BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006
-
Upload
portia-suarez -
Category
Documents
-
view
31 -
download
0
description
Transcript of BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006
![Page 1: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/1.jpg)
BIOL 200 (Section 921)Lecture # 4-5, June 22/23, 2006
• UNIT 4: BIOLOGICAL INFORMATION FLOW - from DNA (gene) to RNA to protein
• Reading: ECB (2nd Ed.) Chap 7, pp. 229-262; Chap 8, pp. 267-286 (focus only on parts covered in lecture). Related questions 7-8, 7-9, 7-11, 7-12, 7-14, 7-16, 7-17, 8-5a,b,d; orECB (1st ed.) Chap 7, pp. 211-240; 263-4; Chap 8, pp. 257-270 (focus only on parts covered in lecture). Related questions 7-9, 7-10, 7-12, 7-13, 7-15, 7-18, 7-19; 8-7b,c,e.
![Page 2: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/2.jpg)
Lecture # 4,5: Learning objectives
• Understand the structural differences between DNA and RNA, and the directionality of transcription.
• Understand the structure of a eukaryotic gene. • Describe the general mechanism of transcription, including
binding, initiation, elongation and termination. Discuss factors regulating transcription.
• Describe processing for all three types of RNA, and discuss why it must occur.
• Describe the structural features of ribosomes.• Describe the genetic code and how it is related to the
mechanisms of transcription and translation. • Describe the coupling of tRNA and discuss the specificity of
amino acid tRNA synthetases.• Describe the general mechanism of translation including
binding, initiation, elongation and termination.
![Page 3: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/3.jpg)
Transcription-same language (nuc. to nuc.)
Translation-different languages (nuc. to protein)
Genetic information flow [Fig. 7-1]
![Page 4: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/4.jpg)
Eucaryotic vs. Procaryotic Biol. Info Flow [Fig. 7-20]
![Page 5: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/5.jpg)
DNA vs. RNA: Differences in chemistry [Fig. 7-3]
![Page 6: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/6.jpg)
DNA vs RNA (Lehninger et al. Biochemistry)
![Page 7: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/7.jpg)
DNA vs. RNA: Intramolecular base pairs in RNA [Fig. 7.5] and Intermolecular base pairs in DNA [Fig.
5-7] assist their folding into a 3D structure
RNA DNA
![Page 8: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/8.jpg)
![Page 9: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/9.jpg)
Fig. 7-12, p. 219Procaryotic vs. eucaryotic transcription [Fig. 7-12]
![Page 10: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/10.jpg)
In procaryotes, clusters of genes called operons can be carried by one mRNA [Fig. 8-6]
![Page 11: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/11.jpg)
Fig. 7-9:Parts of a gene [Fig. 7-9]
Promoter sequence
Transcription start site
terminator
DNA template
![Page 12: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/12.jpg)
Transcription factor binding to DNA [Fig. 8-4]
What types of bonds can you identify between this DNA and protein?
![Page 13: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/13.jpg)
Eukaryotic transcription factors promote RNA Polymerase II binding [Equiv. Fig. 8-10, 2nd Ed.]
![Page 14: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/14.jpg)
![Page 15: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/15.jpg)
Directions of transcription along a short portion of bacterial chromosome [Fig. 7-10, p. 218]
3’
3’
5’
5’
DNA always read 3’ to 5’!
RNA always made 5’ to 3’!
![Page 16: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/16.jpg)
RNA Polymerase: (1) Unwinds and rewinds DNA;(2) Moves along the DNA one nucleotide at a time; (3) Catalyzes The formation of phosphodiester bonds from the energy in the Phosphate bonds of ATP, CTR, GTP and UTP.
![Page 17: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/17.jpg)
Transcription by RNA polymerase in E. coli [Lehninger et al. Principles of Biochemistry]
![Page 18: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/18.jpg)
![Page 19: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/19.jpg)
Fig. 7-37
introns exons
preRNA
5’ cap
polyA tailsplicing
mature mRNA
DNA in nucleus
![Page 20: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/20.jpg)
Fig. 7-12: mRNAs in eukaryotes are processed
Prokaryote
mRNA
5’ cap3’ tail
Eukaryote
mRNA
![Page 21: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/21.jpg)
Fig 7-12B
5’ cap
Functions:- Increased stability- Facilitate transport- mRNA identity
![Page 22: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/22.jpg)
Bacterial vs. Eukaryotic genes [Fig. 7-13]
![Page 23: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/23.jpg)
RNA splicing removes introns [Fig. 7-15]
RNA splicing: (1) done by small nuclear ribonuclear protein molecules [snRNPs, called as SNURPs] and other proteins [together called SPLICEOSOME], (2) Specific nucleotide sequences are recognized at each end of the intron
![Page 24: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/24.jpg)
Fig. 7-17
RNA Splicing by SnRNP+proteins=spliceosome
exon1
intron
5’splice site snRNP 3’ splice site
lariat formation
![Page 25: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/25.jpg)
Fig. 7-17
RNA Splicing
Spliceosome
Lariat=loop of intron
Exons joined
Mature mRNAexons joined together-introns removed
![Page 26: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/26.jpg)
Removal of intron in the form of a lariat [Fig. 7-16]
![Page 27: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/27.jpg)
Detailed mechanism of RNA splicing [Fig. 7-17]
![Page 28: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/28.jpg)
Is RNA splicing biologically important or a wasteful process?
• Pre-mRNA can be spliced in different ways (alternate RNA splicing), thereby generating several different mRNAs which code for several different proteins [e.g. approx. 30,000 human genes can produce mRNAs coding for more than 100,000 proteins]
• Introns quickens the evolution of new and biologically important proteins e.g. three exons of the β-globin gene code for different structural and functional regions (domains) of the polypeptide
![Page 29: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/29.jpg)
Alternative splicing can produce different proteins from the same gene [Fig. 7-18]
![Page 30: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/30.jpg)
Becker et al. The World of the Cell
![Page 31: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/31.jpg)
Transcription of two genes seen be EM [Fig. 7-8]
![Page 32: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/32.jpg)
Becker et al. The World of the Cell
![Page 33: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/33.jpg)
Biological information flow in procaryotes and eukaryotes [Fig. 7-20]
![Page 34: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/34.jpg)
Specialized RNA binding proteins (e.g. nuclear transport receptor) facilitate export of mature mRNA
from nucleus to the cytoplasm [Fig. 7-19]
![Page 35: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/35.jpg)
rRNA processing [Fig. 6-42 in Big Alberts]
45S transcript
18S 5.8S 28S
5S made elsewhereSmall
ribosomal subunit
Large ribosomal subunit
![Page 36: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/36.jpg)
Processing of transfer RNA (tRNA) [Becker et al. The World of the Cell]
![Page 37: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/37.jpg)
From RNA to Protein: translation of the information
• Translation: conversion of language of 4 nucleotides in mRNA into language of 20 amino acids in polypeptide
• Genetic code: a set of rules (triplet code) which govern translation of the nucleotide sequence in mRNA into the amino acid sequence of a polypeptide
• Codon: a group of three consecutive nucleotides in RNA which specifies one amino acid (e.g. ‘UGG’ specifies Trp and ‘AUG’ specifies Met)
![Page 38: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/38.jpg)
Genetic code - triplet, universal, redundant and arbitrary [Fig. 7-21]
mRNA codons
Corresponding amino acid that will be attached onto tRNA
![Page 39: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/39.jpg)
![Page 40: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/40.jpg)
mRNA can be translated in three possible reading frames
![Page 41: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/41.jpg)
“START” and “STOP” codons on mRNA are essential for proper mRNA translation
[Becker et al. The World of the Cell, Fig. 22-6]
![Page 42: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/42.jpg)
Genetic code problem:
5’ AGUCUAGGCACUGA 3’For the RNA sequence above, indicate the amino acids that are encoded by the three possible reading frames.
If you were told that this segment of RNA was close to the3’ end of an mRNA that encoded a large protein, would you know which reading frame was used?
![Page 43: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/43.jpg)
Frame 1-AGU CUA GGC ACU GAFrame 2-A GUC UAG GCA CUG AFrame 3-AG UCU AGG CAC UGA
Frame 1-Ser – Leu – Gly - Thr
![Page 44: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/44.jpg)
What are the main players involved in the process of translation
1. Ribosomes [“protein synthesis machines”]: carry out the process of polypeptide synthesis
2. tRNA [“adaptors”]: : align amino acids in the correct order along the mRNA template
3. Aminoacyl-tRNA synthetases: attach amino acids to their appropriate tRNA molecules
4. mRNA: encode the amino acid sequence for the polypeptide being synthesized
5. Protein factors: facilitate several steps in the translation
6. Amino acids: required as precursors of the polypeptide being synthesized
![Page 45: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/45.jpg)
Fig. 7-28
Eukaryotes
Large=60S
Small=40S
Prokaryotes
Large=50S
Small=30S
Ribosome Assembly
![Page 46: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/46.jpg)
Centrifugation-separates organelles and macromolecules (panel 5-4)
Fixed angle Swinging bucket
Heavy particles move to pellet, e.g. nucleus
![Page 47: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/47.jpg)
Svedberg unit, S, shows how fast a particle sediments when subject to centrifugal force.
From Becker, World of the Cell, p. 327
![Page 48: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/48.jpg)
Fig. 7-23: tRNA structureOld ‘cloverleaf’ model 3-D L-shaped
modelAmino acid attachment
anticodon
H-bonds between complementary bases
![Page 49: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/49.jpg)
Aminoacyl tRNA synthase charge-links tRNA with amino acids [Fig 7-26]
HighEnergyEster bond
![Page 50: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/50.jpg)
Fig. 7-26, part 2
tRNA anticodon
binds mRNA codon
![Page 51: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/51.jpg)
Fig. 7-28
18S
small subunit
28S5.8S5S
large subunit
Ribosomes made of rRNA and protein
Come together during translation
![Page 52: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/52.jpg)
Ribosomes are protein synthesis factories [Fig. 7-29]
![Page 53: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/53.jpg)
Ribosomes can be free in the cytosol or attached to the ER membranes
![Page 54: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/54.jpg)
Fig. 7-35: polyribosomes or polysomes
![Page 55: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/55.jpg)
Fig. 7-32: Initiation of translation
Start codon
Large subunit binds
Initiator rRNA-Met
+small subunit
![Page 56: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/56.jpg)
Fig. 7-32: translation
Aminoacyl-tRNA binds to A site
Initiator tRNA in P site
Peptide bond forms
Ribosome shift: one codon
tRNA1 moves from P site to E site; tRNA2 moves from A site to P site
![Page 57: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/57.jpg)
Fig. 7-30:
Elongation of polypeptide
Bind
Bond
Shift
Bind: aminoacyl-tRNA anticodon to mRNA codon
Bond: make peptide bond
Shift: move ribosome along mRNA, move tRNAs
![Page 58: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/58.jpg)
Fig. 7-34: termination Stop codon at A site
![Page 59: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/59.jpg)
Fig. 7-34:termination
stop codon at A site
Release C terminal from tRNA+shift
Release ribosome from mRNA
Release factor binds
![Page 60: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/60.jpg)
Protein destruction• Proteolysis: digestion of proteins by
hydrolyzing peptide bonds• Proteases: enzymes that digest proteins• Many proteases aggregate to form a
proteasome in eukaryotes• Proteins are tagged for destruction by a
molecule called ubiquitin• Several proteins are also degraded in
lysosomes in eukaryotes
![Page 61: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/61.jpg)
Proteasome-mediated degradation of short-lived and unwanted proteins [Fig. 7-36]
![Page 62: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/62.jpg)
Mechanism of ubiquitin-dependentprotein degradation [Becker et al. The World of the Cell, Fig. 23-38]
![Page 63: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/63.jpg)
SUMMARY1. Transcription2. RNA processing3. Translation4. Protein destruction
![Page 64: BIOL 200 (Section 921) Lecture # 4-5, June 22/23, 2006](https://reader034.fdocuments.us/reader034/viewer/2022052703/56813592550346895d9d0246/html5/thumbnails/64.jpg)
1. Where are Polymerases?2. Where are transcription start/stop sites?3. Where are the 3’ and 5’ ends of the transcript?4. Which direction are the RNA polymerases moving?5. Why are the RNA transcripts so much shorter than the length
of the DNA that encodes them?
Transcription of two genes seen be EM [Fig. 7-8]