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Biology 304101
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Chapters 16,17,18 and19 Quick
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review
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Prof. Dr.Samih Tamimi
Dept.of Biology
University of Jordan
Bio 101 quick review
1/1/2012
Chapter 16
DNA REPLICATION
1.
Basic Outline:
REPLICATION
DNA -----------------------> 2 identical DNAs
TRANSCRIPTION
DNA -----------------------> mRNA
TRANSLATION
mRNA -----------------------> protein
• base sequence of DNA codes for amino acid sequence of protein; one gene
codes for one protein
DNA as Hereditary Material:
• “Transforming principle”: Griffith experiment with S & R strains of
Pneumococcus (fig. 16 – 2); infection with S (pathogenic): lethal, mice died; infection
with R (harmless): mice lived; infection with killed S: harmless, mice lived; infection
with R + killed S - proved lethal; something from killed S rendered R infective (live
S cells were found in blood of dead mouse)
• DNA was confirmed as genetic material in virus infection experiment
(Hershey & Chase); 35S-labeled protein & 32P-labeled DNA study (fig. 16 – 4)
Double Helix & Template Theory:
• DNA structure elucidated by Watson & Crick (modeled X-ray diffraction
data of Wilkins & Franklin) (fig. 16-5, 16 – 6, 16-7)
• Chargaff showed species-specific differences in DNA base content; A = T, C
= G (Chargaff’s rules)
• two antiparallel polynucleotide strands arranged in double helix, Hbonded by complementary base pairing (A - T; C - G) (figs 16 – 5 , 16 – 7 & 16 – 8);
this model explained Chargaff’s rules
• each strand = template for its complementary strand
DNA replication
Replication of DNA (template copy mechanism):
• semiconservative replication (figs. 16 – 9 & 16 – 10)); 14N15N DNA study
(Meselson & Stahl) (fig. 16 – 11)
• mechanisms: replication origins - base sequences recognized by enzymes
which open double strand replication bubbles (replication forks at each end) (fig. 16
– 12) opened up by combined action of helicase & single strand binding proteins
(fig. 16 – 13)
• DNA polymerases add nucleotides in 5’ to 3’ direction (fig. 16 – 14);
antiparallel strands result in continuous synthesis (leading strand) on one template
(fig. 16 – 15) & discontinuous synthesis (lagging strand) on complementary template
(Okazaki fragments joined by DNA ligase) (fig. 16 – 16)
• primer RNA laid down by primase (figs 16 – 15 to 16 – 17)
• errors corrected by repair enzymes (fig. 16 – 18)
Chapter 17
GENE EXPRESSION From gene to protein:
A.TRANSCRIPTION
Genes and Proteins:
• Gene expression: the link between genotype and phenotype involves
enzymes; enzymes (proteins) are determined by the cell’s genetic information in the
nucleus; the implementation of the information involves processes of transcription
& translation
• Evidence that genes code for enzymes:
- Beadle & Tatum conducted metabolic investigations in mold (Neurospora)
- identified nutrient-dependent mutants through growth on minimal
medium + selected nutrients, e.g. arginine-requiring mutants included three classes
of mutant: orn-, cit- & arg-(fig. 17 – 2)
-concluded each enzyme in the metabolic pathway for arginine synthesis
was determined by a separate gene; articulated one gene - one enzyme (now one
gene - one polypeptide) concept
2.
Importance of mRNA:
• DNA is mostly nuclear; protein synthesis is cytoplasmic; RNA content of a
cell correlates with level of protein synthesis; conclusion: RNA is liaison between
nuclear DNA and site of protein synthesis (fig. 17 - 3)
- radioactive tracer studies: RNA synthesized in nucleus moves to
cytoplasm (genetic messenger, a working copy of gene) (fig. 17 – 4)
3.
Transcription: (production of mRNA, rRNA, tRNA)
• RNA polynucleotide: mostly single-stranded, ribose replaces deoxyribose;
uracil substitutes for thymine (fig. 5 - 27)
• promoter: DNA base sequence binds RNA polymerase (+ other
transcription factors in eukaryotes)
- start signal: base sequence near promoter activates RNA polymerase II
to produce RNA single strand (5’-->3’ direction) (figs. 17 – 7 & 17 – 8); RNA
synthesis by template copy mechanism
- termination: special sequence in DNA produces termination sequence in
RNA transcript that causes RNA polymerase & transcript to break away from DNA
• eukaryotic transcription: primary transcript includes intervening sequences
(introns) separating expressed sequences (exons)
• post-transcription processing:
- introns excised in nucleus; small nuclear ribonucleoproteins (snRNPs -”snurps”) collaborate with other proteins in a spliceosome to facilitate excision &
splicing process (figs. 17 – 10 & 17 – 11)
- special fragments added to protect ends of mRNA (5’ cap & poly-A tail)
(fig. 17 – 9)
B. TRANSLATION (protein synthesis)
1.
Translation: (fig. 17 – 13)
• codon: triplet mRNA base sequence coding for 1 amino acid in a protein
(fig. 17 – 4)
• genetic code: 64 triplet (codons) code for 20 amino acids; nearly universal
(fig. 17 – 5) one start codon, 3 stop codons. Codons show redundancy (Fig.17-5)
• ribosomes: rRNAs & proteins: small & large subunits; feature P (peptidyl) ,
A (amino acyl) and E (exit) sites on large subunit (fig. 17 – 17)
- proteins for secretion synthesized on rough ER, passed into cisterna
• transfer RNA (fig. 17 – 15): self-complementary double-stranded regions
separating open loops (including anticodon loop); has specific amino acid binding
site
- anticodon = complement of codon for amino acid bound by stem
- binding of amino acid produces aminoacyl tRNA (catalyzed by
aminoacyl tRNA synthetase) (fig. 17 - 16)
• mechanism of translation:
Initiation
mRNA, initiator tRNA, and small ribosomal subunit combined by initiation
factors; large subunit joins these to form initiation complex (fig. 17 – 18)
Elongation cycle:
1. codon recognition (A site)
2. Peptide bond formation (between the amino group of the new amino acid in the
A site and the at the Carboxyl end of the growing chain in the P site) catalyzed by
large subunit rRNA (ribozyme). The polypeptide from the tRNA at the P site is
removed and is then attached to the tRNA at the A site. - (fig. 17 – 19)
direction (mRNA 5’ to 3’) codon by codon
(These processes require GTP anda group of elongation factors)
3. Translocation : the ribosome and the mRNA move relative to each other in one
direction (5’ to 3’) codon by codon and the elongation cycle is repeated for each
codon until the stop codon reaches the A site..will cause termination
Termination Stop codon at theA site signals release factor that causes the release
of new polypeptide chain & disassembly of ribosome – mRNA – tRNA complex
(fig. 17 – 20)
• polyribosomes: mRNA with several ribosomes concurrently translating the
codons; found in prokaryotes and eukaryotes (fig. 17 - 21)
The signal mechanism for targeting proteins to theER (Fig. 17-22).
Signal peptide (around 20 a.a at the beginning of the polyperptide, recognition and
binding of signal peptide to Signal recognition particle SRP in cytosol. The SRP
ribosome complex binds to SRP receptor protein found at the ER membrane.
Chapter 18
CONTROL OF GENE EXPRESSION
Regulation of transcription of genes
Operon Model:
• regulatory genes control transcription of operon (promoter sequence,
operator sequence, series of structural genes related to metabolic pathway);
regulatory genes code for repressor protein (binds to operator, blocking
transcription)
- trp operon: structural genes code for enzymes of tryptophan production;
presence of tryptophan (corepressor) activates repressor, preventing formation of
enzymes (fig. 18 – 3)
- lac operon: structural genes code for enzymes of lactose catabolism;
presence of allolactose (inducer, formed from lactose) deactivates repressor,
preventing blockage of enzyme formation (fig. 18 – 4)
- CAP (catabolite activator protein) binds at upstream end of promoter
site to facilitate RNA polymerase binding transcription of unrepressed lac operon;
CAP activated by cyclic AMP which accumulates when glucose is scarce (fig. 18 – 5)
Chapter 19
Viruses
• discovered as infectious agents that require access to a host cell to
reproduce; consist of genome (DNA or RNA) enclosed in protein coat (capsid);
some include a viral envelope (membrane derived from a host cell) (fig. 19 – 3)
- reproduction – various strategies for entry into host; viral genome
redirects host cell’s metabolic machinery (enzymes) to produce new viral
components that assemble into thousands of new viruses (fig. 19 – 4); host cell may
or may not be destroyed, but is metabolically debilitated
• viruses that infect bacteria – bacteriophages; 2 types of infective cycle
a. virulent bacteriophages:
lytic cycle (fig. 19 – 5); replication of viral genome, synthesis of new
virus, lysis of host cell, e.g. T-even bacteriophages
b. temperate bacteriophages:
lysogenic cycle (fig. 19 – 6); replication of viral genome, integration of
phage DNA (prophage) into host genome; replicated along with
bacterial genome for many generations; triggering mechanism
subsequently initiates synthesis of new phage & lysis of host cell
(reversion to lytic cycle); e.g.  bacteriophages; many bacteria with
incorporated prophage exhibit increased pathogenicity
• some animal viruses possess viral envelope (enveloped viruses); budding process
rather than lysis of host cell disperses new viruses
- RNA viruses , RNA genome (acts as mRNA) to direct synthesis of viral
protein, including membrane proteins (envelope proteins) (fig. 19 – 7)
- retroviruses e.g HIV (AIDS) virus possess RNA chromosome & reverse
transcriptase; infection leads to production of DNA (from RNA) to yield DNA-RNA
hybrid; single DNA copied to produce double-stranded DNA that is integrated into
host genome (provirus) (fig. 19 – 8). The provirus transcripes the viral genome and
the viral mRNA.
Other infective agents:
• viroids - infective circular RNA molecules (infect plants)
• prions - infectious proteins thought to be abnormally folded versions of
normal brain proteins; capable of inducing abnormal folding on large #s of native
proteins; e. g., mad cow disease (fig. 19 – 11)