Part 418-1 Child Day Care Centers 418-1.1 Definitions, Enforcement ...
Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.
-
Upload
estella-cecilia-owens -
Category
Documents
-
view
213 -
download
0
Transcript of Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.
![Page 1: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/1.jpg)
Biochemistry I(CHE 418 / 5418)
Reading Assignment
Berg et. al (2007) Chapter 30
![Page 2: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/2.jpg)
Central Dogma of Molecular Biology
Replication
DNA RNA Protein mRNA. tRNA, rRNA • Replication - DNA directed DNA synthesis• Transcription - DNA directed RNA synthesis
•Translation - RNA directed Protein synthesis
Transcription Translation
![Page 3: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/3.jpg)
TranslationRNA directed protein synthesis
– Four letters of nucleic acid language translated into 20 amino acids of protein language.• mRNA, tRNA, ribosome (rRNA)• Occurs on ribosome.
•Protein synthesized in N (amino) to C (carboxyl) direction•mRNA read from 5’ to 3’
NN N
N
5’ 3’
![Page 4: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/4.jpg)
InitiationRibosome binds mRNA identifies start codon (AUG). * Met in Eukaryotes * fMet N-formylmethionine in prokaryotes
ElongationProtein synthesized N to C
TerminationPolypeptide releasedupon encountering stop codons (UAA, UAG, UGA)
Translation Divided into 3 Stages
![Page 5: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/5.jpg)
During Translation Ribosome binds:
• mRNA– Contains codon – three nucleotide sequence encoding one amino acid.
• tRNAs (three sites)– Contains Anticodon – three nucleotide sequence complementary to codon.
• Codon and Anticodon interact by hydrogen bonding between complementary bases.
![Page 6: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/6.jpg)
Ribosome contains three tRNA binding sites
• E – Exit– Uncharged tRNA leaves ribosome.
• P – Peptidyl– tRNA in this site has protein covalently attached.
• A – Aminoacyl– Charged tRNA enters. H-bonding established between codon (mRNA) and anticodon of (tRNA).
Sites include regions of large and small subunits of ribosome.
![Page 7: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/7.jpg)
Reaction to Add Amino Acids
• Amino acids are added to the C terminus by transferring existing chain to next amino acid.
![Page 8: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/8.jpg)
Polysome (Polyribosome)
• Polysome -multiple ribosomes bond to the same mRNA.– Each ribosome in a polysome is synthesizing the same protein.
• In Prokayotes, transcription and translation may be coupled, since both are occurring in the same compartment at the same time.
![Page 9: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/9.jpg)
tRNA carry amino acids• Amino acid (C terminus) attached via an ester to 2’or 3’ hydroxyl of A of CCA on tRNA.
• “Charged tRNA” – tRNA with correct amino acid attached.
• Aminoacyl tRNA synthetases – class of enzymes that attach amino acids to tRNA.
![Page 10: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/10.jpg)
Aminoacyl tRNA synthetases
• Enzyme that attaches correct amino acid to CCA of tRNA with high fidelity. (>10-4).
• Binds Activation site and anticodon.
• Two classes– Class I– Class II
![Page 11: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/11.jpg)
Two Classes of Aminoacyl
tRNA synthetase
s
• Two classes differ in:– Sequence alignment / comparison.• 10 tRNA per class.
– Binding to tRNA on different “face” or side
– Attaching amino acid to different hydroxyl• Class 1 to 2’ OH• Class 2 to 3 ‘ OH
– Binding ATP in different comformation
– Subunit comformation• Class 1 are monomers• Class II are dimers
![Page 12: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/12.jpg)
Aminoacyl tRNA synthetases reaction
• Two step reaction– 1. AA + ATP ↔ Aminoacyl-AMP + PPi • Amino acid attached to AMP via mixed anhydride which conserves the energy of phosphodieaster bond in ATP.
• Acyl adenylate
– 2. Amino acid transferred to tRNA. • Ester linkage to 2’ or 3’ hydroxyl of A of CCA on 3’ end of tRNA.
![Page 13: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/13.jpg)
Threonyl-tRNA synthetase
An example of Fidelity• How does Threonyl-tRNA synthetase select between similarly shaped amino acids?
• Thr has almost the same shape as Ser and Val.– 1. Active site selection
– 2. Editing site
![Page 14: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/14.jpg)
Threonyl-tRNA synthetase
An example of Fidelity (Cont’)• 1. Active site
selection by selective binding of substrate.– Zn 2+
• Coordinated to enzyme by 2 his and 1 cys residues
• Binds Thr by amino group and OH of side chain
– Asp of enzyme• Binds OH of thr substrate.
• This interaction prohibits attachment of Val.
![Page 15: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/15.jpg)
Threonyl-tRNA synthetase
An example of Fidelity (Cont’)• 2. Editing site
– Removes Mischarged amino acids (Ser).
• CCA with amino acid attached swings into editing site. Product does not dissociate before editing.
• Increasing fidelity to > 10-4
NOT ALL Aminoacyl tRNA synthetases require editing.
![Page 16: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/16.jpg)
Codon hydrogen bonds to Anticodon
• Codon of mRNA and Anticodon of tRNA are antiparellel.
![Page 17: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/17.jpg)
Wobble• Third base of anticodon (5’ end) allows binding with multiple bases.
![Page 18: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/18.jpg)
Codon Usage Table
• mRNA are “read” three nucleotides (codon) at a time starting from a fixed point.
![Page 19: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/19.jpg)
The Genetic code is unambiguous, degenerate, non-overlapping and universal
• Unambiguous– A given codon either designates a single amino acid or is a stop codon.
• Degenerate– more than one codon can specify the same amino acid, so the genetic code is said to be degenerate.
• Non-overlapping– the code is read sequentially, one codon after another without spacer bases, from a fixed starting point.
• Universal
![Page 20: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/20.jpg)
Initiation (Prokaryotic)
• Prokaryotic start codon = AUG.– Others exist (rare)
• GUG = Val• UUG = Leu
• AUG encodes fMET• Two important interactions – 1. Binding of mRNA to 3’ end of 16S rRNA.
– 2. H bonding of initiator codon with anticodon.
• tRNAf binds to P site of ribosome.
![Page 21: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/21.jpg)
Elongation (Prokaryotic)
• P site is occupied by tRNA holding fMet, or later the growing polypeptide
• Elongation factors bring the correct charged tRNA to the A site. – EF-Tu – brings charged tRNA to A site of ribosome. Requires bond GTP (hydrolyzed to GDP during reaction). GTP binds to p-loop.
– EF-Ts – removes GDP from EF-Tu and replaces with GTP
• The 23 S rRNA of the ribosome catalyzes the attachment of amino acids.
• Translocation is accelerated by EF-G.
![Page 22: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/22.jpg)
Elongation (Prokaryotic)
![Page 23: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/23.jpg)
Termination (Prokaryotic)
• Termination aided by RF = release factors.
![Page 24: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/24.jpg)
Castor Oil• What is Castor Oil?
– Thick, yellowish or almost colorless oil extracted from castor bean (seed).
• Uses of Castor Oil– Laxative– Lubricating oil– Quick-drying oil (when dehydrated)
– used in paints and varnishes.– Competes with linseed and tung oil
– Coating fabrics /protective coverings
– Sebacic acid - basic ingredient in the production of nylon 6, 10 and other synthetic resins / fibers
![Page 25: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/25.jpg)
Castor Bean
• Ricinus communis– (family Euphorbiaceae)
• Source of Castor Oil
http://www.ansci.cornell.edu/plants/alphalist.html
http://waynesword.palomar.edu/plmar99.htm#flow
![Page 26: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/26.jpg)
Synthesis of Nylon 6, 10
– Condensation Polymerization – Sebacic acid + 1, 6-hexanediamine– Sebacic acid
– 10-carbon dicarboxylic acid – carboxylic group (COOH) at each end of the molecule
– 1,6-hexanediamine– 6-carbon molecule with an amino group (C-NH2) at each end.
– Free carboxylic acid of Sebacic Acid reacts with amino group of 1, 6-hexamediamine – water molecule is produced at each link.
![Page 27: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/27.jpg)
What is Ricin?• Protein (64 kda) found in pulp from production of castor oil.– Heterodimer
• A chain– 267 amino acid residues.
– Inhibits protein synthesis.
• B-chain– 262 amino acid residues.
– facilitates transport into cell.
• Connected by disulfide bridge.
![Page 28: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/28.jpg)
Mode of Action of Ricin
• A chain– N-glycosidase which removes specific adenine (depurinates) 28 S ribosomal RNA• A-4323 in rat liver
– prevents the binding of an elongation factor, leaving the ribosome incapable of protein synthesis.
– Extremely toxic• 70 micrograms (equivalent to weight of grain of salt) will kill a 160 pound man.– Merck Index: An Encyclopedia of Chemicals, Drugs, and Biologicals (1997)
![Page 29: Biochemistry I (CHE 418 / 5418 ) Reading Assignment Berg et. al (2007) Chapter 30.](https://reader036.fdocuments.us/reader036/viewer/2022070415/56649ef45503460f94c07584/html5/thumbnails/29.jpg)
Many Antibiotics and Toxins Inhibit Translation