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Biology 13A – Test 1 Lecture Notes
Chapter 1 – Introduction
A. Overview
a. Definitions
i. Anatomy – the study of structure.
ii. Physiology – the study of function.
b. Levels of Organization (Fig. 1.3)
i. Atom, molecule, macromolecule, organelle, cell, tissue, organ, organ system,
organism
B. Homeostasis – “staying the same”
a. Mechanism (Fig. 1.5)
i. Receptor picks up a stimulus
ii. Control center compares stimulus to set point
iii. Effector causes a response
b. Analogy of home thermostat (Fig. 1.6)
c. Regulation of body temperature (Fig. 1.7)
i. Receptors include nerves
ii. Control center is the brain
iii. Effectors are muscles, blood vessels, sweat glands
C. Organ Systems (Fig. 1.12)
a. Body covering
i. Integumentary system – skin, hair, nails, some glands
b. Support and movement
i. Skeletal system – bones, ligaments, and cartilage
ii. Muscular system – muscles
c. Communication
i. Nervous system – nerves carry very fast impulses for short term
ii. Endocrine system – hormone signaling is long term
d. Transport
i. Cardiovascular system – vessels and blood. Overall transport.
ii. Lymphatic system – lymphatic vessels, lymph, and some glands. Specialized
transport, immunity, lipid and fluid balance.
e. Absorption and Excretion
i. Digestive system – gastrointestinal tract. For absorption and elimination
ii. Respiratory system – upper and lower respiratory system. Exchange of gases
with the environment
iii. Urinary system – kidneys filter blood and produces liquid wastes.
f. Reproduction – reproductive system includes discrete male and female components
D. Anatomical Terminology
a. Positions (Fig. 1.13)
i. Superior is closer to the head than inferior
ii. Anterior is closer to the front posterior
iii. Medial is closer to the middle than lateral
iv. Proximal is closer to the trunk than distal
v. Superficial is closer to the surface than deep
b. Sections
i. General terms (Fig. 1.15)
1. Cross cuts the “short way”
2. Oblique cuts at an angle
3. Longitudinal cuts the long way
4. Median cuts through the middle (also is any of the above)
ii. Body sections (Fig. 1.14)
1. Sagittal is a longitudinal section that divides body into left and right.
2. Transverse is a cross section that divides body into superior and inferior
3. Coronal is a longitudinal section that divides body into anterior and
posterior
Chapter 2 – Chemistry
A. The atom (Fig. 2.1)
a. Nucleus in center – made from protons (+) and neutrons (=). Both have an atomic weight
of 1
b. Shell on outside. Made up of electrons (-) with close to zero weight. Electrons orbit the
nucleus.
c. Common elements (Tab. 2.1)
d. Isotopes are atoms with a different number of neutrons. E.g. radioisotopes.
B. Bonds
a. Atoms form bonds with each other mostly because of electron stability. Atoms are
happiest when outer shells have 2 or 8 electrons. If not, they try to share or give them to
achieve this.
b. Bonds
i. Ionic – when electron is transferred. This results in charged atoms called ions.
(Fig. 2.4)
ii. Covalent – when electron is shared. This is how a molecule is formed. (Fig. 2.5,
2.7)
1. Polar – asymmetrical, slight charge
2. Non-polar – symmetrical, no charge.
iii. Hydrogen – weak interaction between polar molecules from slight – and +
charges. (Fig. 2.6)
c. Chemical reactions
i. Reactants  Products, reversable
ii. Synthesis is a building reaction (anabolism) while decomposition is breaking
down (catabolism). Exchange reactions involve both.
C. Water – polarity and size give it unique properties
a. Liquid vs. ice
b. Cohesive and adhesive: surface tension.
c. Solvent – solutes dissolve in it. (Fig. 2.10)
d. Heat sink – water resists temperature change by absorbing or releasing energy in
hydrogen bonds. Heat is also given off by evaporation, e.g. sweating.
e. Acids and bases. Water dissociates into equal numbers of hydrogen ions and hydroxide
ions. H2O  H+ + OH- (Fig. 2.11)
a. pH Scale. Measures H+ concentration. Is logarithmic.
D. Organic molecules contain carbon and hydrogen.
a. Carbohydrates
i. Chemical formula is usually (CH2O)n
ii. Monosaccharides can form disaccharides, polysaccharide (Fig. 2.13)
iii. Examples
1. Starch – a storage polysaccharide in plants
2. Glycogen – storage in animals
3. Cellulose – cell wall structure
b. Lipids – fats
i. Hydrophobic – “water fearing”. Long hydrocarbon chains.
ii. Triglyceride contains 3 fatty acid and 1 glycerol. Saturated vs. unsaturated fats.
Unsaturated has double bonds and is not saturated with hydrogen. (Fig. 2.14)
iii. Phospholipids have a polar head with a phosphate group and non-polar tails. (Fig.
2.15)
iv. Steroids – four ring groups. E.g. cholesterol (precursor to other steroids and
membrane component), estradiol, testosterone (Fig. 2.16)
c. Proteins
i. Amino acids are linked together to form peptides
ii. 20 possible R groups for amino acids.
iii. Function related to final structure. Temperature, pH and salt can affect final
shape.
iv. Levels of structure (Fig. 2.18)
1. Primary – basic sequence
2. Secondary – 3D motif, e.g. helix, sheet
3. Tertiary – whole protein structure
4. Quaternary – more than 1 peptide
d. Nucleic Acids
i. Monomer is nucleotide (phosphate-sugar-base) (Fig. 2.20)
ii. DNA is string of deoxynucleotides. Has four bases ATGC. Genetic material.
(Fig. 2.21)
iii. RNA is less stable. Has AUGC. Genetic messenger.
iv. ATP is a unit of energy. High energy phosphate bond. (Fig. 2.22)
Chapter 3 – Cells
A. Overview
a. Cell Theory
i. All living things are made up of cells.
ii. The smallest living thing is a cell and cells may make up multicellular organisms.
iii. Cells arise from preexisting cells.
b. Small size – micrometer size allows high surface area to volume ratio.
c. Membrane
i. Structure (Fig. 3.3)
1. Phospholipid bilayer
2. Other molecules embedded – proteins, lipids, and carbohydrates
ii. Plasma membrane separates outside of cell from cytoplasm (inside liquid)
B. Cellular Organelles
a. Nucleus (Fig. 3.10)
i. Holds DNA in form of chromatin (DNA + protein). The DNA directs cellular
activities.
ii. Nucleolus is center for ribosome assembly.
iii. Nuclear envelope is a double membrane. Nuclear pores allow molecules to exit.
b. Ribosomes
i. Made from RNA and proteins.
ii. Functions in synthesizing proteins.
iii. Found in cytoplasm, nuclear envelope, and ER.
c. Endomembrane System – all bound by a single membrane
i. Endoplasmic Reticulum (Fig. 3.4)
1. Membranes form flattened tubes. Lumen is on inside.
2. Rough ER has ribosomes. Proteins made here.
3. Smooth ER has no ribosomes. Used for lipid metabolism.
4. Buds vesicles to Golgi. (Fig. 3.5)
ii. Golgi Complex (Fig. 3.5)
1. Sorts incoming proteins and lipids
2. “Tags” or modifies some for destination
3. Packages them for final destination in vesicles.
iii. Lysosomes
1. Contains digestive enzymes
2. Tay-Sach’s disease is genetic and is caused by missing digestive enzyme.
The enzyme digests lipids. Lipids build up and kill cell. Death occurs in
children
iv. Vacuole
1. Store water, food, salts, pigments, and wastes.
2. Structure is that of a large vesicle.
d. Peroxisomes
i. Metabolize small organic compounds. E.g. Hydrogen peroxide and ethanol.
e. Mitochondria – “powerhouse”
i. Produce ATP from glucose
ii. Structure: double membrane, intermembrane space, cristae (folds), matrix that
has enzymes. (Fig. 3.6)
f. Cilia and Flagella – movement and water movement. (Fig. 3.9)
i. Cilia are small and numerous, “eyelash”
ii. Flagella are large and few, “whip”
C. Membrane Transport
a. Passive transport – diffusion
i. Down a concentration gradient (high  low). Can go across a membrane if
permeable (Fig. 3.12)
ii. Facilitated transport – uses a protein (Fig. 3.14)
iii. Osmosis – diffusion of water across a membrane (Fig. 3.15)
1. Tonicity – relation of solute concentrations across a membrane (Fig.
3.16)
1. Isotonic: outside of cell = inside
2. Hypotonic: outside < inside
3. Hypertonic: outside > inside
b. Active transport (Fig. 3.18)
i. Against concentration gradient
ii. Requires energy
iii. Endocytosis and exocytosis transports very large particles and uses vesicles (Fig.
3.19)
D. Cellular Reproduction
a. The Cell Cycle (Fig. 3.21)
i. G1  S  G2  M
1. G1 – Gap 1. Cell grows in size
2. S – Synthesis. DNA duplicates
3. G2 – Gap 2. Cell grows more and organelles duplicate
4. M – Mitosis. Cell physically divides
ii. Checkpoints exist to regulate progression. Cancer can occur if checkpoints are
missing or ignored.
b. Meiosis
i. Used only to produce gametes (egg or sperm). Gametes contain ½ the DNA
content and are unique.
ii. Similar to the cell cycle but contains two M phases.
Chapter 4 – Cellular Metabolism, DNA, and Gene Expression
A. Metabolic Reactions
a. Anabolic reactions
i. Build larger molecules from smaller ones.
ii. Usually requires energy.
iii. Dehydration synthesis is the type of reaction. Releases water. (Fig. 4.1)
b. Catabolic reactions
i. Breaks apart molecules.
ii. Usually releases energy.
iii. Hydrolysis reaction requires water.
B. Enzymes
a. Enzymes are catalysts that speed up reactions by lowering the activation energy
b. Enzyme function: 3 steps
i. Active site binds substrates (reactants).
ii. Reaction occurs on enzyme
iii. Release of products
c. Enzyme regulation
i. Environment
1. Enzymes function at optimal pH, temperature, salt concentration
ii. Activators
1. Coenzymes – organic. e.g. vitamins
2. Cofactors – inorganic. e.g. minerals
C. Cellular Respiration
a. Formula for aerobic respiration: C6H12O6 + 6 O2  6 CO2 + 6 H2O
i. We breathe to deliver oxygen to tissues
ii. Each reaction yields 38 ATP.
iii. ADP + P  ATP (Fig. 4.7)
b. Steps
i. Glycolysis
1. Glucose breaks down to pyruvic acid (C6  2C3)
2. ATP is made and electrons are also released.
3. Takes place in cytoplasm
ii. Acetyl-CoA formation
1. Pyruvic acid is broken down to acetic acid (C2).
2. CO2 is released.
3. Takes place in the mitochondrion.
iii. Citric acid cycle
1. Acetic acid is added into the citric acid cycle to form citric acid (C6)
2. ATP is made and electrons are also released.
3. Takes place in the mitochondrion.
iv. Electron transport chain
1. Electrons are used to power ATP formation
2. Takes place in the mitochondrion.
c. Other compounds can enter at different places into respiration reactions (Fig. 4.9)
D. DNA
a. Review DNA Structure (Fig. 4.10)
i. Nucleotide: P-sugar-base. Linkages using P to sugar.
ii. ATGC bases and complementary base pairing
iii. Double helix with bases forming hydrogen bonds.
iv. Watson/Crick 1953 solved structure. Rosalind Franklin provided key evidence (
b. Replication (Fig. 4.11)
i. Replication occurs during S phase of the cell cycle.
ii. Free nucleotides are linked by the enzyme DNA polymerase
iii. Replication begins at a replication bubble and moves outwards in both directions.
Each side is called a fork
E. Gene Expression
a. Central Dogma: DNA  RNA  Protein. Transcription makes RNA by reading DNA
and translation makes protein by reading RNA.
i. RNA
1. Uses AUGC
2. mRNA, rRNA, tRNA
ii. Genetic Code (Tab 4.2)
1. Each triplet codes for one amino acid (or stop codon)
2. 64 possibilites with 20 a.a., therefore redundancy
3. Practice translation of sequence
b. Transcription (Fig. 4.13)
i. Occurs whenever a gene product needs to be made.
ii. RNA polymerase links together ribonucleotides
c. Translation
i. tRNA: one for each amino acid. Has anticodon that is complementary to mRNA
and site to add the right amino acid.
ii. Ribosome is enzyme that attaches amino acids together.
iii. aa-tRNA comes into empty site in ribosome. Polymerization occurs then shift of
ribosome. Used tRNA exits. (Fig. 4.14)
iv. Stop codon will end the process.