Genetics at the University of Florida

AGR 3303 (3 credits)
University of Florida - Fort Lauderdale
comments to: turf@ufl.edu
Syllabus Guide Exams More classes Turfgrass Science
 
Outline of molecular genetics

THE MOLECULAR BASIS OF HEREDITY (chapters 11-17)

I. Background concepts

A. Organisms (eukaryotes, prokaryotes, and (?) viruses); parts of the cell (cell wall, membranes, nucleus, ribosomes, chromosomes, mitochondria, chloroplasts)

B. Characteristics of the hereditary material include storage, expression, mutation, and replication

C. Very basic chemistry

1. atoms are particles (where have we seen that word before?) of the elements of life: especially C, H, O, N, S, and P; atoms have atomic weight; molecules have molecular weight

2. chemical bonds: especially ionic, covalent, and H

3. isomers

4. hydrophilic versus hydrophobic compounds

5. pH

6. reactions: hydrolysis, dehydration condensation, phosphorylation (phosphodiester bond)

7. major chemicals of living organisms: amino acids (e.g., proteins), fats, sugars (e.g., polysaccharides, cellulose), nucleic acids

8. enzymes and activation energy

9. isotopes, radioactive e.g., 3H, or not, e.g., 15N

10. electromagnetic spectrum (e.g., ultraviolet, X-rays)

11. units of measure (nm, A)

II. Polynucleotide structure (ch. 11)

A. nitrogenous bases (purines and pyrimidines), 5-carbon sugars, and phosphate groups

B. nucleosides, nucleotides, and polynucelotides

C. Watson-Crick model

1. double-helix, antiparallel strands, plectonic

2. A=T, Cº G complementarity & base composition

3. hydrophilic phosphodiester bonds to outside; bases paired by H bonds on inside, stacked flat

4. 34 nm per turn (10.4 bases); 20 nm diam.; major-minor grooves

D. Forms of DNA; supercoiling

III. Nature of the evidence about DNA as the genetic material (ch. 10)

A Avery et al., 1944: heat- killed Diplococcus filtrate transforms rough cells (avirulent) bacteria to smooth (virulent), despite enzyme treatments; DNase inactivates the transforming factor

B. Hershey-Chase: phage T2 injects radioactive phosphorus (32P) into infected bacteria

C. Circumstantial evidence: distribution of DNA; 254-260 nm mutagenesis & absorption spectra

D. Recombinant DNA

E. Base composition, X-ray diffraction analysis

F. Sedimentation velocity (mass=molecular weight & shape) leading to Svedberg coefficient= S; versus sedimentation equilibrium (density gradient)

G. Paper chromatography

H. Melting profiles; hyperchromic shift

I. Reassociation kinetics & genomic complexity; highly repetitive DNA

J. Meselson-Stahl and semiconservative replication based on equilibrium sedimentation in E. coli; autoradiography of labelled broad bean root tips

K. Kornberg & polymerase I

L. Nearest-neighbor analysis

M. F X174 phage and biologically active DNA

IV. RNA (ch. 10)

A. Differences from DNA

B. Types (m, t, r) and function in genetic expression

C. Function as the genetic material (in some viruses)

V. The genetic code (chapter 13)

A. (Review:) Genetic information (in the DNA) is transcribed to an intermediate molecule mRNA, which is translated through an adapter molecule tRNA to form "polypeptides", or long chains of amino acids (these go on to make proteins).

B. The genetic code is a triplet RNA code; it is linear, degenerate (=redundant, which goes with the wobble hypothesis), unambiguous, nonoverlapping, and comma-free. The code is universal (with few exceptions, such as in mitochondria). There are punctuation signals, e.g., termination codons ( = nonsense triplets). There is a colinear 1relationship between nucleotides and amino acids.

C. Circumstantial evidence in deciphering the code

1. Frameshift mutations

2. Cell-free protein synthesizing system and synthetic mRNA (either homopolymers heteropolymers)

D. Smoking gun evidence for deciphering the code

1. Triplet binding technique

2. Repeating copolymers

3. Complete sequencing of a gene with 387 nucleotides, expressed as 129 amino acids.

VI. Replication (ch. 12)

A. Characteristics: semiconservative, bidirectional, fidelity

B. Players: polymerases, ligase, primer, and many others

C. Process: multiple origins (in eukaryotes), leading and lagging strands, unwinding, stabilization, initiation, etc.

VII.Mutations (ch. 17)

A. What are they (i.e., molecular basis)? What good are they?

B. Study and detection, e.g., haploids (even higher plants), ClB system, attached-X method (see p 376-377) [why not just treat normal males? what would be the consequences; comments on Y-chromosome], pedigree testing, chemical methods, the Ames test; minimal media; prototrophs are wild type; auxotrophs lack a metabolic capability

C. Origin and rate; usually during replication

1. UV and T-T dimers; photoreactivation; high-energy radiation

2. Chemical agents; base analogs; tautomeric shifts

3. No threshold/no lower dosage

4. Human examples: O blood type a frameshift mutation; also, muscular dystrophy sometimes

D. Repair; amazing, considering 5000 random depurinations per cell per day; (it's the faulty repair that leaves you with a mutation).

VIII.Recombinant DNA (chs. 18, 21)

IX. Chromosome structure (ch. 2, 20)

A. Nature and kinds of chromosomes=gene packages

B. Viruses and bacteria vary in the genetic material; chromosome is just nucleic acid

C. Eukaryotes

1. Mitochondria and chloroplasts have circular DNA

a. Basis for endosymbiont theory: antibiotics such as erythromycin affect chloroplasts and bacterial ribosomes; variations in genetic code.

b. Interact with nuclear genes in several ways.

c. Leads to maternal inheritance of certain traits (e.g., chlorophyll variations, southern corn leaf blight susceptibility).

2. Chromatin=nucleoprotein contains histones (basic proteins); packing problem, e.g., 12 miles of message in a golf ball! Complexity expected. Why?

a. Subunits nucleosomes » 200 bp repeating units, etc.

b. Heterochromatin is dark-staining, inactive (may be facultative, e.g., Barr body); satellite DNA, highly repetitive, late replicating.

3. Techniques: banding

4. Gene amplification

 

 

GENE EXPRESSION AND REGULATION

I. Transcription, translation, and proteins (chs. 13-14)

A. Both involve chain initiation, elongation, and termination.

B. Transcription

1. Four major players: DNA template, RNA polymerase (an enzyme), Mg++, and nucleoside triphosphates

2. Minor players: sigma subunit, consensus sequences, and promoter sequences, and termination codons

C. Translation

1. Four major players: mRNA, ribosome, charged tRNA, and peptidyl transferase.

2. Many minor players: aminoacyl synthetases (charge tRNA), initiation factors, release factors, RNA maturase, and spliceosomes.

D. Comparison of prokaryotes and eukaryotes

1. Where do events occur?

2. When? (comparative speed; longevity of mRNA; and simultaneity)

3. Complexity (of control, number of factors, modification of pre-mRNAs in eukaryotes; and split genes)

E. Protein structure and function

A. Inborn errors of metabolism

B. One-gene:one-polypeptide

C. Colinearity

II. Gene regulation (chs. 15-16)

A. Why? Not all cells do everything; enzymes may be "adaptive". Commonplace analogies: irrigation valves; how many more can you think of?

B. Importance. Cancer.

C. Two models of gene regulation.

1. Prokaryotes. The lac operon model; 3 structural genes; 2 regulatory genes. Structural gene lac z codes for b -galactosidase. Lactose changes the repressor (a diffusible protein) and prevents it from binding with the operator.

2. Eukaryotes. Steroid hormone binds to a receptor protein in cytoplasm, and migrates to the nucleus. A "cascade of events". Some aspects highly conserved.

3. Similarities: external effector, configuration change, transport, inducible (based on action of substrate). Differences: chromatin structure is altered, signals are external to the cell, and there is more genetic information involved in (multicellular) eukaryotes; also, transcription and translation linked in bacteria, separate in eukaryotes.

D. Major variations on genetic regulation.

1. Catabolite activating protein (CAP) - positive control of lac operon by catabolite glucose (positive because in the absence of glucose the CAP protein makes sure the operon is in the "normally off" position).

2. Tryptophan operon is a repressible gene system; that is, the tryptophan (a co-repressor) acts to reduce the transcription of appropriate mRNA, by activating the repressor. Repressible systems are typical for anabolism.

E. Other variations in gene regulation

1. Post-transcription regulation

2. Transposons

3. Promoters, enhancers, transcription factors, competition for binding sites

III. Molecular warfare; how do you recognize self and non-self? Other basic problems of survival (ch. 20)

A. Antibody diversity; may be caused by recombination

B. Cancer/oncogenes. Proto-oncogenes control cell growth; can be switched "always on".

C. HIV/AIDS

 

OTHER ADVANCED TOPICS

IV.Population and evolutionary genetics (chs. 25-26)

V.Overview of plant and animal improvement

VI.Philosophical and social considerations (ch. 21)

 
  
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comments to: turf@ufl.edu