Biochemistry WGU exam with verified solutions.

RNA polymerase Enzyme that facilitates transcription Transcription synthesis of an RNA molecule from a DNA template Ribosome Large macromolecular complex where proteins are synthesized tRNA (transfer RNA) Form of RNA that is complementary to mRNA. Has a neucleotide anticodon on one end and an amino acid in the other. Translation decoding of a mRNA message into a polypeptide chain Coding strand (DNA) The original strand off which the new nucleotide sequence is based. Almost the same as mRNA template strand (DNA) The strand mRNA uses to make a copy. Complementary to mRNA missense mutation base substitution results in change in an amino acid nonsense mutation changes a normal codon into a stop codon silent mutation change in DNA that codes for the same amino acid Replication process of copying DNA prior to cell division DNA polymerase III synthesizes new DNA only in the 5' to 3' direction Needs a primer to start polymerase chain reaction (PCR) Copying DNA in lab. Used to study/diagnose PCR needs Target DNA dNTPs (deoxyneucleotides) DNA primers Taq polymerase (stable at high temps) Helicase An enzyme that untwists the double helix of DNA at the replication forks. Ligase An enzyme that connects two fragments of DNA to make a single fragment Repair for damage to bases from harmful molecules (like chemicals) Base excision (removes damaged base and replaces it) Mismatch repair Repair for base mismatches due to errors in replication Repair for double stranded breaks in DNA (Radiation/x-rays) Homologous recombination (using sister chromosome as model) Non homologous end joining (no model available) Nucleotide excision Repair for damage from UV which causes adjacent nucleotides to fuse together (thiamine dimers) Amino acid sequence wraps around proteins called Histones Histones organize to form Nucleosomes Nucleosomes organize to form Chromatin Chromatin organizes to form A chromosome Complete dominance When the phenotypes of the heterozygote and dominant homozygote are indistinguishable. Codominance A condition in which neither of two alleles of a gene is dominant or recessive. Both phenotypes are expressed. Incomplete dominance when the phenotypes of the two alleles blend Point mutations chemical changes in just one base pair of a gene frameshift mutations Insertions and deletions 4 parts of an amino acid Carboxyl group Alpha carbon Amino group R side chain COO- I H - C - R I NH3+ Abbreviated structure (amino acid) 3 types of amino acids Hydrophobic Polar Charged Bonds in hydrophobic amino acids C-C, C-H Bonds in polar amino acids O-H N-H S-H Primary protein structure Sequence of amino acids form peptide bonds Secondary protein structure Hydrogen bonding of the peptide backbone causes amino acids to fold into a repeating pattern tertiary protein structure 3-D folding pattern of a protein due to side chain interactions Quaternary protein structure Protein consisting of more than one amino acid chain hydrophobic interactions Weak interactions between amino acids in a protein that come together to avoid water and can be disrupted by heat 2 types of bonds in polar interactions Hydrogen bonds Disulfide bonds Hydrogen bond Weak bond where hydrogen from a polar amino acid attracts an electronegative atom like O & N. Can be disrupted by heat and change in pH. Disulfide bond Very strong covalent bond between two sulfur atoms. Can only be broken by chemical agents. Ionic bonds Bonds in charged interactions between +R group and -R group. Moderately strong, can be broken by change in pH or by salts. Dehydration reaction Creates a peptide bond by removing water. Hydrolysis Breaking peptide bonds by adding water. protein phosphorylation The attachment of a phosphate group of a polar amino acid group. Protein dephosphorylation Removal of a phosphate group of a polar amino acid. competitive inhibitor A molecule similar to a substrate that can bind to the enzymes active site. Reversible Increased substrate=increase in reaction Non competitive inhibitors (allosteric) A molecule that binds to a place on the enzyme other than the active site that changes the shape of the enzyme which interferes with the binding of the substrate. Some reversible, some permanent. Increased substrate does not = increased reaction Feedback inhibition When end product is no longer being consumed and starts accumulating, the end product binds with the initial enzyme, stopping it from bonding with the substrate. Reversible Ways to target enzymes in disease Modify diet (like HFI-removing fructose from diet) Enzyme therapy (like CF to increase digestive enzymes) Drugs that increase substrate of an enzyme(like Parkinson's with LDopa) Drugs that inhibit enzyme activity (like viagra) Myoglobin affinity and location High O2 affinity, stores O2 in muscles Hemoglobin affinity and location Lower O2 affinity, picks up O2 in lungs and delivers to body Myoglobin structure 1 protein subunit (1 heme group and 1 iron) Hemoglobin structure 4 protein subunits Cooperativity In Hgb, if 1 heme gets filled the other 3 want to get filled. If 1 O2 leaves, the others tend to leave. Hemoglobin in the lung -5 qualities Higher O2 affinity Relaxed state Higher pH Low CO2 Low H+ Hemoglobin in muscle-5 qualities Lower O2 affinity Tense state Lower pH High CO2 Lots of H+ The Bohr effect The difference of O2 affinity at different pH Shift to left= in higher pH- higher affinity Shift to right= in lower pH- lower affinity sickle cell anemia cause A mutation in the beta subunit of hemoglobin which leads to insertion of valine into the hydrophobic patches on deoxygenated Hgb. ATP Molecule that fuels our body's activity 3 major steps in aerobic metabolism Glycolysis Citric acid cycle (CAC) or Kreb's cycle Electron transport chain (ETC) Inputs of cellular respiration O2 and sugar Outputs of cellular respiration CO2, H2O, ATP