Chapter12

17 November 2004

1. Fedoroff, N. and N. M. Brown (2004). Mendel in the kitchen : a scientist's view of genetically modified foods. Washington, D.C., Joseph Henry Press. Reviewed in Science 29 Oct 04 - debate on chemical vrs organic

2. new therapeutic silencing of a cholesterol gene via RNAi (RNA interference)

Rossi, J. J. (2004). "Medicine: a cholesterol connection in RNAi." Nature 432(7014): 155-6.

3. source of information on beta globin gene family; the way the information is presented; to get some small idea of the imensity of the genome.

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&db=nucleotide&list_uids=455025&dopt=GenBank&term=HUMHBB&qty=1

4. Another look at the hemoglobin sheet

Through our development there has been a turning on and turning off of several hemoglobin genes

Picture 3 ...the specific timing....../HemoglobinPicture3.gif

Picture 3a ... the specific tetrameres..../HemoglobinPicture3a.gif

Picture 4 .... a close up of the gene families on chromosomes 11 and 16. ../HemoglobinPicture4.gif

Picture 5 ... a long distance view of the beta family ... each functional gene (at least) has a set of promoters ../HemoglobinPicture5.gif

also see Fig 11.5 in your text (not on web) ... ../11x5.gif

Chapter 12 Gene Expression: Translation

Translation

Classes of RNA molecules

rRNA .......ribosomal RNA

tRNA........transfer RNA

from text: . ../../Other%20Graphics/12x16.gif. ../../Other%20Graphics/12x17gif ;

mRNA......messenger RNA

Genetic code

the code.... GeneticCode.GIF

simple code breaking sequences

Ochoa, artificial mRNA

U U U U U U U U U ===== phenylalanine

properties

three letters .... codons

Concept of codon.... three bases in mRNA code for one amino acid

reading frame...cat cat cat cat

redundancy... 64 codons, 20 amino acids, 3 stop translation codons (degeneracy)

wobble...see Table12.1 and Figure 12.8

Figure 12.8 ...... ../../Other%20Graphics/12-8.gif

cut out model for protein synthesis on page 40 of workbook

Gene expression: takes a cast of hundreds; DNA, RNA, and proteins

references:

Lee, Tong Ihn, Young, Richard A. TRANSCRIPTION OF EUKARYOTIC PROTEIN-CODING GENES Annu. Rev. Genet. 2000 34: 77-137

Tupler, Rosella., G. Perini, and M. R. Green. 2001 Expressing the human genome. Nature 409: 832 - 833.

charging of tRNA via amino acyl tRNA synthetase

two kinds of recognition: shape and base pairing (very important)

Crude model for Protein Synthesis ...... ../ProteinSynSequence.html

       1) add tRNA to synthetase WhichtRNA.GIF

        2) add amino acid to synthetase WhichtAminoAcid.GIF

        3) both added to synthetase.....WhichCharged.GIF

        4) charged tRNA.... WhichCharged2.GIF

Ribosomes

Ribosome composition ... RibosomeComposition.gif

Recent paper on ribosome structure

reference: Science volume 285 page 2078; 24 Sept 99

model of ribosome (not on web).. ribosome.gif

reference: American Scientist; Sept-Oct 1998, p.428

Steps in protein synthesis

initiation

elongation

termination

Continuation of Protein synthesis model ..........SingleProtSyn.html

ProteinSynth1.GIF

ProteinSynth1a.GIF

ProteinSynth1b.GIF

ProteinSynth2.GIF

ProteinSynth3.GIF

ProteinSynth4.GIF

ProteinSynth5.GIF

ProteinSynth6.GIF

ProteinSynth7.GIF

ProteinSynth8.GIF

Importance of consensus sequences

Promoter regions; TATA and CAT boxes

Start and stop signals for transcription and translation

Play protein syntheisis movie (not on the web)

..... Campbel protein movie2.gif

Newman's protein synthesis movie.... ProtMovie.gif

...............one step at a time...SingleProtSyn.html

complete translation

The secrets of the molecule table, page 41 of the workbook; the genes are located in the nucleus, synthesis of proteins from mRNA, proteins synthesized in the cytoplasm and RNA in the nucleus. Except for mitochondrial genes.

note third site on ribosome -- the exit site; three sites then, E - P - A

On the problem of turning genes on and off:

"The transformation of a single cell into a complex organism requires an exact system for regulation gene expression. It wouldn't do, say, to have hormone-secreting cells make liver proteing, or even the wrong hormone. Cell biologists don't know exactly how developing cells achieve this precision, but they do know it involves so-called transcription factors - proteins that can turn genes on or off." ....Science 290: 1066

Everything more complicated than indicated here; examples - 3 sites on ribosome; charging of tRNA in nucleus:..... Hopper, A. K. 1998 Nuclear Functions Charge Ahead. Science 282(5396): 2003-2004.

Beautiful and useful article in American Scientist on hemoglobin (also has reference web sites): Hardison, R. 1999 The Evolution of Hemoglobin. American Scientist 87(2): 126-137.

Millard Sussman's Protein synthesis in prokaryotes cartoon(made by Barbara) at: http://www.genetics.wisc.edu/CATG/susman/cartoon.html

click to get. Requires a Mac computer check requirements on Millard's site

polyribosomal complex

PolysomeCx.GIF....Figure 12.12

19 November 2004

Two seminars next week: 23 Nov - Gordon Orians - at 4PM 223 SB2 "Australian Ecology: The Maniford Consequences of Nutrient-Poor Soils and Intense Fire"

at 7PM, 53 Cramer Hall - "Bird Brains: Decision-making by Blackbirds"

We ended the last lecture with a discussion of th4e polyribosomal complex.

We must also consider the problem of defining the gene. Please see the workbook for a discussion of this.

Also, from the text Hartwell, L. H., L. Hood, et al. (2000). Genetics: From Genes to Genomes. Boston, McGraw-Hill.

"gene basic unit of biological information; specific segment of DNA in a discrete region of a chromosome that serves as a unit of function by encoding a particular RNA or protein" Page G-5

The question of gene regulation also came up

reference in: Strachan, T. and A. P. Read (1999). Human molecular genetics 2. New York, Wiley.

see http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=hmg.box.864

ProteinSynth1.GIF	ProteinSynth1a.GIF	ProteinSynth1b.GIF
ProteinSynth2.GIF	ProteinSynth3.GIF	ProteinSynth4.GIF
ProteinSynth5.GIF	ProteinSynth6.GIF	ProteinSynth7.GIF
ProteinSynth8.GIF

17 November 2004

1. Fedoroff, N. and N. M. Brown (2004). Mendel in the kitchen : a scientist's view of genetically modified foods. Washington, D.C., Joseph Henry Press. Reviewed in Science 29 Oct 04 - debate on chemical vrs organic

2. new therapeutic silencing of a cholesterol gene via RNAi (RNA interference)

Rossi, J. J. (2004). "Medicine: a cholesterol connection in RNAi." Nature 432(7014): 155-6.

3. source of information on beta globin gene family; the way the information is presented; to get some small idea of the imensity of the genome.

4. Another look at the hemoglobin sheet

Through our development there has been a turning on and turning off of several hemoglobin genes

Picture 3 ...the specific timing....../HemoglobinPicture3.gif

Picture 3a ... the specific tetrameres..../HemoglobinPicture3a.gif

Picture 4 .... a close up of the gene families on chromosomes 11 and 16. ../HemoglobinPicture4.gif

Picture 5 ... a long distance view of the beta family ... each functional gene (at least) has a set of promoters ../HemoglobinPicture5.gif

also see Fig 11.5 in your text (not on web) ... ../11x5.gif

Chapter 12 Gene Expression: Translation

Translation

Classes of RNA molecules

rRNA .......ribosomal RNA

tRNA........transfer RNA

from text: . ../../Other%20Graphics/12x16.gif. ../../Other%20Graphics/12x17gif ;

mRNA......messenger RNA

Genetic code

the code.... GeneticCode.GIF

simple code breaking sequences

Ochoa, artificial mRNA

U U U U U U U U U ===== phenylalanine

properties

three letters .... codons

Concept of codon.... three bases in mRNA code for one amino acid

reading frame...cat cat cat cat

redundancy... 64 codons, 20 amino acids, 3 stop translation codons (degeneracy)

wobble...see Table12.1 and Figure 12.8

Figure 12.8 ...... ../../Other%20Graphics/12-8.gif

cut out model for protein synthesis on page 40 of workbook

Gene expression: takes a cast of hundreds; DNA, RNA, and proteins

references:

Lee, Tong Ihn, Young, Richard A. TRANSCRIPTION OF EUKARYOTIC PROTEIN-CODING GENES Annu. Rev. Genet. 2000 34: 77-137

Tupler, Rosella., G. Perini, and M. R. Green. 2001 Expressing the human genome. Nature 409: 832 - 833.

charging of tRNA via amino acyl tRNA synthetase

two kinds of recognition: shape and base pairing (very important)

Crude model for Protein Synthesis ...... ../ProteinSynSequence.html

1) add tRNA to synthetase WhichtRNA.GIF

2) add amino acid to synthetase WhichtAminoAcid.GIF

3) both added to synthetase.....WhichCharged.GIF

4) charged tRNA.... WhichCharged2.GIF

Ribosomes

Ribosome composition ... RibosomeComposition.gif

Recent paper on ribosome structure

reference: Science volume 285 page 2078; 24 Sept 99

model of ribosome (not on web).. ribosome.gif

reference: American Scientist; Sept-Oct 1998, p.428

Steps in protein synthesis

initiation

elongation

termination

Continuation of Protein synthesis model ..........SingleProtSyn.html ProteinSynth1.GIF ProteinSynth1a.GIF ProteinSynth1b.GIF ProteinSynth2.GIF ProteinSynth3.GIF ProteinSynth4.GIF ProteinSynth5.GIF ProteinSynth6.GIF ProteinSynth7.GIF ProteinSynth8.GIF

Importance of consensus sequences

Promoter regions; TATA and CAT boxes

Start and stop signals for transcription and translation

Play protein syntheisis movie (not on the web)

..... Campbel protein movie2.gif

Newman's protein synthesis movie.... ProtMovie.gif

...............one step at a time...SingleProtSyn.html

complete translation

The secrets of the molecule table, page 41 of the workbook; the genes are located in the nucleus, synthesis of proteins from mRNA, proteins synthesized in the cytoplasm and RNA in the nucleus. Except for mitochondrial genes.

note third site on ribosome -- the exit site; three sites then, E - P - A

On the problem of turning genes on and off:

Everything more complicated than indicated here; examples - 3 sites on ribosome; charging of tRNA in nucleus:..... Hopper, A. K. 1998 Nuclear Functions Charge Ahead. Science 282(5396): 2003-2004.

Beautiful and useful article in American Scientist on hemoglobin (also has reference web sites): Hardison, R. 1999 The Evolution of Hemoglobin. American Scientist 87(2): 126-137.

Millard Sussman's Protein synthesis in prokaryotes cartoon(made by Barbara) at: http://www.genetics.wisc.edu/CATG/susman/cartoon.html

click to get. Requires a Mac computer check requirements on Millard's site

polyribosomal complex

PolysomeCx.GIF....Figure 12.12

19 November 2004

Two seminars next week: 23 Nov - Gordon Orians - at 4PM 223 SB2 "Australian Ecology: The Maniford Consequences of Nutrient-Poor Soils and Intense Fire"

at 7PM, 53 Cramer Hall - "Bird Brains: Decision-making by Blackbirds"

We ended the last lecture with a discussion of th4e polyribosomal complex.

We must also consider the problem of defining the gene. Please see the workbook for a discussion of this.

Also, from the text Hartwell, L. H., L. Hood, et al. (2000). Genetics: From Genes to Genomes. Boston, McGraw-Hill.

"gene basic unit of biological information; specific segment of DNA in a discrete region of a chromosome that serves as a unit of function by encoding a particular RNA or protein" Page G-5

The question of gene regulation also came up

reference in: Strachan, T. and A. P. Read (1999). Human molecular genetics 2. New York, Wiley.

Continuation of Protein synthesis model ..........SingleProtSyn.html

ProteinSynth1.GIF

ProteinSynth1a.GIF

ProteinSynth1b.GIF

ProteinSynth2.GIF

ProteinSynth3.GIF

ProteinSynth4.GIF

ProteinSynth5.GIF

ProteinSynth6.GIF

ProteinSynth7.GIF

ProteinSynth8.GIF