BCHM 3050 1st EditionExam # 2 Study Guide Lectures: 11-19Lecture 11 (February 4th)How does liquidy syrup inside candies form?Invertase (enzyme) makes candies more creamy than granular; more liquidy than solid.Breaks down sucrose into glucose and fructose to keep it a syrup consistencyWhat is the significance of Km?The lower the Km, the better the enzyme (lowers the Vmax which decreases the energy needed for the enzyme to function at its best). Lower Km à enzyme will bind tighter to the substrate; graph will be more hyperbolic.Lecture 12 (February 6th)Describe the three main types of inhibitors.Competitive- looks very similar to the substrate so it competes with the substrate to try to bind to the activation site and block out substrate- If Malonate binds to the active site à the enzyme changes in shape à inactivating enzyme- Competitive inhibitory causes more substrate needing to be added- Put in more substrate to get the same product of the reaction- Km increases in the presence of an inhibitor à which means you need much more of thesubstrate to achieve the same level of affinity- Vmax is not alerted by competitive inhibitorNon-competitive- Doesn’t bind to active site, doesn’t affect Km, and reduces Vmax- This inhibitor is more permanent than competitive inhibitors; not reversibleUncompetitive- Binds only to the enzyme substrate complex, lowers both Km and Vmax- Km decreases, but velocity also decreasesLecture 13 (February 9th)What is the difference between a purine and a pyrimidine?Purines – bigger and have a two ring structurePyrimidines – smaller and have one ring structureWhat are the three components of a nucleotide?Three components include a nitrogenous base, pentose sugar, and phosphateLecture 14 (February 11th)What is the difference between a phosphanhydride bonds, a phosphodiester bond, and a phosphoester bond?Bonds connecting the different phosphate groups = phosphoanhydrideBond connecting different nucleotides in DNA= phosphodiester Bond connecting phosphate group to OH = phosphoesterWhat form of DNA was discovered by Watson and Crick?B-form of DNA is the form characterized by Watson & Crick. It was originally isolated from aqueous solutions as the partly hydrated “sodium salt”. It is thought that this form represents most native DNA in the cell.Lecture 15 (February 13th)What is the importance of supercoiling DNA?DNA has to be supercoiled in order to fit in such a compact space. Supercoiling makes it inaccessible which is a way the cell protects the DNA from mutagens. Supercoiling makes sure that the replication factors (needed for the DNA replication process) access the DNA only at specific times. Higher organisms have maximum supercoilingWhat composes a nucleosome?Nucleosome is a group of 8 histone proteins that bind to the DNA at certain intervals.Lecture 16 (February 16th)When does a cruciform DNA form?Cruciform DNA is a cross-like DNA structure that forms when DNA contains a palindrome. Palindrome should read the same top on the top and the bottom strand; can be slightly staggeredExplain how gel electrophoresis works.Buffer conducts electricity. Make use of the negative charge of DNA. Negative charge at one endof the gel and positive charge at the other end. When electricity is turned on, the DNA will migrate towards the positive end of the gel à DNA is separated in agarose.Lecture 17 (February 20th)What did Sanger generate in his sequencing technique?Sanger generated di-deoxynucleotides - ddGtP, ddCTP, ddTTP, ddATP. He replaced the OH with just an H, which cannot form a phosphodiester bond à cannot extended the DNA chain.What did Sanger’s four tubes contain?#1 adds 1 strand of DNA + dATP/CTP/GTP/TTP+ ddATP#2 adds 1 strand of DNA + dATP/CTP/GTP/TTP+ ddGTP#3 adds 1 strand of DNA + dATP/CTP/GTP/TTP+ ddCTP#4 adds 1 strand of DNA + dATP/CTP/GTP/TTP+ ddTTPLecture 18 (February 23rd)What are transposons?Transposons = “jumping genes”Transposons cause random mutation – some parts of DNA moves from one chromosome to anotherWhat are some general characteristics of DNA replication?- Chemically uni-directional (5’ à 3’)- Semi-conservative- Spatially bi-directional – DNA goes in both direction from a single point- Semi-discontinuousLecture 19 (February 25th)Describe the three main steps of DNA Synthesis.Initiation1) Origins of replication bind to initiation factors2) Helicase binds3) Topoisomerase binds and prevents supercoiling (occurs almost at same time as #2)4) ssBP- No protein can work alone; it’s a concerted effort- Grand finale of Initiation is the helicase unwinding the DNA strands- Initiation Factors – DnaA proteins- Bring helicase to origin of replication- Helicase – DnaB proteins- Helicase needs energy from ATP to break bonds - Some mode of tension exists all the time in DNA- Topoisomerases – bind on either side of the origin and introduce a small cut in DNA that helps to prevent tangling/supercoiling in DNA (relax stress)- ssDNA – “single stranded binding proteins” – prevent strands of DNA from coming back togetherElongation - Elongation – new 5’ à 3’ DNA strand is created- Primase – NEEDS a primer to start synthesis (flaw of primase); primer = small RNA nucleotide chain- Primase is a type of RNA polymerase- Gaps between lagging strands are filled by DNA ligase- DNA polymerases are just named with numbers in the order of their discovery- DNA polymerase II is involved in proofreading and DNA repair- DNA polymerase 3 is also involved in DNA repairTermination- Specific termination proteins and termination sites (similar to palindromes)- Termination binding proteins bind to termination sites on opposite side of the DNA
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