Lecture 4: DNA and Proteins

I. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” three parts: - pentose sugar (ribose in RNA, deoxyribose in DNA)

I. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” three parts: - pentose sugar (ribose in RNA, deoxyribose in DNA) - nitrogenous base (A, C, G, U in RNA A, C, G, T in DNA)

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” three parts: - pentose sugar - nitrogenous base Nitrogenous base binds to the 1’ carbon

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” three parts: - pentose sugar - nitrogenous base - phosphate group PO 4 binds to the 5’ carbon

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” three parts: - pentose sugar - nitrogenous base - phosphate group Diphosphates and triphosphates occur, also. In fact, here is ATP, the energy currency of the cell. The nucleotides exist as free triphosphates before they are linked into a nucleic acid chain.

OH O-P-O O OH H2OH2O V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ Between the PO 4 (which always has free H+ ions binding and unbinding) of the free nucleotide and the –OH group on the 3’ carbon of the last sugar in the chain. OH O-P-O O OH O-P-O O Energy released by cleaving the diphosphate group can be used to power the dehydration synthesis reaction

5’ 3’ V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ Polymerization results in a polymer of DNA (or RNA). This single polymer is a single- stranded helix It has a ‘polarity’ or ‘directionality’; it has different ends… there is a reactive phosphate at one end (5’) and a reactive –OH at the other (3’). So, the helix has a 5’-3’ polarity.

A purine (A or G) always binds with a pyrimidine (T or C) In fact, A with T (2 h-bonds) And G with C (3 h-bonds) V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) (although some viruses have genetic material that is signle-stranded DNA (ss-DNA)) a. The nitrogenous bases on the two helices are ‘complementary’ to one another, and form weak hydrogen bonds between the helices.

5’ V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) a. bases are complementary b. the strands are anti-parallel: they are aligned with opposite polarity

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) 4. RNA performs a wide variety of functions in living cells: a. m-RNA is a ‘copy’ of a gene, read by the ribosome to make a protein

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) 4. RNA performs a wide variety of functions in living cells: a. m-RNA is a ‘copy’ of a gene, read by the ribosome to make a protein b. R-RNA is made the same way, is IN the Ribosome, and ‘reads’ the m-RNA

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) 4. RNA performs a wide variety of functions in living cells: a. m-RNA is a ‘copy’ of a gene, read by the ribosome to make a protein b. r-RNA is made the same way, is IN the Ribosome, and ‘reads’ the m-RNA c. t-RNA is made the same way, and brings amino acids to the ribosome

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) 4. RNA performs a wide variety of functions in living cells: a. m-RNA is a ‘copy’ of a gene, read by the ribosome to make a protein b. r-RNA is made the same way, is IN the Ribosome, and ‘reads’ the m-RNA c. t-RNA is made the same way, and brings amino acids to the ribosome d. mi-RNA (micro-RNA) and si-RNA (small interfering RNA) bind to m-RNA and splice it; inhibiting the synthesis of its protein. This is a regulatory function.

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) 4. RNA performs a wide variety of functions in living cells: a. m-RNA is a ‘copy’ of a gene, read by the ribosome to make a protein b. r-RNA is made the same way, is IN the Ribosome, and ‘reads’ the m-RNA c. t-RNA is made the same way, and brings amino acids to the ribosome d. mi-RNA (micro-RNA) and si-RNA (small interfering RNA) bind to m-RNA and splice it; inhibiting the synthesis of its protein. This is a regulatory function. e. Sn-RNA (small nuclear RNA) are short sequences that process initial m-RNA products, and also regulate the production of r-RNA, maintain telomeres, and regulate the action of transcription factors. Regulatory functions.

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure B. Chromosome Structure 1. Prokaryotes - usually one circular chromosome, tethered to the membrane, with some associated, non-histone proteins.

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure B. Chromosome Structure 1. Prokaryotes 2. Eukaryotes – usually many linear chromosomes, highly condensed with histone proteins into several levels of structure.

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure B. Chromosome Structure 1. Prokaryotes 2. Eukaryotes – usually many linear chromosomes, highly condensed with histone proteins into several levels of structure. a. Level 1: ds-DNA is wrapped around histone proteins, creating the “beads on a string’ level of organization.

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure B. Chromosome Structure 1. Prokaryotes 2. Eukaryotes – usually many linear chromosomes, highly condensed with histone proteins into several levels of structure. a.Level 1: ds-DNA is wrapped around histone proteins, creating the “beads on a string’ level of organization.

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure B. Chromosome Structure 1. Prokaryotes 2. Eukaryotes – usually many linear chromosomes, highly condensed with histone proteins into several levels of structure. a.Level 1: ds-DNA is wrapped around histone proteins, creating the “beads on a string’ level of organization. b.Level 2: string is coiled, 6 nucleosomes/turn (solenoid)

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure B. Chromosome Structure 1. Prokaryotes 2. Eukaryotes – usually many linear chromosomes, highly condensed with histone proteins into several levels of structure. a.Level 1: ds-DNA is wrapped around histone proteins, creating the “beads on a string’ level of organization. b.Level 2: string is coiled, 6 nucleosomes/turn (solenoid) c.Level 3: the coil is ‘supercoiled’

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure B. Chromosome Structure 1. Prokaryotes 2. Eukaryotes – usually many linear chromosomes, highly condensed with histone proteins into several levels of structure. a.Level 1: ds-DNA is wrapped around histone proteins, creating the “beads on a string’ level of organization. b.Level 2: string is coiled, 6 nucleosomes/turn (solenoid) c.Level 3: the coil is ‘supercoiled’ d.Level 4: the supercoil is folded into a fully condensed metaphase chromosome

V. DNA, RNA, and Chromosome Structure A. DNA and RNA Structure B. Chromosome Structure 1. Prokaryotes 2. Eukaryotes – usually many linear chromosomes, highly condensed with histone proteins into several levels of structure. To read a gene, the chromosome must be diffuse (uncondensed) in that region. Even when condensed, these ‘euchromatic’ coding regions are less condensed and more lightly staining than non-coding regions. DNA that has few genes can remain condensed and closed (heterochromatic), and appears as dark bands on condensed chromosomes.

II. Protein Synthesis

Why is this important? Well…what do proteins DO?

Why is this important? Well…what do proteins DO? Think about it this way: 1)sugars, fats, lipids, nucleic acids and proteins, themselves, are broken down and built up through chemical reactions catalyzed by enzymes. 2)So everything a cell IS, and everything it DOES, is either done by proteins or is done by molecules put together by proteins.

II. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C Genes are read by enzymes and RNA molecules are produced… this is TRANSCRIPTION U G C U G A C U A C U (m-RNA) (r-RNA) (t-RNA)

II. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C Genes are read by enzymes and RNA molecules are produced… this is TRANSCRIPTION U G C U G A C U A C U (m-RNA) Eukaryotic RNA and some prokaryotic RNA have regions cut out… this is RNA SPLICING (r-RNA) (t-RNA)

II. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C U G C U G A C U A C U (m-RNA) (r-RNA) (t-RNA) R-RNA is complexed with proteins to form ribosomes. Specific t-RNA’s bind to specific amino acids. ribosome Amino acid

II. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C U G C U G A C U A C U (m-RNA) (r-RNA) (t-RNA) The ribosome reads the m-RNA. Based on the sequence of nitrogenous bases in the m-RNA, a specific sequence of amino acids (carried to the ribosome by t-RNA’s) is linked together to form a protein. This is TRANSLATION. ribosome Amino acid

II. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C U G C U G A C U A C U (m-RNA) (r-RNA) (t-RNA) The protein product may be modified (have a sugar, lipid, nucleic acid, or another protein added) and/or spliced to become a functional protein. This is POST-TRANSLATIONAL MODIFICATION. ribosome Amino acid glycoprotein

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription a. The message is on one strand of the double helix - the sense strand: 3’ 5’ “TAG A CAT” message makes ‘sense’ “ATC T GTA” ‘nonsense’ limited by complementation A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A sense nonsense

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription a. The message is on one strand of the double helix - the sense strand: 3’ 5’ In all eukaryotic genes and in some prokaryotic sequences, there are introns and exons. There may be multiple introns of varying length in a gene. Genes may be several thousand base-pairs long. This is a simplified example! A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A sense nonsense intronexon

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription b. The cell 'reads' the correct strand based on the location of the promoter, the anti- parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase. 3’ 5’ Promoters have sequences recognized by the RNA Polymerase. They bind in particular orientation. A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A sense nonsense intronexon Promoter

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription b. The cell 'reads' the correct strand based on the location of the promoter, the anti- parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase. 3’ 5’ 1)Strand separate 2)RNA Polymerase can only synthesize RNA in a 5’  3’ direction, so they only read the anti-parallel, 3’  5’ strand (‘sense’ strand). A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A sense nonsense intronexon Promoter G C A U GUUU G C C A A U AUG A U G A

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. Terminator sequences destabilize the RNA Polymerase and the enzyme decouples from the DNA, ending transcription 3’ 5’ A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A sense nonsense intronexon Promoter G C A U GUUU G C C A A U AUG A U G A Terminator

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. 3’ 5’ A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A sense nonsense intronexon Promoter G C A U GUUU G C C A A U AUG A U G A Terminator Initial RNA PRODUCT:

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. 3’ 5’ A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A sense nonsense PromoterTerminator intronexon G C A U GUUU G C C A A U AUG A U G A Initial RNA PRODUCT:

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing intronexon Initial RNA PRODUCT: Introns are spliced out, and exons are spliced together. Sometimes these reactions are catalyzed by the intron, itself, or other catalytic RNA molecules called “ribozymes”. G C A U GUUU G C C A A UAUG AU G A

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing intron exon Final RNA PRODUCT: This final RNA may be complexed with proteins to form a ribosome (if it is r-RNA), or it may bind amino acids (if it is t-RNA), or it may be read by a ribosome, if it is m- RNA and a recipe for a protein. G C A U GUUU G C C A A U AUG A U G A

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. M-RNA:G C A U G U U U G C C A A UU G A

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. M-RNA:G C A U G U U U G C C A A UU G A It then reads down the m-RNA, one base at a time, until an ‘AUG’ sequence (start codon) is positioned in the first reactive site.

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex. M-RNA:G C A U G U U U G C C A A UU G A Meth

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex. c. A second t-RNA-AA binds to the second site M-RNA:G C A U G U U U G C C A A UU G A MethPhe

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex. c. A second t-RNA-AA binds to the second site d. Translocation reactions occur M-RNA:G C A U G U U U G C C A A UU G A Meth Phe The amino acids are bound and the ribosome moves 3-bases “downstream”

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation e. polymerization proceeds M-RNA:G C A U G U U U G C C A A UU G A MethPhe The amino acids are bound and the ribosome moves 3-bases “downstream” AlaAsn

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation e. polymerization proceeds M-RNA:G C A U G U U U G C C A A UU G A MethPhe The amino acids are bound and the ribosome moves 3-bases “downstream” Ala Asn

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation e. polymerization proceeds f. termination of translation M-RNA:G C A U G U U U G C C A A UU G A Some 3-base codon have no corresponding t-RNA. These are stop codons, because translocation does not add an amino acid; rather, it ends the chain. MethPheAlaAsn

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation 4. Post-Translational Modifications Most initial proteins need to be modified to be functional. Most need to have the methionine cleaved off; others have sugar, lipids, nucleic acids, or other proteins are added. MethPheAlaAsn

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription - DNA bound to histones can’t be accessed by RNA Polymerase - but the location of histones changes, making genes accessible (or inaccessible) Initially, the orange gene is “off”, and the green gene is “on” Now the orange gene is “on” and the green gene is “off”.

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 3’ 5’ Transcription factors can inhibit or encourage the binding of the RNA Polymerase. And, through signal transduction, environmental factors can influence the activity of these transcription factors. So cells can respond genetically to changes in their environment. A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A sense nonsense intronexon Promoter RNA POLY

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing intronexon Initial RNA PRODUCT: Mi-RNA’s and si-RNA’s are small RNA molecules that can bind to m-RNA and disrupt correct spicing, creating non-functional m-RNA’s. G C A U GUUU G C C A A UAUG AU G A U A U A Cut not made

M-RNA:G C A U G U U U U G A A A UU G A Incorrect splicing can result in a ‘premature’ stop codon, terminating translation early, resulting in a non-functional protein. MethPhe II. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing 3. Regulating Translation

The patterns of cleavage and modification can vary. MethPheAlaAsn II. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing 3. Regulating Translation 4. Regulating Post-Translational Modification

II. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing 3. Regulating Translation 4. Regulating Post-Translational Modification Protein ? Affected by other genes Affected by other cells Affected by the environment Gene activity is responsive to cellular and environmental cues

III. Evolution of a Genetic System - remember the Requirements of a Living System? 1.Evolution of a Membrane 2.Metabolic Pathways 3.Evolution of a Genetic System DNA RNA (m, r, t) protein

III. Evolution of a Genetic System A.Problem: - conundrum... which came first, DNA or the proteins they encode? DNA RNA (m, r, t) protein DNA stores info, but proteins are the metabolic catalysts...

III. Evolution of a Genetic System A.Problem B.Solution - Ribozymes – RNA enzymes info storage AND cataylic ability

III. Evolution of a Genetic System A.Problem B.Solution - Ribozymes – RNA enzymes - Three stage hypothesis

RNA Stage 1: Self-replicating RNA evolves

RNA Stage 1: Self-replicating RNA evolves Stage 2: RNA molecules interact to produce proteins... if these proteins assist replication (enzymes), then THIS RNA will have a selective (replication/reproductive) advantage... chemical selection. m-, r-, and t- RNA PROTEINS (REPLICATION ENZYMES)

Stage 3: Mutations create new proteins that read RNA and make DNA; existing replication enzymes replicate the DNA and transcribe RNA. m-, r-, and t- RNA PROTEINS (REPLICATION ENZYMES) DNA Reverse transcriptases

Can this happen? Are their organisms that read RNA and make DNA?

yes - retroviruses....

Stage 3: Mutations create new proteins that read RNA and make DNA; existing replication enzymes replicate the DNA and transcribe RNA. m-, r-, and t- RNA PROTEINS (REPLICATION ENZYMES) DNA Already have enzymes that can make RNA...

Stage 3: Mutations create new proteins that read RNA and make DNA; existing replication enzymes replicate the DNA and transcribe RNA. m-, r-, and t- RNA PROTEINS (REPLICATION ENZYMES) DNA Already have enzymes that can make RNA...

Stage 4: Mutations create new proteins that replicate the DNA instead of replicating the RNA... m-, r-, and t- RNA PROTEINS (REPLICATION ENZYMES) DNA This is adaptive because the two-step process is more productive, and DNA is more stable (less prone to mutation).

Stage 4: Mutations create new proteins that replicate the DNA instead of replicating the RNA... m-, r-, and t- RNA PROTEINS (REPLICATION ENZYMES) DNA This is adaptive because the two-step process is more productive, and DNA is more stable (less prone to mutation). And that's the system we have today....

D. Summary: STEPS REQUIRED FOR THE SPONTANEOUS, NATURAL FORMATION OF LIFE, and the evidence to date: 1. Spontaneous synthesis of biomolecules - strong evidence; Miller- Urey experiments. 2. Polymerization of monomers into polymers (proteins, RNA, sugars, fats, etc.) - strong evidence; Fox and Cairns-Smith experiments. 3. Formation of membranes - strong evidence; behavior of phospholipids in solution. 4. Evolution of metabolic systems - reasonable hypotheses, and genetic similarity in genes involved in particular pathways (suggesting gene duplication and subsequent evolution of new genes and elaboration of existing pathways) 5. Evolution of a genetic system - a reasonable hypothesis and significant corroborating evidence that it could happen. But no experimental evidence of the process evolving through all three steps. 6. How did these three elements (membrane, metabolism, genetic system come together?) a few untested hypotheses.