Power Point to Accompany

Principles and Applications of Inorganic, Organic, and Biological Chemistry Denniston, Topping, and Caret 4th ed Chapter 24

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24.1Structure of the Nucleotide

DNA and RNA are polymers whose monomer units are called nucleotides A nucleotide itself consists of: 1. a nitrogen containing heterocyclic base 2. a ribose or deoxyribose sugar ring 3. a phosphoric acid unit
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Major Purine Bases

NH2 N1 HC
2

O
7

C
6

C 5

N
8 CH

HN C H2N

C C

N CH N H

9 3 4C

N H

adenine in DNA and RNA

guanine in DNA and RNA

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Major Pyrimidine Bases

O O NH2 C CH3 C C HN CH N3 4 5CH HN C C CH C2 1 6CH C CH O N O N O N H H H

cytosine in DNA and RNA thymine in DNA and some RNA uracil in RNA
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Nucleotides-1
A nucloetide is the base NH2 repeating unit of the C DNA or RNA N C phosphate N polymer. The CH nitrogen base is ester C N HC attached to the N 2ribose (RNA) or O3PO CH2 O deoxyribose (DNA) ring. The sugar is H H phosphorylated at H H carbon 5

deoxyribose sugar 24-5

OH H

Nucleotides-2: Names
Begin with the name of the nitrogenous base. Remove ine ending and replace with: -osine for purines or idine for pyramidines. Uracil: -acil with idine. ribose then ribonucleotide deoxyribose then deoxyribonucleotide deoxy before base name for deoxyribonucleotide Add prefix for number of phosphoryl groups Monophosphate, diphosphate, 24-6 triphosphate

Nucleotides-3
NH2 C CH3 C HN N O 2O3PO CH2 O H H H H OH H C C

Deoxythymidine 5-monophosphate dTMP

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Nucleotides-4
NH2 N O HC C C N CH O O H O H OH N C

NH2 C N CH CH

C N N O P O CH2 O O H H H H OH H

O P O CH2

O H H H

Deoxyadenosine 5-monophosphate dAMP

2-deoxy

Deoxycytidine 5-monophosphate 24-8 dCMP

Nucleotides-5
Uridine O 5-monophosphate C UMP HN CH
O 2O3PO CH2 H H OH C O H H H N CH
2-

HN H2N C

O C

N CH

C N N O H H H

O3PO CH2 H H

OH

Guanosine 5-monophosphate, GMP 24-9

24.2 DNA/RNA Chains

When nucleotides polymerize, the 5 phosphate on one unit esterifies to the 3 OH on another unit. The terminal 5 unit retains the phosphate. An example of a three nucleotide DNA product is shown on the next slide .

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Segment of One DNA Chain 5-end

N O C C N C N C H2N N -2 O3PO CH2 O H H H H H O CH O C

guanine
C CH CH3

3-5 link

O N O P O CH2 O O H H H H H O

N C

thymine cytosine

3-end

NH2 C N CH C CH O N O P O CH2 O O H H H H OH H

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DNA-Secondary Structure
The most common form of DNA is the form . Its structure was determined by Watson and Crick in 1953. This DNA consists of two chains of nucleotides coiled around one another in a right handed double helix. The chains run antiparallel and are held together by hydrogen bonding between complimentary base pairs: A=T, G=C.

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Insert Fig 24.4

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DNA-Secondary Structure, cont.

Hydrogen CH3 N H||||||||||| O N HC bonding between C C C C N C CH A and T or G and N|||||||||||H N C N N CH C helps to hold A TO the chains in the H double helix O ||||||||||| H N N
HC N C N H ||||||||||| N C N H ||||||||||| H C C C CH CH N The strands C N said to be O H

are

complimentary 24-14

B DNA segment
Chain 2 Sugar-phosphate backbone Chain 1

Hydrogen bonded base pairs in the core of the helix 24-15

B DNA: 2
Major groove Outside diameter, 2 nm Interior diameter, 1.1 nm Minor groove

Length of one turn of helix is 3.4 nm and contains 10 base pairs.

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Chromosomes
Chromosomes are pieces of DNA that contain the genetic instructions, or genes, of an organism. Prokaryotes (single chromosome) No true nucleus. Chromosome is a circular DNA molecule that is supercoiled, that is, the helix is coiled on itself. At approximately 40 sites a complex of proteins is attached, forming a series of loops. This structure is the nucleoid. 24-17

Chromosomes, cont.
Eukaryotes (Number and size of chromosomes vary.) True nucleus. Membrane bound organelles that separate cellular functions. Nucleosome which consists of a strand of DNA wrapped around a disk of histone proteins. Larger structure is the 30 nm fiber. Coiled in to a 200 nm fiber
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RNA Structure
Sugar-phosphate backbone for ribonucleotides linked by 3-5 phosphodiester bonds. RNA molelcules usually single stranded. Ribose replaces deoxyribose. Uracil replaces thymine. Base pairing between U and A and G and C results in portions of the single strand that become double stranded.
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24.4 Information Flow

DNA RNA Protein

Replication: DNA duplicates itself Transcription: RNA is made on a DNA template Translation: Protein is synthesized from AAs and the three RNAs. Reverse Transcription: RNA directs synthesis of DNA
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Classes of RNA Structure

transfer RNA (tRNA) Transfers amino acids to the site of protein synthesis (ribosomes). Has the anticoden. ribosomal RNA (rRNA) rRNA forms ribosomes by reacting with proteins messenger RNA (mRNA) mRNA directs the AA sequence of proteins and is a complimentary copy of a gene. It has the codon for an AA in a protein,
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tRNA
There is at least one tRNA (and often several) for each AA to be incorporated into a protein. tRNA is single stranded with typically about 80 nucleotides. Intrachain hydrogen bonding (A=U and G=C) occurs to gives regions called stems with an -helix The overall structure is called a cloverleaf in a L-shaped conformation.
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tRNA
Transfer RNA (tRNA) transfers AA to the site of protein synthesis. Has the anticoden Attachment to mRNA here

AA attaches here
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Transcription
Transcription is catalyzed by RNA polymerase. Initiation binds RNA polymerase to the promoter region at the beginning of the gene. Cain elongation then occurs forming a 3-5 phosphodiester bond. Termination is the final step of transcription.

Will Fig 24.12 fit here??

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Post Transcription Processing, mRNA

Prokaryote mRNA is continuous. Eukaryote mRNA must be processed: A 5 cap structure is added A 3 poly A tail (100 to 200 units) is added The introns (noncoding base sequences) are cut out and the introns (coding sequences) are spliced together. Splicosomes help recognize intron-exon boundaries. They are composed of small nuclear ribonucleoproteins (snRNPs, snurps). 24-25

24.5 The Genetic Code (DNA)

The message on DNA translated to mRNA: 1. Degenerate: more than one three base codon can code for the same AA. 2. Specific: each codon specifies one AA 3. Nonoverlapping and commaless : none of the bases are shared between consecutive codons and no noncoding bases appear in the base sequence. 4. Universal: except in a few instances, all organisms use the same code.
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The Genetic Code-2

All 64 codons have meaning; 61 code for an AA and three code for the stop signal. Multiple codes for an AA tend to have two bases in common. E. g. CUU, CUC, CUA, CUG code for leu (codons are written: 5-> 3 sequence.) A partial table for the genetic code follows on the next slide. See your text for a complete table.
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The Genetic Code-3

5 end U Middle base U C A phe ser tyr phe ser tyr leu ser end leu ser end leu pro his leu pro his leu pro gln leu pro gln 3 end G cys cys end trp arg arg arg arg U C A G U C A G

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The Genetic Code-4

Use the table in slide 6 to answer the questions. Click for the answer. 1. CCU codes for: ? pro arg 2. CGA codes for: ? ser 3. UCA codes for: ?

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24.6 Protein Synthesis

Protein synthesis is called translation. It is carried out on ribosomes, complexes of rRNA and proteins. Protein synthesis occurs in multiple places on one mRNA. The mRNA plus the multiple ribosomes are called a polysome, tRNA binds a specific AA aided by aminoacyl tRNA synthethase and recognizes the appropriate codon on the mRNA.

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Translation Process-1
Initiation Initiation factors (proteins), mRNA, initiator tRNA, and small and large ribosomes come together. Ribosome has two sites to bind tRNA P-site binds to the growing peptide A-site binds the aminoacyl tRNA Chain Elongation An aminoacyl tRNA binds to A site Peptide bond formation occurs Translocation (movement) of ribosome down the mRNA chain to next codon. 24-31

Translation Process-2
Termination Upon finding a stop codon a release factor binds a the empty A site. The bond between the last AA and peptidyl tRNA is hydrolyzed releasing the protein. The protein released may not be in its final form. Cleavage, association with other proteins, and bonding to carbohydrate or lipid groups may occur before a protein is fully functional.
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Insert Fig 24.19

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24.7 Mutation and Repair

Mutations are mistakes introduced into the DNA sequence of an organism. They can be classified as: Point: substitution of a single nucleotide for another. Deletion: one or more nucleotides are lost. Insertion: one or more nucleotides are added. Many mutagens (chemicals causing a change in the DNA sequence) are also carcinogens and cause cancer. 24-34

UV Damage and DNA Repair

UV light causes formation of a pyrimidine dimer on a DNA strand. Failure to repair this defect can lead to xeroderma pigmentosum. People who suffer from this genetic skin disorder are very sensitive to UV light and develop multiple skin cancers.

Insert Fig 24.20

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24.8 Recombinent DNA

Restriction enzymes are bacterial enzymes that cut the backbone of DNA at specific nucleotide sequences. Donor and plasmid (bacteria) DNA are cleaved by the same restriction enzyme. Donor and plasmid DNA are mixed and donor fragment joins to a complimentary plasmid fragment due to hydrogen bonding. Plasmid ring is restored using using DNA ligase. Engineered plasmid (recombinent DNA) is introduced to a bacterium to be reproduced.

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24.9 Polymerase Chain Reaction

DNA is mixed with Taq polymerase (a heat stable DNA polymerase), a primer DNA sequence for a specific gene, and the four nucleotide triphosphates. A thermocycler raises the temperature to 9496 oC to separate the DNA strands, lowers the temperature to 50-56 oC to the primers to hybridize to the DNA, and raises the temperature to 72 oC to allow the Taq polymerase to act. Repeating the cycle doubles the new DNA strands each cycle. (12481632 etc) 24-37

24.10 Human Genome Project

The DNA to be sequenced is placed in four test tubes (tt) with all the enzymes and nucleotides necessary for DNA synthesis. In addition, each tt contains a small amount of one species of dideoxynucleotide with an H at the 3 position. Once this is incorporated in the growing chain, chain synthesis stops. The DNA fragments are separated by gel electrophoresis in four wells side by side. The sequence is read from the gel as shown in the figure on the next slide.
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Insert Fig 24.26

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The End
Introduction to Molecular Genetics
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