Advanced Topics in RNA and DNA. DNA Microarrays Aptamers

Size: px
Start display at page:

Download "Advanced Topics in RNA and DNA. DNA Microarrays Aptamers"

Transcription

1 Quiz 1

2 Advanced Topics in RNA and DNA DNA Microarrays Aptamers 2

3 Quantifying mrna levels to asses protein expression 3

4 The DNA Microarray Experiment 4

5 Application of DNA Microarrays 5

6 Some applications of microarrays Identification of tumor markers Distinguish between clinically distinct subgroups of leukemia, lymphoma, breast cancer, and melanoma Alterations in gene expression in response to therapeutics to identify genes involved in sensitivity and resistance 6

7 Aptamers DNA, RNA, or protein that bind a specific target Can be engineered or natural occurring Riboswitches are naturally occuring aptamers that regulate gene expression 7

8 8

9 How do RNA aptamers work? Ligand induces conformational change allowing translation Ligand induces conformational change inhibiting translation 9

10 Structures of RNA aptamers Flavin Mononucleotide FMN 10

11 FMN aptamer binding site 11

12 The Genetic Code All the codons have meaning: 61 specify amino acids, and the other 3 are "nonsense" or "stop" codons The code is unambiguous - only one amino acid is indicated by each of the 61 codons The code is degenerate - except for Trp and Met, each amino acid is coded by two or more codons Codons representing the same or similar amino acids are similar in sequence 2nd base pyrimidine: usually nonpolar amino acid 2nd base purine: usually polar or charged aa 12

13 Biochemists Break the Code Assignment of "codons" to their respective amino acids was achieved by in vitro biochemistry Marshall Nirenberg and Heinrich Matthaei showed that poly-u produced polyphenylalanine in a cellfree solution from E. coli Poly-A gave polylysine Poly-C gave polyproline Poly-G gave polyglycine But what of others? 13

14 The Nirenberg Experiment deciphering the genetic code Ribosome-free cell extract with radiolabeled single amino acid Ribosomes alone Ribosome-free cell extract with radiolabeled single amino acid Ribosomes Trinucleotide 14

15 The Genetic Code is Nearly Universal Codon Standard code Mitochondrial code UGA Stop Trp UGG Trp Trp AUA Ile Met AUG Met Met AGA Arg Stop AGG Arg Stop 15

16 trna The trna molecules translate the mrna codon to a protein sequence There is a trna for each amino acid trna synthetase (one for each amino acid) load the amino acid onto the trna 16

17 How does each trna syntetase recognize which Amino acid to load each trna with? trna synthetase recognition elements Single letter amino acid code U70 G3 17

18 Structure of trna synthetase/trna complexes Threonyl-tRNA synthetase/trna Thr Glutaminyl-tRNA synthetase/trna Gln 18

19 trna synthetase classes Feature Class I enzymes Class II enzymes Structure of the enzyme active site Parallel β-sheet Antiparallel β-sheet Interaction with the trna Minor groove of the acceptor stem Major groove of the acceptor stem Orientation of the bound trna Amino acid attachment Enzymes for * V loop faces away from the enzyme To the 2 -OH of the terminal nucleotide of the trna Arg, Cys, Gln, Glu, Ile, Leu, Lys1, Met, Trp, Tyr, Val V loop faces the enzyme To the 3 -OH of the terminal nucleotide of the trna Ala, Asn, Asp, Gly, His, LysII, Phe, Pro, Thr, Ser 19

20 Aminoacyl-tRNA synthetase reaction 20

21 Ribosomes 21

22 Getting oriented with the ribosome 22

23 Protein synthesis Initiation Binding of mrna by small ribosomal subunit at the mrna ribosomal binding site (a purine rich sequence) Association of initiator trna to the first codon Association of the large ribosomal subunit Elongation Synthesis of all peptide binds by successive association of the appropriate (dictated by the codons) trna molecules Termination At the stop codon, releasing factor 1 and 2 along with GTP bind, the peptide chain is released from the trna at the P site, the trna is moved to the E site and the ribosome dissociates 23

24 Initiation Initiator trna (fmet-trna) recognizes start (AUG) codon and is unique because the N-terminal is formylated Initiation requires initiation factors (IFs) that assemble the ribosomal initiation complex IF-2 is a GTPase that delivers the fmettrna to the ribosome P site 24

25 Mechanism of Protein Synthesis Peptidyl transferase 25

26 Peptidyl transferase Mechanism is not thought to be catalyzed by acid-base chemistry (reaction ph independent) Catalyzed by several other mechanisms Proximity Proton shuttle 26

27 Protein synthesis overview A bit more detail Elongation requires GTPases EF-Tu loads the aminoacyl-trna into position A EF-G pushes the trna in position A into position P and the trna in position P to E 27

28 Termination RF-1 and RF-2 Binding of RF1/RF2/GTP complex triggers Cleavage of the polypeptide chain from the trna and then the dissociation of the ribosome complex 28

29 tmrna Bacterial 29

30 Eukaryotic and Prokaryotic Protein Synthesis Differences 1. Ribosomes. Eukaryotic ribosomes are larger. (Slide 29 lecture 4) 2. Initiator trna. In eukaryotes, the initiating amino acid is methionine rather than N-formylmethionine. However, as in prokaryotes, a special trna participates in initiation. 3. Initiation. The initiating codon in eukaryotes is always AUG. Eukaryotes, in contrast with prokaryotes, do not use a specific purine-rich sequence (RBS) on the 5 side to distinguish initiator AUGs from internal ones. Instead, the AUG nearest the 5 end of mrna is usually selected as the start site. A 40S ribosome attaches to the cap at the 5 end of eukaryotic mrna and searches for an AUG codon by moving step-by-step in the 3 direction. The 5 cap provides an easily recognizable starting point. 4. Elongation and termination. Eukaryotic elongation factors EF1α and EF1βγ are the counterparts of prokaryotic EF-Tu and EF-Ts. The GTP form of EF1α delivers aminoacyl-trna to the A site of the ribosome, and EF1βγ catalyzes the exchange of GTP for bound GDP. Eukaryotic EF2 mediates GTP-driven translocation in much the same way as does prokaryotic EF-G. Termination in eukaryotes is carried out by a single release factor, erf1, compared with two in prokaryotes. Finally, eif3, like its prokaryotic counterpart IF3, prevents the reassociation of ribosomal subunits in the absence of an initiation complex. 30

31 Eukaryotic Initiation Binding of 5 cap of mrna Ratchet search of AUG dependent on ATP Association of ribosome 31

32 Antibiotics inhibit protein synthesis Antibiotic Streptomycin and other aminoglycosides Tetracycline Chloramphenicol Cycloheximide Erythromycin Puromycin Action Inhibit initiation and cause misreading of mrna (prokaryotes) Binds to the 30S subunit and inhibits binding of aminoacyl-trnas (prokaryotes) Inhibits the peptidyl transferase activity of the 50S ribosomal subunit (prokaryotes) Inhibits the peptidyl transferase activity of the 60S ribosomal subunit (eukaryotes) Binds to the 50S subunit and inhibits translocation (prokaryotes) Causes premature chain termination by acting as an analog of aminoacyltrna (prokaryotes and eukaryotes) 32

BCH 4054 Spring 2001 Chapter 33 Lecture Notes

BCH 4054 Spring 2001 Chapter 33 Lecture Notes BCH 4054 Spring 2001 Chapter 33 Lecture Notes Slide 1 The chapter covers degradation of proteins as well. We will not have time to get into that subject. Chapter 33 Protein Synthesis Slide 2 Prokaryotic

More information

Gene Expression: Translation. transmission of information from mrna to proteins Chapter 5 slide 1

Gene Expression: Translation. transmission of information from mrna to proteins Chapter 5 slide 1 Gene Expression: Translation transmission of information from mrna to proteins 601 20000 Chapter 5 slide 1 Fig. 6.1 General structural formula for an amino acid Peter J. Russell, igenetics: Copyright Pearson

More information

Translation. Genetic code

Translation. Genetic code Translation Genetic code If genes are segments of DNA and if DNA is just a string of nucleotide pairs, then how does the sequence of nucleotide pairs dictate the sequence of amino acids in proteins? Simple

More information

9 The Process of Translation

9 The Process of Translation 9 The Process of Translation 9.1 Stages of Translation Process We are familiar with the genetic code, we can begin to study the mechanism by which amino acids are assembled into proteins. Because more

More information

CHAPTER4 Translation

CHAPTER4 Translation CHAPTER4 Translation 4.1 Outline of Translation 4.2 Genetic Code 4.3 trna and Anticodon 4.4 Ribosome 4.5 Protein Synthesis 4.6 Posttranslational Events 4.1 Outline of Translation From mrna to protein

More information

Protein synthesis II Biochemistry 302. Bob Kelm February 25, 2004

Protein synthesis II Biochemistry 302. Bob Kelm February 25, 2004 Protein synthesis II Biochemistry 302 Bob Kelm February 25, 2004 Two idealized views of the 70S ribosomal complex during translation 70S cavity Fig. 27.25 50S tunnel View with 30S subunit in front, 50S

More information

Translation. A ribosome, mrna, and trna.

Translation. A ribosome, mrna, and trna. Translation The basic processes of translation are conserved among prokaryotes and eukaryotes. Prokaryotic Translation A ribosome, mrna, and trna. In the initiation of translation in prokaryotes, the Shine-Dalgarno

More information

Molecular Biology (9)

Molecular Biology (9) Molecular Biology (9) Translation Mamoun Ahram, PhD Second semester, 2017-2018 1 Resources This lecture Cooper, Ch. 8 (297-319) 2 General information Protein synthesis involves interactions between three

More information

Lecture 9 Translation.

Lecture 9 Translation. 1 Translation Summary of important events in translation. 2 Translation Reactions involved in peptide bond formation. Lecture 9 3 Genetic code Three types of RNA molecules perform different but complementary

More information

Introduction to the Ribosome Overview of protein synthesis on the ribosome Prof. Anders Liljas

Introduction to the Ribosome Overview of protein synthesis on the ribosome Prof. Anders Liljas Introduction to the Ribosome Molecular Biophysics Lund University 1 A B C D E F G H I J Genome Protein aa1 aa2 aa3 aa4 aa5 aa6 aa7 aa10 aa9 aa8 aa11 aa12 aa13 a a 14 How is a polypeptide synthesized? 2

More information

GENETICS - CLUTCH CH.11 TRANSLATION.

GENETICS - CLUTCH CH.11 TRANSLATION. !! www.clutchprep.com CONCEPT: GENETIC CODE Nucleotides and amino acids are translated in a 1 to 1 method The triplet code states that three nucleotides codes for one amino acid - A codon is a term for

More information

ومن أحياها Translation 2. Translation 2. DONE BY :Nisreen Obeidat

ومن أحياها Translation 2. Translation 2. DONE BY :Nisreen Obeidat Translation 2 DONE BY :Nisreen Obeidat Page 0 Prokaryotes - Shine-Dalgarno Sequence (2:18) What we're seeing here are different portions of sequences of mrna of different promoters from different bacterial

More information

TRANSLATION: How to make proteins?

TRANSLATION: How to make proteins? TRANSLATION: How to make proteins? EUKARYOTIC mrna CBP80 NUCLEUS SPLICEOSOME 5 UTR INTRON 3 UTR m 7 GpppG AUG UAA 5 ss 3 ss CBP20 PABP2 AAAAAAAAAAAAA 50-200 nts CYTOPLASM eif3 EJC PABP1 5 UTR 3 UTR m 7

More information

-14. -Abdulrahman Al-Hanbali. -Shahd Alqudah. -Dr Ma mon Ahram. 1 P a g e

-14. -Abdulrahman Al-Hanbali. -Shahd Alqudah. -Dr Ma mon Ahram. 1 P a g e -14 -Abdulrahman Al-Hanbali -Shahd Alqudah -Dr Ma mon Ahram 1 P a g e In this lecture we will talk about the last stage in the synthesis of proteins from DNA which is translation. Translation is the process

More information

Lecture 25: Protein Synthesis Key learning goals: Be able to explain the main stuctural features of ribosomes, and know (roughly) how many DNA and

Lecture 25: Protein Synthesis Key learning goals: Be able to explain the main stuctural features of ribosomes, and know (roughly) how many DNA and Lecture 25: Protein Synthesis Key learning goals: Be able to explain the main stuctural features of ribosomes, and know (roughly) how many DNA and protein subunits they contain. Understand the main functions

More information

Section 7. Junaid Malek, M.D.

Section 7. Junaid Malek, M.D. Section 7 Junaid Malek, M.D. RNA Processing and Nomenclature For the purposes of this class, please do not refer to anything as mrna that has not been completely processed (spliced, capped, tailed) RNAs

More information

ومن أحياها Translation 1. Translation 1. DONE BY :Maen Faoury

ومن أحياها Translation 1. Translation 1. DONE BY :Maen Faoury Translation 1 DONE BY :Maen Faoury 0 1 ومن أحياها Translation 1 2 ومن أحياها Translation 1 In this lecture and the coming lectures you are going to see how the genetic information is transferred into proteins

More information

Protein synthesis I Biochemistry 302. February 17, 2006

Protein synthesis I Biochemistry 302. February 17, 2006 Protein synthesis I Biochemistry 302 February 17, 2006 Key features and components involved in protein biosynthesis High energy cost (essential metabolic activity of cell Consumes 90% of the chemical energy

More information

Laith AL-Mustafa. Protein synthesis. Nabil Bashir 10\28\ First

Laith AL-Mustafa. Protein synthesis. Nabil Bashir 10\28\ First Laith AL-Mustafa Protein synthesis Nabil Bashir 10\28\2015 http://1drv.ms/1gigdnv 01 First 0 Protein synthesis In previous lectures we started talking about DNA Replication (DNA synthesis) and we covered

More information

Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus:

Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus: m Eukaryotic mrna processing Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus: Cap structure a modified guanine base is added to the 5 end. Poly-A tail

More information

Chapter 19 Overview. Protein Synthesis. for amino acid. n Protein Synthesis genetic info encoded in nucleic acids translated into standard amino acids

Chapter 19 Overview. Protein Synthesis. for amino acid. n Protein Synthesis genetic info encoded in nucleic acids translated into standard amino acids Chapter 19 Overview Protein Synthesis n Protein Synthesis genetic info encoded in nucleic acids translated into standard amino acids n Genetic code dictionary defining meaning for base sequence n Codon

More information

Information Content in Genetics:

Information Content in Genetics: Information Content in Genetics: DNA, RNA and protein mrna translation into protein (protein synthesis) Francis Crick, 1958 [Crick, F. H. C. in Symp. Soc. Exp. Biol., The Biological Replication of Macromolecules,

More information

Translation and the Genetic Code

Translation and the Genetic Code Chapter 11. Translation and the Genetic Code 1. Protein Structure 2. Components required for Protein Synthesis 3. Properties of the Genetic Code: An Overview 4. A Degenerate and Ordered Code 1 Sickle-Cell

More information

Reading Assignments. A. Genes and the Synthesis of Polypeptides. Lecture Series 7 From DNA to Protein: Genotype to Phenotype

Reading Assignments. A. Genes and the Synthesis of Polypeptides. Lecture Series 7 From DNA to Protein: Genotype to Phenotype Lecture Series 7 From DNA to Protein: Genotype to Phenotype Reading Assignments Read Chapter 7 From DNA to Protein A. Genes and the Synthesis of Polypeptides Genes are made up of DNA and are expressed

More information

Degeneracy. Two types of degeneracy:

Degeneracy. Two types of degeneracy: Degeneracy The occurrence of more than one codon for an amino acid (AA). Most differ in only the 3 rd (3 ) base, with the 1 st and 2 nd being most important for distinguishing the AA. Two types of degeneracy:

More information

Translation and Operons

Translation and Operons Translation and Operons You Should Be Able To 1. Describe the three stages translation. including the movement of trna molecules through the ribosome. 2. Compare and contrast the roles of three different

More information

Molecular Genetics Principles of Gene Expression: Translation

Molecular Genetics Principles of Gene Expression: Translation Paper No. : 16 Module : 13 Principles of gene expression: Translation Development Team Principal Investigator: Prof. Neeta Sehgal Head, Department of Zoology, University of Delhi Paper Coordinator: Prof.

More information

Chapter

Chapter Chapter 17 17.4-17.6 Molecular Components of Translation A cell interprets a genetic message and builds a polypeptide The message is a series of codons on mrna The interpreter is called transfer (trna)

More information

TRANSLATION: How to make proteins?

TRANSLATION: How to make proteins? TRANSLATION: How to make proteins? EUKARYOTIC mrna CBP80 NUCLEUS SPLICEOSOME 5 UTR INTRON 3 UTR m 7 GpppG AUG UAA 5 ss 3 ss CBP20 PABP2 AAAAAAAAAAAAA 50-200 nts CYTOPLASM eif3 EJC PABP1 5 UTR 3 UTR m 7

More information

From Gene to Protein

From Gene to Protein From Gene to Protein Gene Expression Process by which DNA directs the synthesis of a protein 2 stages transcription translation All organisms One gene one protein 1. Transcription of DNA Gene Composed

More information

Biochemistry Prokaryotic translation

Biochemistry Prokaryotic translation 1 Description of Module Subject Name Paper Name Module Name/Title Dr. Vijaya Khader Dr. MC Varadaraj 2 1. Objectives 2. Understand the concept of genetic code 3. Understand the concept of wobble hypothesis

More information

Conceptofcolinearity: a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein

Conceptofcolinearity: a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein Translation Conceptofcolinearity: a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein Para além do fenómeno do wobble, há que considerar Desvios ao código

More information

Types of RNA. 1. Messenger RNA(mRNA): 1. Represents only 5% of the total RNA in the cell.

Types of RNA. 1. Messenger RNA(mRNA): 1. Represents only 5% of the total RNA in the cell. RNAs L.Os. Know the different types of RNA & their relative concentration Know the structure of each RNA Understand their functions Know their locations in the cell Understand the differences between prokaryotic

More information

Central Dogma. DNA is the genetic material within the nucleus. The process of replication creates new copies of DNA.

Central Dogma. DNA is the genetic material within the nucleus. The process of replication creates new copies of DNA. Protein Synthesis Outline Central dogma Genetic code Ribosome Structure and Assembly Mechanics of Protein Synthesis Protein Synthesis in Eukaryotes Inhibitors of Protein Synthesis Postranslation modification

More information

Part IV => DNA and RNA. 4.6 RNA Translation 4.6a Genetic Code 4.6b Translational Machinery

Part IV => DNA and RNA. 4.6 RNA Translation 4.6a Genetic Code 4.6b Translational Machinery Part IV => DNA and RNA 4.6 RNA Translation 4.6a Genetic Code 4.6b Translational Machinery Section 4.6a: Genetic Code Synopsis 4.6a - In order to translate the genetic information (or genetic code) carried

More information

Organic Chemistry Option II: Chemical Biology

Organic Chemistry Option II: Chemical Biology Organic Chemistry Option II: Chemical Biology Recommended books: Dr Stuart Conway Department of Chemistry, Chemistry Research Laboratory, University of Oxford email: stuart.conway@chem.ox.ac.uk Teaching

More information

Chapter 12. Genes: Expression and Regulation

Chapter 12. Genes: Expression and Regulation Chapter 12 Genes: Expression and Regulation 1 DNA Transcription or RNA Synthesis produces three types of RNA trna carries amino acids during protein synthesis rrna component of ribosomes mrna directs protein

More information

Ribosome readthrough

Ribosome readthrough Ribosome readthrough Starting from the base PROTEIN SYNTHESIS Eukaryotic translation can be divided into four stages: Initiation, Elongation, Termination and Recycling During translation, the ribosome

More information

Chapter 17. From Gene to Protein. Biology Kevin Dees

Chapter 17. From Gene to Protein. Biology Kevin Dees Chapter 17 From Gene to Protein DNA The information molecule Sequences of bases is a code DNA organized in to chromosomes Chromosomes are organized into genes What do the genes actually say??? Reflecting

More information

mrna and Genetic code standard

mrna and Genetic code standard Synthesis and Processing of the Proteome. (mrna and Genetic code: standard and variations; codon anti codon interactions), The role of trna in protein synthesis, Role of Ribosome in Protein synthesis (Ribosome

More information

Protein Biosynthesis: The Overall Picture

Protein Biosynthesis: The Overall Picture Protein Biosynthesis: The Overall Picture From: Biochemistry Berg, Tymoczko, Stryer 5 th Ed. The Nature of the Genetic Code Three bases code for one amino acid WHY? Consider 4 n then 1 base can only code

More information

BCMB Chapters 39 & 40 Translation (protein synthesis)

BCMB Chapters 39 & 40 Translation (protein synthesis) BCMB 3100 - Chapters 39 & 40 Translation (protein synthesis) Translation Genetic code trna Amino acyl trna Ribosomes Initiation Elongation Termination How is the nucleotide code translated into a protein

More information

BCMB Chapters 39 & 40 Translation (protein synthesis)

BCMB Chapters 39 & 40 Translation (protein synthesis) BCMB 3100 - Chapters 39 & 40 Translation (protein synthesis) Translation Genetic code trna Amino acyl trna Ribosomes Initiation Elongation Termination How is the nucleotide code translated into a protein

More information

L I F E S C I E N C E S

L I F E S C I E N C E S 1a L I F E S C I E N C E S 5 -UUA AUA UUC GAA AGC UGC AUC GAA AAC UGU GAA UCA-3 5 -TTA ATA TTC GAA AGC TGC ATC GAA AAC TGT GAA TCA-3 3 -AAT TAT AAG CTT TCG ACG TAG CTT TTG ACA CTT AGT-5 NOVEMBER 7, 2006

More information

Molecular Biology - Translation of RNA to make Protein *

Molecular Biology - Translation of RNA to make Protein * OpenStax-CNX module: m49485 1 Molecular Biology - Translation of RNA to make Protein * Jerey Mahr Based on Translation by OpenStax This work is produced by OpenStax-CNX and licensed under the Creative

More information

1. In most cases, genes code for and it is that

1. In most cases, genes code for and it is that Name Chapter 10 Reading Guide From DNA to Protein: Gene Expression Concept 10.1 Genetics Shows That Genes Code for Proteins 1. In most cases, genes code for and it is that determine. 2. Describe what Garrod

More information

What is the central dogma of biology?

What is the central dogma of biology? Bellringer What is the central dogma of biology? A. RNA DNA Protein B. DNA Protein Gene C. DNA Gene RNA D. DNA RNA Protein Review of DNA processes Replication (7.1) Transcription(7.2) Translation(7.3)

More information

Protein synthesis I Biochemistry 302. Bob Kelm February 23, 2004

Protein synthesis I Biochemistry 302. Bob Kelm February 23, 2004 Protein synthesis I Biochemistry 302 Bob Kelm February 23, 2004 Key features of protein synthesis Energy glutton Essential metabolic activity of the cell. Consumes 90% of the chemical energy (ATP,GTP).

More information

NO!!!!! BCMB Chapters 39 & 40 Translation (protein synthesis) BCMB Chapters 39 & 40 Translation (protein synthesis)

NO!!!!! BCMB Chapters 39 & 40 Translation (protein synthesis) BCMB Chapters 39 & 40 Translation (protein synthesis) BCMB 3100 - Chapters 39 & 40 Translation How is the nucleotide code translated into a protein code? translation DNA RNA protein transcription 5 UCA 3 NH 2 Ser COO -????? Adapter Molecule Hypothesis (Crick,

More information

Lecture 13: PROTEIN SYNTHESIS II- TRANSLATION

Lecture 13: PROTEIN SYNTHESIS II- TRANSLATION http://smtom.lecture.ub.ac.id/ Password: https://syukur16tom.wordpress.com/ Password: Lecture 13: PROTEIN SYNTHESIS II- TRANSLATION http://hyperphysics.phy-astr.gsu.edu/hbase/organic/imgorg/translation2.gif

More information

Videos. Bozeman, transcription and translation: https://youtu.be/h3b9arupxzg Crashcourse: Transcription and Translation - https://youtu.

Videos. Bozeman, transcription and translation: https://youtu.be/h3b9arupxzg Crashcourse: Transcription and Translation - https://youtu. Translation Translation Videos Bozeman, transcription and translation: https://youtu.be/h3b9arupxzg Crashcourse: Transcription and Translation - https://youtu.be/itsb2sqr-r0 Translation Translation The

More information

From gene to protein. Premedical biology

From gene to protein. Premedical biology From gene to protein Premedical biology Central dogma of Biology, Molecular Biology, Genetics transcription replication reverse transcription translation DNA RNA Protein RNA chemically similar to DNA,

More information

Energy and Cellular Metabolism

Energy and Cellular Metabolism 1 Chapter 4 About This Chapter Energy and Cellular Metabolism 2 Energy in biological systems Chemical reactions Enzymes Metabolism Figure 4.1 Energy transfer in the environment Table 4.1 Properties of

More information

TRANSLATION: How to make proteins?

TRANSLATION: How to make proteins? TRANSLATION: How to make proteins? EUKARYOTIC mrna CBP80 NUCLEUS SPLICEOSOME 5 UTR INTRON 3 UTR m 7 GpppG AUG UAA 5 ss 3 ss CBP20 PABP2 AAAAAAAAAAAAA 50-200 nts CYTOPLASM eif3 EJC PABP1 5 UTR 3 UTR m 7

More information

RNA & PROTEIN SYNTHESIS. Making Proteins Using Directions From DNA

RNA & PROTEIN SYNTHESIS. Making Proteins Using Directions From DNA RNA & PROTEIN SYNTHESIS Making Proteins Using Directions From DNA RNA & Protein Synthesis v Nitrogenous bases in DNA contain information that directs protein synthesis v DNA remains in nucleus v in order

More information

Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013

Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013 Hydration of protein-rna recognition sites Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India 1 st November, 2013 Central Dogma of life DNA

More information

7.05 Spring 2004 February 27, Recitation #2

7.05 Spring 2004 February 27, Recitation #2 Recitation #2 Contact Information TA: Victor Sai Recitation: Friday, 3-4pm, 2-132 E-mail: sai@mit.edu ffice ours: Friday, 4-5pm, 2-132 Unit 1 Schedule Recitation/Exam Date Lectures covered Recitation #2

More information

Chapter 17 The Mechanism of Translation I: Initiation

Chapter 17 The Mechanism of Translation I: Initiation Chapter 17 The Mechanism of Translation I: Initiation Focus only on experiments discussed in class. Completely skip Figure 17.36 Read pg 521-527 up to the sentence that begins "In 1969, Joan Steitz..."

More information

Properties of amino acids in proteins

Properties of amino acids in proteins Properties of amino acids in proteins one of the primary roles of DNA (but not the only one!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids repeated

More information

Lesson Overview. Ribosomes and Protein Synthesis 13.2

Lesson Overview. Ribosomes and Protein Synthesis 13.2 13.2 The Genetic Code The first step in decoding genetic messages is to transcribe a nucleotide base sequence from DNA to mrna. This transcribed information contains a code for making proteins. The Genetic

More information

Gene regulation II Biochemistry 302. February 27, 2006

Gene regulation II Biochemistry 302. February 27, 2006 Gene regulation II Biochemistry 302 February 27, 2006 Molecular basis of inhibition of RNAP by Lac repressor 35 promoter site 10 promoter site CRP/DNA complex 60 Lewis, M. et al. (1996) Science 271:1247

More information

(Lys), resulting in translation of a polypeptide without the Lys amino acid. resulting in translation of a polypeptide without the Lys amino acid.

(Lys), resulting in translation of a polypeptide without the Lys amino acid. resulting in translation of a polypeptide without the Lys amino acid. 1. A change that makes a polypeptide defective has been discovered in its amino acid sequence. The normal and defective amino acid sequences are shown below. Researchers are attempting to reproduce the

More information

BME 5742 Biosystems Modeling and Control

BME 5742 Biosystems Modeling and Control BME 5742 Biosystems Modeling and Control Lecture 24 Unregulated Gene Expression Model Dr. Zvi Roth (FAU) 1 The genetic material inside a cell, encoded in its DNA, governs the response of a cell to various

More information

Protein Synthesis. Unit 6 Goal: Students will be able to describe the processes of transcription and translation.

Protein Synthesis. Unit 6 Goal: Students will be able to describe the processes of transcription and translation. Protein Synthesis Unit 6 Goal: Students will be able to describe the processes of transcription and translation. Types of RNA Messenger RNA (mrna) makes a copy of DNA, carries instructions for making proteins,

More information

7.012 Problem Set 1. i) What are two main differences between prokaryotic cells and eukaryotic cells?

7.012 Problem Set 1. i) What are two main differences between prokaryotic cells and eukaryotic cells? ame 7.01 Problem Set 1 Section Question 1 a) What are the four major types of biological molecules discussed in lecture? Give one important function of each type of biological molecule in the cell? b)

More information

UNIT 5. Protein Synthesis 11/22/16

UNIT 5. Protein Synthesis 11/22/16 UNIT 5 Protein Synthesis IV. Transcription (8.4) A. RNA carries DNA s instruction 1. Francis Crick defined the central dogma of molecular biology a. Replication copies DNA b. Transcription converts DNA

More information

PROTEIN SYNTHESIS: TRANSLATION AND THE GENETIC CODE

PROTEIN SYNTHESIS: TRANSLATION AND THE GENETIC CODE PROTEIN SYNTHESIS: TRANSLATION AND THE GENETIC CODE HLeeYu Jsuico Junsay Department of Chemistry School of Science and Engineering Ateneo de Manila University 1 Nucleic Acids are important for their roles

More information

Geometrical Concept-reduction in conformational space.and his Φ-ψ Map. G. N. Ramachandran

Geometrical Concept-reduction in conformational space.and his Φ-ψ Map. G. N. Ramachandran Geometrical Concept-reduction in conformational space.and his Φ-ψ Map G. N. Ramachandran Communication paths in trna-synthetase: Insights from protein structure networks and MD simulations Saraswathi Vishveshwara

More information

Gene regulation II Biochemistry 302. Bob Kelm February 28, 2005

Gene regulation II Biochemistry 302. Bob Kelm February 28, 2005 Gene regulation II Biochemistry 302 Bob Kelm February 28, 2005 Catabolic operons: Regulation by multiple signals targeting different TFs Catabolite repression: Activity of lac operon is restricted when

More information

Regulation and signaling. Overview. Control of gene expression. Cells need to regulate the amounts of different proteins they express, depending on

Regulation and signaling. Overview. Control of gene expression. Cells need to regulate the amounts of different proteins they express, depending on Regulation and signaling Overview Cells need to regulate the amounts of different proteins they express, depending on cell development (skin vs liver cell) cell stage environmental conditions (food, temperature,

More information

Molecular Biology of the Cell

Molecular Biology of the Cell Alberts Johnson Lewis Morgan Raff Roberts Walter Molecular Biology of the Cell Sixth Edition Chapter 6 (pp. 333-368) How Cells Read the Genome: From DNA to Protein Copyright Garland Science 2015 Genetic

More information

Chapter 16 Lecture. Concepts Of Genetics. Tenth Edition. Regulation of Gene Expression in Prokaryotes

Chapter 16 Lecture. Concepts Of Genetics. Tenth Edition. Regulation of Gene Expression in Prokaryotes Chapter 16 Lecture Concepts Of Genetics Tenth Edition Regulation of Gene Expression in Prokaryotes Chapter Contents 16.1 Prokaryotes Regulate Gene Expression in Response to Environmental Conditions 16.2

More information

Translation Part 2 of Protein Synthesis

Translation Part 2 of Protein Synthesis Translation Part 2 of Protein Synthesis IN: How is transcription like making a jello mold? (be specific) What process does this diagram represent? A. Mutation B. Replication C.Transcription D.Translation

More information

Name: SBI 4U. Gene Expression Quiz. Overall Expectation:

Name: SBI 4U. Gene Expression Quiz. Overall Expectation: Gene Expression Quiz Overall Expectation: - Demonstrate an understanding of concepts related to molecular genetics, and how genetic modification is applied in industry and agriculture Specific Expectation(s):

More information

C CH 3 N C COOH. Write the structural formulas of all of the dipeptides that they could form with each other.

C CH 3 N C COOH. Write the structural formulas of all of the dipeptides that they could form with each other. hapter 25 Biochemistry oncept heck 25.1 Two common amino acids are 3 2 N alanine 3 2 N threonine Write the structural formulas of all of the dipeptides that they could form with each other. The carboxyl

More information

ATP. P i. trna. 3 Appropriate trna covalently bonds to amino acid, displacing AMP. Computer model Hydrogen bonds

ATP. P i. trna. 3 Appropriate trna covalently bonds to amino acid, displacing AMP. Computer model Hydrogen bonds mino acid attachment site nticodon Hydrogen bonds mino acid T i denosine i i denosine minoacyl-trn synthetase (enzyme) trn 1 ctive site binds the amino acid and T. 2 T loses two groups and bonds to the

More information

From DNA to protein, i.e. the central dogma

From DNA to protein, i.e. the central dogma From DNA to protein, i.e. the central dogma DNA RNA Protein Biochemistry, chapters1 5 and Chapters 29 31. Chapters 2 5 and 29 31 will be covered more in detail in other lectures. ph, chapter 1, will be

More information

Lecture 5. How DNA governs protein synthesis. Primary goal: How does sequence of A,G,T, and C specify the sequence of amino acids in a protein?

Lecture 5. How DNA governs protein synthesis. Primary goal: How does sequence of A,G,T, and C specify the sequence of amino acids in a protein? Lecture 5 (FW) February 4, 2009 Translation, trna adaptors, and the code Reading.Chapters 8 and 9 Lecture 5. How DNA governs protein synthesis. Primary goal: How does sequence of A,G,T, and C specify the

More information

Genetics 304 Lecture 6

Genetics 304 Lecture 6 Genetics 304 Lecture 6 00/01/27 Assigned Readings Busby, S. and R.H. Ebright (1994). Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79:743-746. Reed, W.L. and

More information

GCD3033:Cell Biology. Transcription

GCD3033:Cell Biology. Transcription Transcription Transcription: DNA to RNA A) production of complementary strand of DNA B) RNA types C) transcription start/stop signals D) Initiation of eukaryotic gene expression E) transcription factors

More information

protein synthesis and the ribosome

protein synthesis and the ribosome protein synthesis and the ribosome Central dogma of biology DNA codes for DNA DNA codes for RNA RNA codes for proteins not surprisingly, many points for regulation of the process RNA codes for proteins

More information

Lecture 15: Realities of Genome Assembly Protein Sequencing

Lecture 15: Realities of Genome Assembly Protein Sequencing Lecture 15: Realities of Genome Assembly Protein Sequencing Study Chapter 8.10-8.15 1 Euler s Theorems A graph is balanced if for every vertex the number of incoming edges equals to the number of outgoing

More information

Objective: You will be able to justify the claim that organisms share many conserved core processes and features.

Objective: You will be able to justify the claim that organisms share many conserved core processes and features. Objective: You will be able to justify the claim that organisms share many conserved core processes and features. Do Now: Read Enduring Understanding B Essential knowledge: Organisms share many conserved

More information

Biophysics Lectures Three and Four

Biophysics Lectures Three and Four Biophysics Lectures Three and Four Kevin Cahill cahill@unm.edu http://dna.phys.unm.edu/ 1 The Atoms and Molecules of Life Cells are mostly made from the most abundant chemical elements, H, C, O, N, Ca,

More information

Proteins: Characteristics and Properties of Amino Acids

Proteins: Characteristics and Properties of Amino Acids SBI4U:Biochemistry Macromolecules Eachaminoacidhasatleastoneamineandoneacidfunctionalgroupasthe nameimplies.thedifferentpropertiesresultfromvariationsinthestructuresof differentrgroups.thergroupisoftenreferredtoastheaminoacidsidechain.

More information

UNIT TWELVE. a, I _,o "' I I I. I I.P. l'o. H-c-c. I ~o I ~ I / H HI oh H...- I II I II 'oh. HO\HO~ I "-oh

UNIT TWELVE. a, I _,o ' I I I. I I.P. l'o. H-c-c. I ~o I ~ I / H HI oh H...- I II I II 'oh. HO\HO~ I -oh UNT TWELVE PROTENS : PEPTDE BONDNG AND POLYPEPTDES 12 CONCEPTS Many proteins are important in biological structure-for example, the keratin of hair, collagen of skin and leather, and fibroin of silk. Other

More information

Quiz answers. Allele. BIO 5099: Molecular Biology for Computer Scientists (et al) Lecture 17: The Quiz (and back to Eukaryotic DNA)

Quiz answers. Allele. BIO 5099: Molecular Biology for Computer Scientists (et al) Lecture 17: The Quiz (and back to Eukaryotic DNA) BIO 5099: Molecular Biology for Computer Scientists (et al) Lecture 17: The Quiz (and back to Eukaryotic DNA) http://compbio.uchsc.edu/hunter/bio5099 Larry.Hunter@uchsc.edu Quiz answers Kinase: An enzyme

More information

9/11/18. Molecular and Cellular Biology. 3. The Cell From Genes to Proteins. key processes

9/11/18. Molecular and Cellular Biology. 3. The Cell From Genes to Proteins. key processes Molecular and Cellular Biology Animal Cell ((eukaryotic cell) -----> compare with prokaryotic cell) ENDOPLASMIC RETICULUM (ER) Rough ER Smooth ER Flagellum Nuclear envelope Nucleolus NUCLEUS Chromatin

More information

Protein Synthesis. Unit 6 Goal: Students will be able to describe the processes of transcription and translation.

Protein Synthesis. Unit 6 Goal: Students will be able to describe the processes of transcription and translation. Protein Synthesis Unit 6 Goal: Students will be able to describe the processes of transcription and translation. Protein Synthesis: Protein synthesis uses the information in genes to make proteins. 2 Steps

More information

CHMI 2227 EL. Biochemistry I. Test January Prof : Eric R. Gauthier, Ph.D.

CHMI 2227 EL. Biochemistry I. Test January Prof : Eric R. Gauthier, Ph.D. CHMI 2227 EL Biochemistry I Test 1 26 January 2007 Prof : Eric R. Gauthier, Ph.D. Guidelines: 1) Duration: 55 min 2) 14 questions, on 7 pages. For 70 marks (5 marks per question). Worth 15 % of the final

More information

Regulation of Gene Expression at the level of Transcription

Regulation of Gene Expression at the level of Transcription Regulation of Gene Expression at the level of Transcription (examples are mostly bacterial) Diarmaid Hughes ICM/Microbiology VT2009 Regulation of Gene Expression at the level of Transcription (examples

More information

Computational Cell Biology Lecture 4

Computational Cell Biology Lecture 4 Computational Cell Biology Lecture 4 Case Study: Basic Modeling in Gene Expression Yang Cao Department of Computer Science DNA Structure and Base Pair Gene Expression Gene is just a small part of DNA.

More information

Physiochemical Properties of Residues

Physiochemical Properties of Residues Physiochemical Properties of Residues Various Sources C N Cα R Slide 1 Conformational Propensities Conformational Propensity is the frequency in which a residue adopts a given conformation (in a polypeptide)

More information

Prokaryotic Regulation

Prokaryotic Regulation Prokaryotic Regulation Control of transcription initiation can be: Positive control increases transcription when activators bind DNA Negative control reduces transcription when repressors bind to DNA regulatory

More information

9/2/17. Molecular and Cellular Biology. 3. The Cell From Genes to Proteins. key processes

9/2/17. Molecular and Cellular Biology. 3. The Cell From Genes to Proteins. key processes Molecular and Cellular Biology Animal Cell ((eukaryotic cell) -----> compare with prokaryotic cell) ENDOPLASMIC RETICULUM (ER) Rough ER Smooth ER Flagellum Nuclear envelope Nucleolus NUCLEUS Chromatin

More information

TWO PARTNERS OF THE RIBOSOME, EF-TU AND LEPA EVELINA INES DE LAURENTIIS. B.Sc. University of Lethbridge, A Thesis

TWO PARTNERS OF THE RIBOSOME, EF-TU AND LEPA EVELINA INES DE LAURENTIIS. B.Sc. University of Lethbridge, A Thesis TWO PARTNERS OF THE RIBOSOME, EF-TU AND LEPA EVELINA INES DE LAURENTIIS B.Sc. University of Lethbridge, 2007 A Thesis Submitted to the School of Graduate Studies of the University of Lethbridge in Partial

More information

Final Chem 4511/6501 Spring 2011 May 5, 2011 b Name

Final Chem 4511/6501 Spring 2011 May 5, 2011 b Name Key 1) [10 points] In RNA, G commonly forms a wobble pair with U. a) Draw a G-U wobble base pair, include riboses and 5 phosphates. b) Label the major groove and the minor groove. c) Label the atoms of

More information

Any protein that can be labelled by both procedures must be a transmembrane protein.

Any protein that can be labelled by both procedures must be a transmembrane protein. 1. What kind of experimental evidence would indicate that a protein crosses from one side of the membrane to the other? Regions of polypeptide part exposed on the outside of the membrane can be probed

More information

GENE ACTIVITY Gene structure Transcription Transcript processing mrna transport mrna stability Translation Posttranslational modifications

GENE ACTIVITY Gene structure Transcription Transcript processing mrna transport mrna stability Translation Posttranslational modifications 1 GENE ACTIVITY Gene structure Transcription Transcript processing mrna transport mrna stability Translation Posttranslational modifications 2 DNA Promoter Gene A Gene B Termination Signal Transcription

More information