Bio1A Quiz 1 Study Guide

Lecture 1 Introduction to Molecular Biology

A. Module 1: Evolutionary Principles
a. Evolution of Cells
i. All organisms made from cells (Fig. 2)
1. Prokaryotic simple, no membrane-bound organelles
2. Eukaryotic complex, has membrane-bound organelles
ii. DNA exists in all cells. They may be packaged differently.
iii. Membranes are all the same (Fig. 11)
b. Unity and Diversity
i. Homologous structures different function/structure but common ancestor (Fig.
9)
ii. Changes in DNA explain diversity. Genetic code of DNA is the same in all
organisms (Tab. 1)
iii. Energy usage is virtually the same in all organisms. Breaking ATP releases
energy (Fig. 12)
iv. Reproduction
c. Evolutionary relationships can be described by trees. (Fig. 14)
B. Module 1: Biological Information
a. Genetic information is stored in nucleic acids
i. DNA bases are A, T, G, C. Their sequence provides information (Fig. 10a)
b. Information flow in a cell
i. The Central Dogma states information is expressed by being passed from DNA
RNA Protein. Protein is the functional part of this information (Fig. 10b)
c. Heredity
i. Genetic information is passed down to the next generation of cells. DNA
replication allows this. DNA has evolved to be a great molecule for this.
C. Module 3: Practicing Science
a. Scientific Method: Question (Observation) Hypothesis Experiment Conclusion
(Fig. 3)
i. Hypothesis is an answer or prediction to the question. It must be falsifiable.
ii. Experiment includes: design, data collection, and evaluation.
1. Controls (control variables) factors held constant for verification of
results.
2. Independent variable factor manipulated by researcher.
3. Dependent variable what is measured by researcher.
iii. Conclusion accepts or rejects hypothesis.
b. Reductionism vs. systems approach.
i. Reductionism break down mechanism to simplest components
ii. Systems looks at relationship of components with the whole organism.
Bioinformatics with computers allows this approach today.
c. Social Context: the use of powerful technologies, ethics, social responsibility

Lecture 2 Chemistry of Water and Acids/Bases

A. Module 6: Properties of Water

a. Water is a polar molecule with a slight positive charge on the hydrogen atoms and slight
negative charge on the oxygen atom. This allows hydrogen bonding between water
molecules and other molecules. (Fig. 1, 2)
i. Hydrophilic water loving molecules
ii. Hydrophobic water fearing molecules (non-polar)
b. Heat sink.
i. High specific heat. Water requires much heat energy to raise its temperature, and
releases heat slowly; this helps maintain a constant body temperature.
ii. Evaporation. Water requires heat when changed to vapor; sweating therefore
cools animals rapidly.
c. Cohesion/Adhesion. Water columns allow transport in organisms (Fig. 4)
d. Solvent. Dissolver is solvent, dissolved is solute. (Fig. 5)
e. Liquid. Hydrogen bonds form and break at equilibrium. Lower temperature lower
kinetic energy so water freezes. Structure of ice and water (Fig 8)
B. Module 7: Acids and Bases
a. Water can dissociate into equal numbers of hydrogen ions and hydroxide ions.
i. H2O H+ + OHii. In reality: 2 H2O H3O+ + OH- (Fig. 1)
b. pH Scale. Defined as negative logarithm of the hydrogen ion concentration; neutral water
dissociates into 10-7 moles/liter of hydrogen ions. pH = - log [H+]. Log is a ten-fold scale.
(Fig. 2)
i. Acids contribute to hydrogen ion when dissolved (Fig. 3, 4)
ii. Bases contribute hydroxide ion, or remove hydrogen ion when dissolved (Fig. 5)
c. Buffers resist pH change. (bicarbonate) HCO3- + H+ H2CO3 (carbonic acid) in blood.
(Fig. 6)
d. Ocean acidification is detrimental to coral reefs. (Fig. 7)

Lecture 3 Organic Chemistry

A. Module 5: Basic Principles of Organic Chemistry
a. Carbon
i. Organic molecules contain carbon.
ii. Carbon is tetravalent
b. Hydrocarbons are backbones for many organic compounds: double/triple bonds, rings,
branching, etc. (Fig. 5)
c. Isomers (Fig. 6)
i. Structural different covalent partners
ii. Geometric different arrangement across double bond
iii. Enantiomer handedness. e.g. amino acid and ibuprofen
d. Important functional groups (Fig. 8)
i. Hydroxyl: -OH polar, reactive
ii. Carbonyl: C=O polar
iii. Carboxyl: COOH polar, reactive, ionizing (acid)
iv. Amino: NH2 polar, reactive, ionizing (base)
v. Sulfhydryl: SH polar, reactive
vi. Phosphate: PO42- polar, reactive, ionizing (acid)
vii. Methyl: CH3 nonpolar
e. Macromolecules
i. Monomer polymer
ii. Most formed by dehydration synthesis
iii. Broken by hydrolysis

iv. Bonds
1. Ether: bond formed from two alcohols
2. Ester: bond between alcohol and carboxylic acid
f. Stanley Miller Experiment shows possible synthesis in prebiotic conditions (Fig. 10)
B. Module 8: Carbohydrates
a. Functions: energy, structure
b. Structure
i. Monosaccharides have general structure of (CH2O)n
ii. Linear forms have hydroxyl and carbonyl groups (Fig. 1)
iii. Ring form is used to create polymers (Fig. 6)
c. Examples of polysaccharides (Fig. 10)
i. Cellulose has beta 1-4 linkages that are difficult to break.
ii. Starch/glycogen have alpha 1-4 linkages that are breakable.
iii. Chitin has decoration to make it hard.
C. Module 9: Lipids
a. Functions: energy, insulation, membranes, signaling
b. Structure
i. Largely nonpolar
c. Examples
i. Fatty acids hydrocarbon chains usually containing 16 - 18 carbons and ending
with an acid group. (Fig. 6)
1. Saturated have no double bonds (Fig. 8)
2. Unsaturated have double bonds (Fig. 9)
ii. Triacylglycerols: formed by one glycerol reacting with three fatty acid
molecules. (Fig. 7)
iii. Phospholipids.
1. Two fatty acids linked to glycerol. One phosphocholine on last OH of
glycerol. Has hydrophilic and hydrophobic regions = amphipathic. (Fig.
1)
2. Forms various structures in water (Fig. 3)
3. Membranes are lipid bilayers. (Fig. 4)
iv. Steroids e.g. cholesterol, stiffens membranes and precursor to hormones (Fig.
5)
D. Module 10: Proteins
a. Diverse and numerous functions (Tab. 1)
b. Structure
i. Amino acid peptide
1. Amino acid (Fig. 1)
2. R groups 3 types (polar, non-polar, charged), 20 amino acids (Fig. 2).
3. Peptide bond (Fig. 3)
4. N-C termini
ii. Levels of structure (Fig. 6)
1. Primary linear amino acid sequence
2. Secondary internal folding. Examples: beta-sheets, alpha-helices. Uses
almost exclusively hydrogen bonds (Fig. 4)
3. Tertiary final structure. Uses more bonds (e.g. hydrogen, ionic,
covalent, hydrophobic) (Fig. 5)
4. Quaternary if there is more than 1 peptide
5. Sickle-Cell Anemia is an extreme example of what can go wrong with
structure.
iii. Conformation

1. Naturation and denaturation

2. Factors: temp, pH, salt, other proteins
E. Module 12 Nucleic Acids
a. Functions: hereditary information, energy molecule, coenzymes, signaling.
b. Structure
i. Nucleotides are made of a phosphate, a pentose sugar, and a nitrogenous base. PSugar-Base. Nucleoside is without phosphate. (Fig. 2, 9)
ii. Bases are purines (double ring) and pyrimidines (Fig. 1)
iii. Linkage is phosphodiester bond: P-sugar-P-sugar etc.
iv. 4 bases for DNA, 4 (and more) for RNA
1. Base pairing rules A=T, G=C (Fig. 4)
2. For RNA A=U, G=C
v. DNA and RNA differences
1. 2OH on RNA
2. DNA exists as double helix (Fig. 5) while RNA is single-stranded but
binds to itself (Fig. 7)

Lecture 4 Energy and Enzymes

A. Module 2: Energy - ability to do work
a. Types of Energy
i. Kinetic (motion) vs. potential (stored)
ii. Chemical is potential energy
iii. Free energy available energy in a system to do work
b. Types of chemical reactions (Fig. 2)
i. Endergonic requires energy
ii. Exergonic releases energy
iii. Coupled use energy from an exergonic to drive an endergonic (e.g. ATP)
c. Metabolism the sum of all reactions in a cell
i. Catabolism breakdown molecules
ii. Anabolism build
iii. Reactions tend to be organized in pathways
B. Module 11: Enzymes
a. Enzymes are catalysts that lower energy of activation (Fig. 1, 2)
b. Enzyme
i. Specific for certain substrates
ii. Reaction must already be exergonic
iii. Reusable
c. Substrate Product
d. Catalytic cycle: E + S ES EP E + P (Fig. 3)
i. Substrate binding: binds to active site of enzyme. Uses induced fit model
instead of lock-and-key.
ii. Reaction: active site provides correct environment to create product.
iii. Release: enzyme releases product and can be reused.
e. Regulation
i. Environmental factors
1. Optimal pH, temperature, salt produce bell curves (Fig. 4)
2. Substrate concentration (Fig. 5)
ii. Activators
1. Cofactors (non-organic)

2. Coenzymes (organic)
iii. Inhibitors (Fig. 6)
1. Competitive binds active site
2. Noncompetitive binds allosteric site
iv. Complex Regulation
1. Feedback inhibition
2. Enzyme complexes
a. Allosteric activation and inhibition as a complex
b. Cooperativity when substrate binding assists further substrate
binding of other enzymes in complex
3. Localization enzymes are held in separate compartments