Amino Acids, Peptide Bonds and Protein Structure Study Guide 2

Enzymes catalyse reactions by: speeding up reactions by lowering activation energy How do enzymes affect reaction rate & activation energy? Enzymes speed up reactions by reducing activation energy. How do environmental changes affect enzymes? • temperature: raising the temp usually speeds up a reaction, & lowing it slows it down. Extreme high temps can cause enzyme to denature/lose shape & stop working • pH: each enzyme has optimal pH range; changing pH outside of this range will slow enzyme activity; extreme pH values can denature enzymes • enzyme concentration: increasing enzyme concentration will speed up reaction, as long as there is a substrate available for binding; when all substrate is bound, reaction will no longer speed up r/t nothing for enzymes to bind to • substrate concentration: increasing substrate concentration increases rate of reaction to a point; once all enzymes are bound, substrate increase no longer affects rate of reaction allosteric regulation: any case in which a proteinÕs function at one site, is affected by the binding of a regulatory molecule to a separate site allosteric site: the place where an activating or inhibiting regulatory molecule, binds to a regulatory site feedback inhibition: a mode of metabolic control; a metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early in the pathway Differences between competitive & noncompetitive inhibitors: • competitive inhibitor: binds to the active site & prevents the substrate from binding there • noncompetitive inhibitor: binds to a different site on the enzyme; it doesnÕt block substrate binding, but causes other changes in the enzyme so it can no longer catalyze the reaction efficiently What property of enzymes is illustrated in the Þnal step of the enzymatic cycle? Enzymes are reusable In the enzyme cycle, which step immediately follows induced Þt? formation of the enzyme-product complex What type of inhibition occurs when a particular drug binds to the active site of an enzyme? competitive Salivary amylase, an enzyme responsible for partial digestion of carbs, has optimum activity at a pH level of 6.8. What is the impact on the activity if pH is decreased to 4.0? signiÞcantly decreased In the synthesis of gluthiaone, gluthiaone accumulates & binds to an enzyme in the pathway to prevent synthesis. Which type of inhibition is displayed? feedback Lipase is an enzyme with an optimum temp of 98.6 & optimum pH of 7.0 in the duodenum. If a person has a fever of 99.8, what will increase the activity of the lipase enzyme? decrease in temperature The enzyme glucokinase only binds to its substrate glucose, and converts glucose into the product glucose-6-phosphate. Which property of enzymes is described? speciÞcity Two enzymatic reactions are involved in the synthesis of glutathione. In the second reaction, glutathione synthetase converts glycine to glutathione. What would potentially decrease risks r/t low levels of glutathione? Increasing the amount of glycine in the diet. Which class of enzymes temporarily removes a phosphate? phosphatase A Þnal product of a 4-step metabolic pathway serves as a noncompetitive inhibitor, binding to an enzyme in the pathway & temporarily turning the pathway off. Which enzyme is most likely to be targeted by this inhibitor? The Þrst enzyme in the pathway. Unit 4: DNA and RNA Nucleotides/Bases of DNA Nucleotides/Bases of RNA A Adenine A Adenine C Cytosine C Cytosine G Guanine G Guanine T Thymine U Uracil Base-Pairing: A with T C with G Flow of genetic info: DNA > RNA > protein gene expression: DNA provides instructions for its own replication • DNA directs RNA synthesis • DNA controls protein synthesis (through RNA) antiparallel: expresses that the sugar phosphate backbone of the DNA double helix side rails, run in opposite directions of each other transcription: occurs when speciÞc DNA is used as a template to make mRNA; the synthesis of RNA using info in the DNA stages of transcription: • initiation • elongation • termination complementary: expresses that the two strands of the double helix are the predictable counterparts of each other translation: the synthesis of a polypeptide/protein using the info in the mRNA replication: process by which DNA makes a copy of itself during cell division Template DNA: a strand used by DNA polymerase to attach to complementary bases during DNA replication or RNA transcription Coding DNA: a sequence of DNA that codes for protein RNA polymerase: the main transcription enzyme; uses a template DNA strand to make a new, complementary RNA molecule promoter: the DNA sequence where RNA polymerase attaches & initiates transcription mRNA: messenger RNA; plays vital role in protein synthesis; carries the genetic info copied from DNA in the form of a series of 3 base code ÔwordsÕÉ each of which speciÞes a particular amino acid tRNA: transfer RNA; the key to deciphering the code ÔwordsÕ in mRNA; function is to transfer an amino acid from the cytoplasmic pool of amino acids, to a growing polypeptide in a ribosome ribosomes: the sites of translation; molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains codons: a triplet of nucleotide bases that form a unit of genetic code in a DNA or RNA molecule anticodons: sequence of nucleotides complementary to codons How do we make complementary DNA? (Coding to template, or template to coding?) A molecule of DNA polymerase runs the length of each DNA strand; acts as blueprint to produce a complementary strand; template to coding How do we make mRNA? Made from DNA via transcription in the nucleus; uses nucleotide sequence of DNA as a template Which strand of DNA is complementary to mRNA? • lower strand • upper strand is coding strand, lower strand is template strand How do we make proteins? • DNA promoter attaches to RNA polymerase • RNA polymerase separates strands & codes for RNA • DNA processed into mRNA inside nucleus • mRNA leaves nucleus to be translated into protein What type of nucleotide sequence is used, and in which direction? • A sequence of 20 amino acids • can only extend on the 3Õ end of the RNA How do we read the codon table? • Left = position 1 • Top = position 2 • Right = position 3 What is the relationship between tRNA and mRNA? Transfer ribonucleic acid (tRNA) is a type of RNA molecule that helps decode a messenger RNA (mRNA) sequence into a protein. When a tRNA recognizes and binds to its corresponding codon in the ribosome, the tRNA transfers the appropriate amino acid to the end of the growing amino acid chain. splicing • mRNA: introns are removed & exons are joined together • tRNA: cleaving that introduces 1 intron & 2 exons introns: noncoding segments of nucleic acid that lie between coding regions; also called intervening sequences exons: segments of DNA or RNA that code for a protein or peptide sequence histones: family of basic proteins that associate w/ DNA in the nucleus & condense it into chromatin nucleosomes: fundamental protein subunits of chromatin methylation: • process where methyl groups are added to the DNA molecule • can change the activity of a DNA segment without changing itÕs sequence • decreases gene expression acetylation: introduces an acetyl group to a compound How does mRNA splicing allow us to create multiple proteins from a single gene/mRNA? Splicing allows for different combinations if exons to be included in the Þnal, mature mRNA, making many different versions of proteins. What factors increase gene expression? • increased acetylation • decreased methylation • widely spaced nucleosomes What factors decrease gene expression? • increased methylation • decreased acetylation • tightly packed nucleosomes How do these factors work together to control transcription? • Methylation packs nucleosomes tightly; transcription factors cannot bind & genes are not expressed • Acetylation causes loose packing of nucleosomes; transcription factors bind and genes are expressed point mutations: changes in a single nucleotide pair of a gene • silent mutations • missense mutations • nonsense mutations nonsense mutations: causes production of the STOP codon; most lead to shortened, non-functional proteins missense mutations: substitutions that change one amino acid to another one; may have little effect on the protein silent mutations: mutations that have no effect r/t the redundancy go the genetic code; more than one codon codes for each amino acid Frameshift mutations: when the insertion or removal of a letter from the DNA sequence, causes everything after it to be altered. • insertion mutations • deletion mutations insertion mutations: addition of nucleotide pairs in a gene; can have disastrous effect on resulting protein deletion mutations: loss of nucleotide pairs in a gene; can have disastrous effect on resulting protein base excision repair: • one base is damaged • one enzyme cuts out the damaged base • other enzymes come in & trim around the site & replace nucleotides nucleotide excision repair: • team of proteins removes a long strand (approx 24) of nucleotides • replaces them with fresh ones mismatch repair: • enzyme usually catches these errors; if not, cuts off a few nucleotides & replaces them • second set of proteins follows behind to check for accuracy • if mismatch is found, they cut it out & replace it Homologous Recombination: • used to repair strand breaks • uses undamaged section of similar DNA as template • enzymes interlace the damaged & undamaged strands • prompts them to exchange sequences of nucleotides • Þlls in missing gaps to end up w/ 2 complete double-stranded segments Non-Homologous End-Joining • used to repair strand breaks when no sister DNA is available • series of proteins trims off a few nucleotides & fuses the broken ends back together • not as accurate as homologous; can cause genes to get mixed up/ moved around What type of DNA damage does each repair pathway Þx? • base excision = when one base is damaged • nucleotide excision = replaces a whole strand of nucleotides • mismatch = replaces mismatchedÉ • homologous = strand breaks • non-homologous = strand breaks PCR/Polymerase Chain Reaction: technique using repeated steps of heating & cooling, to make copies of a speciÞc region of DNA • after 3 cycles, 2 molecules match the target sequence exactly • after 30 cycles, over 1 billion molecule match the target sequence • used to provide speciÞc DNA fragments for cloning