input: 2 Acetyl CoA
-Net Output: 6 NADH, 2 FADH2, 2 ATP
-Occurs in mitochondrial matrix
-Substrate level phosphorylation
Oxidative Phosphorylation:
-Input: 10 NADH, 2 FADH2, O2
-Net Output: 26-28 ATP, H2O
-Occurs in inner mitochondrial membrane
-Oxidative Phosphorylation

Cohesion: the hydrogen bonds in water molecules hold the substance together. Contributes to the transport of water and dissolved nutrients against gravity in plants. Also related to surface tension.
Moderation of Temperature: due to its high specific heat, water can moderate air temperature bu absorbing heat from air that is warmer and releasing the stored heat to air that is cooler. Keeps temperature fluctuations on land and in water within limits that permit life.
Density: due to hydrogen bonding, water is less dense as a solid than as a liquid i.e. it expands when it freezes. Permits life under water in cold temperatures.
Versatility as a Solvent: the polarity of water molecules allows it to dissolve many things.

Hydrophobic: substance that fears or repels water
Hydrophilic: any substance that has an affinity for water
Amphipathic: both hydrophilic and hydrophobic

Protein Folding
-Primary Structure
-Secondary Structure
-Tertiary Structure
-Quaternary Structure

1s

Cytoskeleton: a network of fibers exteding throughout the cytoplasm
-Microtubules: made of a golbular protein called tubulin. Shape and support the cell and also serve as tracks along which organelles equipped with motor proteins can move. Also involved in the seperation of chromosomes during cell division.
-Microfilaments: built from molecules of actin protein. structural role is to bear tension (pulling forces). Cytoplasmic streaming, muscle contraction, and ameoboid movement.
-Intermediate Filaments: maintenance of cell shape, anchorage of nucleus and other organelles, and formation of nuclear lamina.

Cell Junctions:
-Plants:
-Plasmodesmata: see plant organelles
-Animals:
-Tight Junction: prevent leakage of extra-cellular fluid across a layer of epithelial cells.
-Desmosomes: function like rivets, fastening cells together into strong sheets, semi-permeable
-Gap Junctions: similar to plasmodesmata, provide cytoplasmic channels from one cell to another.

Transcription: the synthesis of RNA using DNA information. Just as DNA strand provides a template for making a new complementary strand during DNA replication, it can also serve as a template for complementary sequence of RNA nucleotides.
-Eukaryotes:
-DNA Template
-Seperation of 2 strands
-RNA Polymerase II
-5'-3'
-pre-mRNA product
-5'Cap and Poly A Tail
-Spliceosomes
-Prokaryotes:
-DNA template
-Seperation of 2 strabds
-RNA Polymerase
-5'-3'
-mRNA product

Translation: synthesis of polypeptide using information in mRNA. The sites of translation are called ribosomes.

Local Signaling:
-Direct Contact: the use of cell junctions to communicate
-Paracrine Signaling: messenger molecules are secreted by the signaling cell, influencing cells in the vicinity.
-Synaptic Signaling: occurs in the anumal nervous system. An electrical signal along a nerve cell triggers the secretion of neurotransmitter molecules carrying a chemical signal.
Long Distance:
-Endocrine Signaling: specialized cells release hormone molecules, which travel via the circulatory system to other parts of the body, where they reach target cells can recognize and respond to the hormones.

Stages of Cell Communication:
1. Reception
-G Protein Receptors
-Receptor Tyrosine Kinases
-Ion Channel Receptors
-Intracellular Receptors (for hydrophobic signaling molecules)
2. Transduction
-Siganl Transduction Pathways
3. Response

Somatic Cells: all body cells except reproductive cells. 46 chromosomes each, 23 from each parent. (diploid, 2n)
Gametes: reproductive cells, one set of 23 chromosome. (haploid, n)
Sister Chromatids: each duplicated chromosome has two sister chromatids, which are joined copies of the original chromosome
Homologous Chromosomes: 2 chromosomes with genes for the same traits, one from each parent.
Autosomes: the 22 pairs of chromosome that don't determine sex.

Mitosis:
-Inherit 46 chromosomes, 23 from each parent
-Combined in the nucleusof a single cell when a sperm unites with an egg
Phases:
1.Prophase
2.Prometaphase
3.Metaphase
4.Anaphase
5.Telophase
Meiosis:
-produce gametes
-yields non-identical daughter cells that have only one set of chromosomes, half as many as parent cell
-occur only in the gonads
-in each generation, meiosis reduces the chromosome number from 46 to 23
-fertilization fuse 2 gametes together and returns the chromosome number to 46
Phases:
1.Meiosis I
2.Meiosis II
Cytokinesis:
-cleavage furrow in animal cells
-cell plate in plant cells

Phases of the Cell Cycle:
-Mititic (M1) Phase: mitosis and cytokinesis
-Interphase: a cell grows and copies its chromosomes in preperation for cell division
-G1 Phase: a cell grows
-S Phase: continues to grow as it copies chromosomes
-G2 Phase: grows more as it completes preperation for cell division

The Light Reactions:
-carried out by molecules in the thylakoid membranes
-convert light energy to the chemical energy of ATP and NADPH
-split H2O and release O2 to the atmosphere
The Calvin Cycle
-take place in the stroma
-use ATP and NADPH to convert CO2 to the sugar G3P
-return ADP, inorganic phosphate and NADP+ to the light reactions