Chapter 9 Objectives
Chapter 9 Objectives Biol 450
Popular in Modern genetics
Popular in Biology
verified elite notetaker
This 8 page Class Notes was uploaded by Kseniya Notetaker on Tuesday October 13, 2015. The Class Notes belongs to Biol 450 at Kansas State University taught by Dr. Katherine Schrick in Fall 2015. Since its upload, it has received 34 views. For similar materials see Modern genetics in Biology at Kansas State University.
Reviews for Chapter 9 Objectives
Report this Material
What is Karma?
Karma is the currency of StudySoup.
You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!
Date Created: 10/13/15
Chapter 9 Proteins and Their Synthesis OBJECTIVES amp PROBLEM ASSIGNMENTS Lecture 18 19 READING ASSIGNMENT CHAPTER 9 p 319344 Section 91 Protein Structure 1 Be able to draw the general structure of an amino acid State the number of different amino acids used in the translation process and comment on the chemical diversity of the R groups found in these amino acids Egraup or side chain R 3 carbon I ct hydrogen r J I I Emma I carbaxyi graup graup The Rgroup is the only structure that differs There are 20 amino acids known to exist in proteins Each have a different R group that gives it its unique properties There are 4 general classes polar vs nonpolar aromatic vs charged side chains 0 Hydrophilic 0 Hydrophobic 0 Charged 0 Uncharged R groups determine 0 Protein folding hydrophobic effect ionic interactions 0 Protein function catalytic activity ability to bind other molecules like RNA polymeraseDNA 2 Define the term polypeptide An average polypeptide would contain about 4 40 49974999 amino acids Polypeptide is a chain of amino acids usually contains about 10100 amino acids A peptide bond is formed by linkage of amino end NH2 of one amino acid with carboxyl end COOH of another amino acid 3 Draw amino acids general structure as joined by peptide bonds and indicate the amino and carboxyl ends of the amino acid chain HJ tat Hi n w E a nu c r H H H EIIIH Peptide d E iE fill i H H H EH 4 Peptide bonds are covalent weak bonds and are formed by condensation hydrolysis reactions Peptide bonds are covalent bonds and are formed by condensation reactions condensationchemical process where 2 molecules are joined together to make a larger more complex molecule with the loss of water 5 Distinguish between the primary secondary tertiary and quaternary organizational levels of protein structure 0 Primary the linear sequence of the amino acids in a polypeptide chain 0 Held by strong covalent bonds 0 Secondary structure local regions of the chain that fold into specific shapes each shape arises from the bonding forces between amino acids that are close together in the linear sequence 0 Comes in either Alpha Helix or Beta Pleated Sheet 0 Interaction between nearby amino acids 0 Tertiary produced by the folding of the secondary structure into 3D shape 0 Necessary for proper function of protein 0 Example enzymes have active site into which substrate fits 0 Quaternary two or more separate folded polypeptides also called subunits joined by weak bonds Hemoglobin is an example of a four subunit protein 6 Name the key bond in determining a polypeptide s primary structure and the key bond in determining a polypeptide s alpha helical structure State which structural level requires two or more polypeptides Primary structure is determined by peptide bond between adjacent amino acids peptide bond is strong covalent bond Alpha helix is made by hydrogen bonds between amino acids at different locations in polypeptide chain Quaternary structure require 2 or more polypeptides 7 How is hemoglobin an example of a protein with quaternary structure How many polypeptides are part of one hemoglobin protein complex Hemoglobin is a heterotetramer a 4subunit protein made of 2 copies each of 2 different polypeptides 8 Define the active site of an enzyme The active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction 9 Explain why disruption of weak bonds hydrogen electrostatic and Van der Waal s causes an enzyme to lose its catalytic activity When a protein is denatured by such disruptions is the peptide bond destroyed Denaturations of proteins involves disruption of both the secondary and tertiary structures Denaturation reactions are not strong enough to break the peptide bonds Section 92 The Genetic Code 10 Describe the genetic code in terms of number of nucleotides per codon total number of codons codons specifying amino acids and universality or lack thereof of codon specificities across a diversity of species mRNA has 4 nucleotides A C G U How do these code for 20 amino acids Must use combination of nucleotides Must be at least 3 nucleotides long 4x4x464 3 letter oneseven though there are 64 combination several different ones code for the same amino acid Start codon AUG Methionine Met Stop codon UAG UAA UGA These DO NOT SPECIFY any amino acid Universal code is in all organisms 11 Be able to explain what the degeneracy of the genetic code refers to Degenerate code more than one codon for amino acids 0 Phenylalanine has 2 codons 0 Proline has 4 codons 0 Leucine has 6 codons 12 Describe the genetic code in terms of directionality in which the code is read 539 gt339 339 gt539 both and reading frame Understand the effect on the translation process of the insertion of an extra nucleotide or two into the gene or mRNA or the removal of a nucleotide or two from the gene or mRNA Genetic code is nonoverlapping Ribosome is the site of translation Ribosome reads nucleotide sequence of mRNA 3 nucleotides at a time in 5 to 3 direction The info in mRNA is read by an adaptor molecule to link codons and amino acids Section 93 tRNA The Adapter 13 Describe transfer RNAs tRNAs with respect to a function b number of different kinds found in a cell c size compared to mRNAs d occurrence of unusual N bases common or rare and possession of a specific 3D structure yes or no a tRNA is an adaptor molecule to link codons and amino acids a KEY FEATURES Acceptor arm and anticodon loop Number of different kinds found in a cell 35 tRNA s Size 80 bases long May contain rare N bases Has a stemloop secondary structure so NO 3D structure 9906 14 Sketch the Cloverleaf representation of a tRNA molecule indicating the 539 and 339 ends the location and function of the anticodon and the location of the amino acid attachment site 0 One of the leaves of the clover has the i ri39lil liil acid 39 quot a nhmw aim anticodon 0 Anticodon goes 35 0 Codon goes from 53 0 Anticodons in tRNA pair with codons in mRNA to specify the amino acids Strands are antiparallel 0 Amino acid attachment side is on the opposite side of the clover 0 Each tRNA is covalently linked to a specific amino acid almi 3quot gr O 15 Sketch an mRNA molecule indicating 539 and 339 ends with one of its codons paired with a tRNA indicating 539 and 339 ends and indicate the wobble position Table Eaquot Eudon ntimdun Pairings Ellawed by the Wobble Rules 5 End Bf 3m A tIHiHIA rant rodon Jinanp anticodon of coder 5 I or a 39 uWoliljle position E only 3 G 5 31 J ril ll39y g L A M G u C j 54quot 39 U5 393quot I quot391 5quot Ewan 339 mm 16 What is the significance of wobble Because of wobble the number of tRNAs needed to recognize the six serine codons is 1 3 6 18 Its relaxed base pairing rules between tRNA and mRNA at the 3 end of the codon Serine recognizes 3 tRNA s which means a total of 35 17 Give the function of aminoacyl tRNA synthetases A specific tRNA synthetase enzyme will bind to enlyhene leind more than one kind of amino acid A specific tRNA synthetase enzyme e g serine tRNA synthetase will bind to only 1 speci c class of ser tRNA with a speci c anticodon or all ser Ms Hence the number of different types of aminoacyl tRNA synthetases a cell requires for normal translation is 1 610 20 61 or more Aminoacyl tRNA attaches amino acids to the 3 end of tRNA Section 94 Ribosomes 18 Describe a complete ribosome With respect to function chemical composition number of subunits and number of tRNA binding sites Prokaryotic and eukaryotic ribosomes are similar in composition and size lib Euhnmi ndll Erxmying unwind F uw ti39 g m1 IHHH release i from site P p dyll trainiferaae tanker 7 L email131 Mmemwntuf Mammal h Ribos ome binds mRNA and tRNA simultaneously forms peptide bonds between amino acids carried by charged tRNAs Contain A P E binding sites for tRNA s 0 A aminoacyl just the charged tRNA 0 P peptidyl tRNA attached to growing peptide chain 0 E exit tRNA with no amino acid 19 Distinguish between a 70S and SOS ribosome with respect to cellular origin prokaryotic or eukaryotic If the 70S ribosome has 3 rRNA molecules then the SOS ribosome has 3 more than 3 rRNA molecules If the 70S ribosome has 52 polypeptides then the SOS ribosome has 52 many more than 52 polypeptides Prokaryotic has 7OS ribosome Eukaryotic has SOS ribosome If 7OS ribosome has 3rRNA molecules then the SOS ribosome has more than 3 rRNA molecules If 7OS ribosome has 52 polypeptides then the SOS ribosome has more than 52 20 Sketch a ribosome in the process of protein synthesis showing the mRNA molecule with specific codons and indicating 539 and 339 ends the ribosome with labeled large and small subunits and labeled A P and E sites and tRNA molecules one with a growing polypeptide chain and one with an amino acid Indicate in sketch the direction of movement of the ribosome along the mRNA IIl mama mailI I WI3 rming Elamyiltad F ypeptmg than IHHJEI release A I A A r imm E ante HWid tramferase tanner I V l EEEiil llgl MWEMEHET Mammal h 21 Recognize that during protein synthesis the tRNA first occupies the A site and then the P site Recognize the direction of polypeptide synthesis is from the free amino end to the free carboxyl end 22 In the termination stage of translation a stop codon is recognized by a terminator tRNA a protein release factor nothing at all At termination of translation the polypeptide is is not released from the tRNA and the ribosome does does not dissociate into 2 subunits 23 Memorize the translation initiation and the 3 translation stop codons Determine if given a mRNA sequence and without the use of the genetic code table the number of amino acids that will be in the polypeptide The translation initiation 0 begins in the Psite in prokaryotes its near start codon at shine Dalgarno 0 in Eukaryotes its at 5 cap ESSENTIAL small subunit binds at start codon tRNAMet binds to AUG Elongation 0 Charged tRNA with elongation factor EF Tu enters A site anticodon pairs with codon EF Tu leaves 0 Peptide bond formation COOH group of 1st amino acid at P site is joined to NH2 group of 2nd amino acid at A site 0 Translocation uncharged initiator tRNA moves into E site then exists tRNA from A site moves into P site attached to polypeptide chain 0 A site is now available for next tRNA Termination 0 No tRNA recognizes stop codons 0 Release factor a protein recognizes stop codons bind in A site 0 Protein cleaved from last tRNA ribosome dissociates Section 95 The Proteome 24 Understand the definitions of the terms proteome and interactome Proteome is the entire complement of proteins that is expressed by a cell tissue organism 0 Humans have fewer genes than proteins Interactome is the complete set of proteinprotein interactions in a given organism organ tissue or cell 0 There are 3186 interactions among 1705 human proteins 25 Explain how alternative splicing leads to a larger number of proteins Alternative splicing is a process which allows the production of a variety of different proteins from one gene only 3 4 Figure 1 Most genes in eukaryotic genomes consist of exons and introns After transcription introns need to be removed from the premRNA by a step called splicing Sometimes an exon can be either included or excluded from the final transcripts or there can be two splice sites at one end of an exon that are recognized by the spliceosome the complex which carries the splicing reaction 26 Understand that proteins are folded into their final shape with the help of special proteins called chaperones Chaperones are A large group of unrelated protein families whose role is to stabilize unfolded proteins unfold them for translocation across membranes or for degradation and or to assist in their correct folding and assembly 27 Understand that most proteins are modified after translation Once a protein is made it has to move to the correct part of the cell depending on its function so there could be post translational modifications 28 Explain how phosphorylation affects protein activity Phosphorylation acts like a switchcell is always ready to respond but only does when stimulated It can cause conformation change change in shape of the protein 29 Explain how proteins are targeted for degradation Via ubiquitination Small proteins are attached to other proteins and that usually targets them for destruction 30 Know that different sequences such as the signal sequence or the nuclear localization sequence NLS control the final location of a newly made protein Assigned Textbook Problems Chapter 9 12 l3 16 17 28 34 35
Are you sure you want to buy this material for
You're already Subscribed!
Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'