Unit 2

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Metabolism: all of the chemical reactions of the cell
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Terms in this set (44)
Metabolism: all of the chemical reactions of the cell
1. Catabolism: degradative; breaks the bonds of larger molecules formingsmaller molecules; releases energy
2. Anabolism: biosynthesis; process that formslarger macromoleculesfrom smaller molecules; requires energy input
Importance of enzymes
1. Enzymes are biological catalysts that increase the rate of a chemical reaction by lowering the energy of activation (the resistance to a reaction)
2. The enzyme is not permanently altered in the reaction
3. Enzyme promotes a reaction by serving asa physical site for specific substrate molecules
Enzyme structure
1. Simple enzymes - consist of protein alone
2. Conjugated enzymes or holoenzymes - contain protein and nonprotein molecules
Apoenzyme
protein portion
Cofactors
> nonprotein portion
> Metallic cofactors: iron, copper, magnesium
> Coenzymes: organic molecules, vitamins
Exoenzymes
produced and transported outside of the cell to participate in chemical reactions
Endoenzymes
stays intracellular
Constitutive enzymes
alwayspresent irrespective of substrate concentration
Regulated enzymes
induced or repressed in response to substrate concentrations
Labile
chemically unstable enzymes
Denaturationweak bonds that maintain the shape of the protein portion (apoenzyme) are brokenCondensation reactionsanabolic, form bonds and release waterHydrolysis reactioncatabolic, break bonds and require waterEndergonic reactionsconsume energyExergonicrelease energyATP "metabolic currency of the cell"> Consists of adenine (nitrogenous base), ribose and 3 phosphate groups > Energy isin the bond between the last two phosphates3 mechanisms in the cell that produce ATP1. Substrate level phosphorylation - phosphate is transferred from a substrate to ADP to make ATP. (Glycolysis and Kreb's Cycle also known as TCA 2. Oxidative phosphorylation - ATP is produced by the respiratory pathway (Electron transport chain) 3. Photophosphorylation - ATPis produced by energy from sunlight (Photosynthesis)Breakdown of glucose occurs through 3 coupled pathways1. Glycolysis: producesATP; electron carriers NADHand FADH shuttle the electrons to the Electron Transport Chain (ETC) 2. Kreb's cycle: produces ATP; electron carriers NADH and FADH shuttle the electrons to the Electron Transport Chain (ETC) 3. Respiratory chain (Electron transport chain) found in the cell membrane in bacteria3 pathways that convert glucose to ATP1. Aerobic respiration - uses all 3 pathways, 38 ATP produced, molecular oxygen is the last electron acceptor 2. Anaerobic respiration - used all 3 pathways, 36 ATP produced, final electron acceptor is something other than molecular oxygen such asnitrite or sulfite 3. Fermentation - uses only glycolysis, 2 ATP produced, final electron acceptor is an organic compoundChemiosmosisNADH and FADH from Glycolysis and Kreb's Cyle release their electrons to the first protein in the ETC. As electrons are passed to successive proteins in the ETC, hydrogen ions (proteins) are actively pumped across the membrane setting up a gradient of hydrogen ions called the proton motive force. The hydrogen ions then diffuse back through the membrane via the ATP synthase complex resulting in the production of ATP.Genomesum of total genetic material; chromosomes, plasmids, mitochondrial DNA, chloroplast DNAcompare prokaryotic genomes to eukaryotic and viral genomesGenesfundamental unit of heredity in the chromosome3 basic categoriesof genes1. Structural - code for proteins; messenger RNA (mRNA) 2. RNA - code for RNA 3. Regulatory - code for genes that regulate gene expressionGenotypeall types of genes constitute the genetic makeupPhenotypesThe expression of the genotype creates observable traitsStructure of DNA double helix is the nucleotide containing1. 5 carbon deoxyribose 2. Phosphate group 3. Nitrogenous bases-adenine (A),thymine (T), cytosine (C) and guanine (G) > Phosphates connect the riboses of each nucleotide forming the phosphate backbone on the outside of each strand Nitrogenous bases form hydrogen bonds inside of the DNA molecule between the two strands; 2 hydrogen bonds between A and T, 3 hydrogen bonds between C and G Anti-parallel strands, 5' to 3' for one strand and 3' to 5' for the other strandBacterial DNA replication process1. Helicase: unzips or unwinds the DNA double helix to separate strands 2. Primase: lays down an RNA primer to help initiate DNA replication 3. DNA polymerase III: begins adding bases to new DNA chain 4. DNA polymerase I: removes the RNA primer and closes gaps 5. Ligase: final binding of nicks in DNA during synthesis and repair 6. Gyrase: supercoils DNA after replicationSemi-conservative replicationreplication results in each daughter cell having one newly replicated DNA strand and one parental DNA strandUnderstand the DNA code and how this information is conveyed through transcription and translationDNA is read in triplicates of nucleotides (ATGGCCCAG) A. Transcription: DNA is transcribed into: > 3 types of RNA and functions 1. Messenger RNA (mRNA): carries DNA message through complementary copy; message isin tripletscalled codons 2. Transfer RNA (tRNA): secondary structure creates loops; bottom loop exposes a triplet of nucleotides called anticodon which designatesspecificity and complements mRNA; carriesspecific amino acids to ribosomes 3. Ribosomal RNA (rRNA): component of ribosomes where protein synthesis occurs B. Translation: only mRNAis translated into protein3 types of RNA and functions1. Messenger RNA(mRNA): carriesDNA message through complementary copy; message isin tripletscalled codons 2. Transfer RNA (tRNA): secondary structure creates loops; bottom loop exposes a triplet of nucleotides called anticodon which designatesspecificity and complements mRNA; carriesspecific amino acids to ribosomes 3. Ribosomal RNA (rRNA): component of ribosomes where protein synthesis occursRegulation of protein synthesis by operons involves a set of genes regulated together as a single unit> 1. Inducible- operon isnormally turned off and is turned on when a substrate is available to be metabolized so these are catabolic reactions a. Lactose operon: repressor protein binds on the stretch of DNA in the operator region not allowing the RNA polymerase to set down and begin transcription of the genes in the operon. When the inducer (in this case lactose) is present it binds with the repressor which fallsoff the DNA and now those genes can be transcribed that will break down the lactose > 2. Repressible-operon is normally turned on and is turned off when the product of the pathway is no longer required b. Arginine operon: the repressor is the wrong shape to bind to the DNA and sto transcription by RNA polymerase. As the arginine accumulates to a certain concentration it can then bind to the repressor. The repressor now has the right shape to bind to the DNA and stop transcription of the genes in the operonCauses of Mutations on the DNA1. Spontaneous mutations - random changes due to replication errors 2. Induced mutations - exposure to chemical or physical (radiation) mutagensCategories of mutations> Nonsense mutation - changes a normal codon into a stop codon > Silent mutation - altersa base but does not change the amino acid > Back-mutation - when a mutated gene reverses to its original base composition > Frameshift mutation - when the readingframe of the mRNAis altered3 ways for bacteria to undergo genetic recombination-when an organism can receive DNA from another organism. May be advantageous for the bacteria if say an antibiotic resistance gene is acquired or may not have an impact.1. Conjugation - donor bacteria must have a fertility plasmid (F+) in order to make a sex pilus to attach to another organism to transfer the plasmid DNA. Donor and recipient are usually closely related 2. Transformation - chromosome fragments (DNA) from lysed cells around the recipient are taken in through a receptor and converted to a single strand of DNA. That DNA then aligns with the chromosomal DNA and recombines, so now the DNA is part of the chromosome. Donor and recipient don't need to be related. Very useful as a tool in recombinant DNA technology 3. Transduction-a bacteriophage acts as the carrier to deliver the DNA to the recipient. Once phage has injected its DNA, some of the host's cell's DNA can be randomly packages into the phage particle.When this phage then infects another cell the new piece of DNA can be incorporated into this new recipient.Transposonsjumping genes capable of moving within genomeGriffith's experimentshowed that transformation occurs in vivo using live capsular and heat-killed capsular strains.Physical properties of DNA> double strand comes apart at 90-95o C due to breaking of hydrogen bonds between nitrogenous bases. > Useful to then be identified by sequencing, replicated by amplification or transcribed into mRNA, once the DNA is cooled down it will re-hybridize back to the double stranded formUseful enzymes for genetic engineeringRestriction enzymes - recognize palindromes (DNA is identical when read from 5' to 3' on either strand) in the double strand DNA and cleave the DNA resulting in restriction fragments.Molecular methods employed in genetic engineering1. Gel electrophoresis - separates DNA fragments according to size, an electric current is applied and the negatively charged DNA moves toward the positive pole 2. Polymerase chain reaction (PCR) - developed by Kary Mullins to rapidly amplify DNA. Each subsequent cycle of amplification doubled the amount of DNA.Recombinant DNA Technology> the removal of DNA from one organism and combining it with that of another organism. > To do this we need to clone the desired gene by inserting it into an appropriate vector which is usually a plasmid, but can be a bacteriophage as well. To ensure compatibility between the target DNA and the plasmid, both are treated with the same endonuclease (restriction enzyme). This plasmid containing the genes is then transformed into the cloning host. The cloning host will then be able to produce large amounts of your gene of interest.Desirable features of a cloning host1. Capable of accepting a vector 2. Gene you insert is maintained through many generations 3. High expression of the protein 4. NonpathogenicPlasmid being used as a vector needs to have an antibiotic gene present to be able to select for organisms that have taken up that plasmid. This is called selectionGene therapy used to correct or repair a defective gene in humans> used to correct or repair a defective gene in humans 1. Ex vivo therapy 2. In vivo therapy