REVIEW FOR EXAMS
This list is intended as a study guide to the material covered. It may not include all figures or topics discussed in lecture or lab.
Basic Chemistry:
structure of atom and atomic orbitals
bonds: ionic, covalent, polar covalent and hydrogen
water and polarity of water molecule
consequences of hydrogen bonds found in water
hydrophilic vs hydrophobic molecules
acids, bases and pH
buffers: bicarbonate
Biological Chemistry:
Carbon
Hydrocarbons
Functional groups
Monomers
Condensation/hydrolysis reactions
Biological molecules: function, solubility and composition of the following:
Carbohydrates: monosaccharides, disaccharides, polysaccharides
Lipids: saturated and unsaturated fatty acids, triglycerides, phospholipids,
cholesterol
Proteins: amino acids, polar, ionic and nonpolar R groups, peptide bonds,
dipeptides, polypeptides, structure (levels of organization): primary, secondary,
tertiary, quaternary (bonds at each level), relate protein structure to protein
function
Nucleic Acids: DNA, RNA, ribonucleotides, deoxyribonucleotides, ATP, NAD+
Enzymes:
Examples of catalyzed reactions: catalase-Fe
Function of enzymes
Activation energy and catalytic activity of enzymes
Folding of enzyme and active site
Specificity of enzyme and structure
Induced Fit Hypothesis
Coenzymes, cofactors
Factors affecting enzyme activity: enzyme concentration, substrate concentration,
cofactors/coenzymes, physical factors including pH and temperature
Competitive and noncompetitive inhibitors
Cell Membrane and Transport:
Function of cell membrane: compartmentalization, barriers/transport,
reception, enzymes
Fluid Mosaic Model and membrane structure: lipids (phospholipids, cholesterol,
glycolipids), proteins (enzymes, nonenzymatic ion channels, receptors, glycoproteins),
carbohydrates
Phospholipid bilayer formation
Factors that contribute to fluidity of bilayer: unsaturated fatty acids, cholesterol
Permeability of lipid bilayer to hydrophobic, hydrophilic, ionic, large polar,
small polar molecules
Diffusion
Osmosis
Solvent, solute, hypertonic, hypotonic, isotonic solutions in animal and plant
cells
Transport mechanisms: carrier assisted (passive or facilitated and active);
vesicle-medicated (exocytosis and endocytosis)
Examples of transport mechanisms: glucose transporter, Na+K+-ATPase, cotransport
Energy and Living Cells
Flow of energy in the living world
Laws of Thermodynamics
Forms of energy: potential and kinetic
Endergonic and exergonic reactions
Coupled reactions: examples including the condensation reaction between glucose
and fructose,
Na+K+ATPase
Structure of ATP and phosphate bonds
Function of high energy electrons in energy transfer reactions of photosynthesis
and cellular respiration
Redox Reactions: examples including formation of NaCl, oxidation of glucose
Overview of cellular respiration: oxidized components, reduced components,
removal of hydrogen
Formation of membrane potential as source of energy in mitochondria and chloroplasts
Electron Transport systems in general
Carrier molecules in electron transport
Cellular Respiration:
Steps and location of reactions involved in cellular respiration
Redox reactions in cellular respiration
Reduction of NAD+ to NADH + H+
Glycolysis: hydrogens and oxidation of glucose, NADH, ATP formation and usage,
pyruvate, aerobic vs anaerobic conditions: animals vs plant cells
Formation of acetyl CoA: CO2, NADH
TCA Cycle: OAA, products, carriers, direct substrate level phosphorylation
and formation of ATP
Electron transport: chemiosmotic ATP production, oxidative phosphorylation,
proton gradient (H+concentration gradient), proton pumping, proteins involved,
role of oxygen
Summary energy yield of glucose oxidation: direct substrate level phosphorylation
via oxidative phosphorylation
Photosynthesis:
Characteristics of light
Electromagnetic spectrum, absorption spectrum
Ability of pigments to absorb light: fluorescence, electron acceptors
Structure of chlorophyll: Mg++-containing ring and hydrophobic tail
Structure of leaf: chloroplast, outer, inner and thylakoid membranes, thylakoid
space, stroma, grana
Stages of photosynthesis and location of each stage:
Light dependent (Energy-Capturing Reactions): photosystems (PS700, PS680),
fate of electrons, products of reactions, role of water, electron transport
systems involved, ATP and NADPH formation
Light independent (Carbon-fixation Reactions): C3, Calvin, PGAL formation,
urns to yield PGAL/glucose, ribulose bisphosphate, rubisco, NADPH, ATP
Cell Cycle:
Stages of interphase: G1, S, G2, G0
Restriction point
DNA replication (DNA synthesis = S)
When do mutations occur?
Why is skin cancer more common than liver cancer?
Define cancer
DNA:
Chromosome: haploid, diploid
Investigations into the source of the genetic material:
Experiments by Griffith; Avery, MacLoed and McCarth; Hershey and Chase
Structure of DNA
Antiparallel strands
Double helix
Four DNA nucleotides: adenine, thymine, cytosine, quanine
Complementary base pairing: A:T, C:G
DNA replication: semiconservative
Parental strand and new daughter strand
DNA polymerase and formation of the sugar-phosphate bond, forms backbone of
molecule
DNA polymerase can form bonds only in the 5'--> 3' direction on the newly
forming strand
Leading (continuous), replications proceeds toward the replication fork
Lagging (discontinuous), replication proceeds away from the replication fork,
also called
Okazaki fragments
DNA polymerase requires a primer
Primers are a series of RNA nucleotides at the 5' end of the new strand
Primers are made by RNA polymerase
What are the differences between DNA polymerase and RNA polymerase?
RNA polymerase does not require a primer
RNA polymerase makes RNA on a DNA template
DNA polymerase makes DNA on a DNA template
RNA polymerase forms sugar-phosphate bonds of new strand in the 5'-->3'
direction
(same as DNA polymerase)
Replication origins in prokaryotes and in eukaryotes
DNA Fingerprint Lab: Lab Handout
Coding and non-coding regions
Alleles
Homozygous
Heterozygous
Paternal alleles and maternal alleles
Variable number tandem repeats (VNTR)
Agarose gel electrophoresis
Polymerase chain reaction (PCR)
Materials for PCR:
1. Your DNA
2. Primer
3. Taq polymerase (buffers, MgCl2)
4. DNA nucleotides
RNA/Protein Synthesis (Chapter 12)
Central dogma of molecular biology: DNA--> RNA--> amino
acid sequence of a protein (primary structure)
Structure of RNA vs DNA
General Steps in Protein synthesis
Transcription: role of RNA polymerase, promoters, termination signals
Genetic code: written in mRNA!!!
Codons, STOP codons, START codon (methionine), 61 codons to 20 amino acids
(more than one codon per amino acid), position of nucleotides in codons: first
and second are the same coding for the same amino acid, third position may
be different---> why is this important?
Differences and similarities between prokaryotic transcription and eukaryotic
transcription:
Postranscriptional modification of eukaryotic mRNA (RNA processing): introns
and exons
Structure and role of rRNA: small subunit and binding sites on small subunit;
large subunit and binding sites on large subunit
Structure and role of tRNA: binding sites for mRNA (anticodon) and binding
sites for appropriate amino acid
Details of translation: initiation, elongation and termination
Mutations
Gene Regulation:
Constitutive genes
Regulated genes
Operons: regulated gene clusters
Promoter
Structural genes
Operator
Repressor gene
Lac Operon: Inducible
Role of lactose in regulating operon
Eukaryotic gene regulation
Enhancers
DNA binding proteins (ex. Receptors for steroid hormones)
Euchromatin
Heterochromatin
Animal Development:
Fertilization
Types of eggs and quantity of yolk, relationship to cleavage patterns: equal,
unequal, animal and vegetal ples
General function of cleavage: no growth in size of developing embryo, partitioning
of zygote into many small, easily movable cells
Morula
Blastula
Gastrulation: derivatives of mesoderm, ectoderm, endoderm
Neurulation and induction by mesoderm
Embryonic Induction
Formation of lens of eye
Sample Exam 2 Questions:
1. A significant paper in development appeared in the early 1900's. In the
study a small amount of mesoderm was removed from one embryo in the gastrula
stage and transplanted into a second embryo also in the gastrula stage. The
second embryo with the transplanted mesoderm developed two neural tubes and
two nervous systems. Explain why. (5 pts.)
2. Explain the similarities and differences between the blastulas of eggs with a small amount of yolk, a moderate amount of yolk and large quantity amount of yolk. (5 pts.)
3. Cancer is due to mutations that disrupt the normal cell cycle. Cancers of nerve cells are extremely rare. Propose why a cancer of nerve cells is seldom observed. (5 pts.)
4. If you were to stretch out the 46 molecules of DNA found in a human cell and lay them end-to-end they would measure 2 meters long. However, these 46 molecules when fully condensed have a combined length of only 200 nanometers. What accounts for this? Describe how molecules of DNA are condensed. (5 pts.)
5. Explain why each of following terms/statements is important to the replication of DNA.(10 pts.)
Semiconservative
Role of DNA Polymerase
Okazaki fragments
Leading strand
Primers
6. What is the difference between heterochromatin and euchromatin? What is the difference in terms of gene expression? (5 pts.)
7. DNA replication in prokaryotes occurs in the cytoplasm, while in eukaryotes
it occurs in the nucleus. If the DNA of a eukaryotic cell was replicated exactly
like the DNA of a prokaryotic cell, DNA replication in eukaryotes might take
several days instead of minutes. How does DNA replication differ in prokaryotes
and eukaryotes, and why do you think this difference might speed-up eukaryotic
DNA replication. (5 pts.)
8. A common way of regulating gene expression in prokaryotes is via operons. What are the components of an operon? Describe how the presence of lactose in the environment of a bacterium controls the Lac operon. (10 pts.)
9. In prokaryotes, ribosomes attach to a mRNA molecule and begin its translation into protein even before transcription is completed. However, in eukaryotes transcription and translation occur separately. One reason for this is due to transcription occurring in the cytoplasm of prokaryotes and in the nucleus of eukaryotes. Discuss a second reason for this unrelated to the location of these processes. (5 pts.)
10. Explain the statement: When the fertilized egg of a sea urchin is separated into two halves, the future development of the resulting halves depends on how the cytoplasm is divided. (5 pts.)
11. Chromosomes contain both proteins and DNA. Describe how the "Waring Blender" experiment of Hershey and Chase using bacteriophages confirmed that DNA contains genetic information and protein does not. (5 pts.)
12. Suppose a mutation occurs in the following segment of DNA nucleotides in a prokaryote that involves a deletion of the marked nucleotide.
G-C-T-A-C-G-C-A-A-T-A-G-G-A-T-G-T-A-T-G-T-G-C-A-C-T-C-G-A
How could this mutation change the amino acid sequence of the protein coded for by this DNA sequence? Using a copy of the genetic code at your desk, what is the amino acid sequence of the original protein and of the mutated protein. (5 pts.)
13. Using the same nucleotide sequence as the question above, list the tRNA in order that would be necessary to translate the original sequence (without the mutation). (5 pts.)
14. Discuss the role of mRNA, rRNA and tRNA in gene expression. Compare the functions of each of the types of RNA. (10 pts.)
1. An animal living with free access to fresh water typically excretes a large quantity of urine that is hypotonic in relation to their blood. Terrestrial animals such as mammals excrete a hypertonic urine (a urine that is more concentrated than their blood). Discuss how the structure of the nephrons of these two types of animals might differ to explain the tonicity of their respective urine.
2. Discuss how the processes of filtration, reabsorption and secretion contribute to the final content of urine.
3. Describe how each of the situations would affect the response of the target neuron.
a decreased concentration of extracellular calcium.
the opening of chemical-regulated channels in the target neuron for chloride ions (Cl-).
4. There are three "states" or conditions of the voltage
regulated Na+ channel. Describe the state of the Na+ voltage regulated channel
at each of the following times.
a. at the resting membrane potential (Vrest)
b. just after threshold potential has been reached
c. during the absolute refractory period
d. during the relative refractory period
e. during repolarization
5. What is the importance of the myelin sheath that occurs around axons of neurons? What cells form the myelin sheath?
6. Acquired immunity includes humoral and cell-mediated immunity. Match each
of the following to either humoral or cell-mediated immunity or to both. Then,
explain the role of each term.
· B-lymphocyte
· Antibody
· Antigen presenting cell
· T-Helper cell
· T-Killer cell
· Cytokines
7. What types of pathogens are handled by Humoral immunity and what type of pathogens are handled by Cell-mediated immunity?
8. Explain why the concentrations of thyroid stimulating hormone from the pituitary and thyroid releasing factor from the hypothalamus are high when thyroid hormone from the thyroid gland is low.
9. Throughout this course we have encountered a multitude of uses for the ribonucleotide adenosine triphosphate (ATP). State three different uses for ATP within a cell. Give an example of each.
10. Oxytocin and Antidiuretic Hormone are secreted by the posterior pituitary gland. Where are these hormones actually produced? How does this differ from the hormones secreted from the anterior pituitary gland?
11. Chemical signals can be hydrophobic (example: steroid hormones) or hydrophilic (example: proteins). Describe the differences between these two types of signals and how they are able to cause a response in target cells.
12. Insulin is a small protein and cortisol is a steroid. What types of molecules would you look for in the cytoplasm of liver cells responding to insulin? What types of molecules would you look for in the cytoplasm of liver cells responding to cortisol? Where would the receptors for each of these hormones be located?
13. In general, what is the response of a target cell to a steroid hormone? How does this differ from the response of a target cell to a hormone derived from an amino acid?
14. Contraction of skeletal muscle involves the movement of protein filaments called myofilaments (thin and thick filaments). Describe these myofilaments and their arrangement in skeletal muscle cells. What is the role of calcium in muscle contraction?
· T-tubules
· Sarcoplasmic reticulum
· Troponin
· Tropomyosin
· Actin
· Myosin
· Ca++ATPase