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What is the basic structure of an amino acid? What do they look like? correct answers >> amino group (NH2 or NH3), carboxyl group (COO or COOH), alpha carbon (C), and variable group How do you identify the 3 different types of side chains: non- polar/hydrophobic, polar, and charged? correct answers >> Non-polar/hydrophobic - end with CH or "can't have" water. Polar - end with OH, SH, or NH. Charged - end with a charge what kinds of bonds do each of the 3 different types of side chains make? correct answers >> ionic, hydrophobic/non-polar, charged What are the 4 levels of protein structure? correct answers >> Primary - linear structure, Secondary - Folded into helix or pleated sheet caused by hydrogen bonding, tertiary - 3D structure caused by side chain interactions, quaternary - 1+ amino acid chains combine = multiple subunits MUST have 1+ subunit What enviormental change breaks each type of bond? correct answers >> hydrophobic - temperature change, ionic - salt or decreased pH, hydrogen - temperature, change in pH, disulfide - reducing agents what type of amino acid side chain leads to protein aggregration? correct answers >> hydrophobic bonds
how do environmental changes affect protein folding? correct answers >> Extreme temp can cause hydrogen bonds to break apart = malformation of protein folding how do mutations affect protein structure? correct answers >> Can cause structure to change. Protein loses form = loses function. May form a different protein. What is an electron? correct answers >> Negatively charged atom on outer ring for bonding What is energy: correct answers >> Power derived fro chemical interaction what are covalent bonds? correct answers >> chemical bond, atoms share 1+ valence electrons what is an ionic bond? correct answers >> bond between positive and negative what is a hydrogen bond? correct answers >> weak bond between positive and negative with an amino? correct answers >> piece of amino acid, NH or NH what is a carboyxl? correct answers >> piece of amino acid, COO or COOH
what is denaturation? correct answers >> loss of shape duet o interruption of chemical bonds; occurs via extreme salt, temp, pH what is aggregation? correct answers >> clumping of inner or outer cellular proteins caused by misfolded proteins leading to diseases such as Alzheimers, ALS, Parkinson's how do enzymes catalyze reactions? correct answers >> bind with substrates to decrease activation energy required and decrease reaction rate how do enzymes affect reaction rate and activation energy? correct answers >> decrease activation energy and decrease reaction rate what are the 4 steps of the enzymatic cycle? correct answers
enzyme recognizes substrate, substrate attracts the enzyme; enzyme-substrate complex is formed; enzyme-product complex formed; product is released, enzyme recycled how do environmental changes affect enzymes? correct answers >> High heat, pH change, high salt concentration, and reducing agents can cause an enzyme to lose its form/lose function what is a competitive inhibitor? correct answers >> Mimics substrate and takes its place on the active binding site
what is a noncompetitive inhibitor? correct answers >> Binds to allosteric site causing active site to change shape = preventing substrate from binding with enzyme what molecules increase/build up or decrease given a specific inhibitor? A -> (enzyme 1) -> B -> (enzyme 2) -> C -> (enzyme 3) -> D. Pretend Enzyme 2 is inhibited. correct answers >> Inhibitor would cause a build up for product B, decrease product C. Enzyme 3 and product D would not be created. what is substrate? correct answers >> the substance on which an enzyme acts what is a product? correct answers >> result of a reaction what is an intermediate? correct answers >> products produced in an enzyme pathway before final product what is an active site? correct answers >> location where substrate binds with enzyme what is enzyme specificity? correct answers >> Enzymes bind with certain substrate or type of substrate to create a certain reaction what is induced fit? correct answers >> Enzyme changes shape in enzyme-substrate complex to facilitate formation of enzyme-product complex
which nucleotides base-pair together in DNA? correct answers
T-A, G-C which nucleotides base-pair together in RNA? correct answers U-A, G-C how to we make complementary DNA? (i.e. coding to temple et reverse) correct answers >> Taking coding DNA, write in reverse, then pair them up to make template. Template DNA, write in reverse, then pair up to make coding how do we make mRNA? correct answers >> template DNA to mRNA by switching back and forth OR coding DNA to mRNA by switching out T's for U's which strand of DNA is complementary to mRNA? correct answers >> Template DNA how do we make protein? correct answers >> DNA -> RNA - Protein which type of nucleotide sequence is used and in which direction? correct answers >> RNA is used 5' to 3' what is the relationship between mRNA and tRNA? correct answers >> tRNA is complementary to mRNA
how does mRNA splicing allow use to create multiple proteins from a single gene/mRNA? correct answers >> Alternative splicing allows for all introns to be cut and some exons = multiple proteins form from same MRNA what factors increase gene expression? correct answers >> Decreased methylation, increased acetylation, Widely spaced neucleosomes, exposed promoter, use of transcription factors, use RNA polymerase what factors decrease gene expression? correct answers >> Increased methylation/decreased acetylation, tightly packed nucleosomes, hidden promoter, no transcription factors, no RNA polymerase what steps do you take to determine what type of mutation occurred between a normal and mutated DNA/RNA sequence? correct answers >> look between the two strands, determine what changed, name the mutation What are the types of mutations? correct answers >> silent, missense, nonsense, frameshift what type of DNA damage does each repair pathway fix? correct answers >> base excision - single nucleotide, nucleotide excision repair - multiple nucleotides, missmatch - mistakes made in DNA replication, homologous recombination/nonhomologous end joining - double stranded breaks
how are primers used to assist in a PCR reaction? correct answers >> Primers allow DNA polymerase to bind to target DNA how do you calculate the number of copies of DNA produced by specific number of PCR cycles? correct answers >> Each cycle produces doubles the amount of DNA how does PCR compare to normal DNA replication in the cell? correct answers >> RNA primers used instead of DNA in normal replication. Helicase enzymes separate DNA strands instead of heat in normal replication. DNA polymerase is not heat stable in normal replication. what is gene expression? correct answers >> process by which info coded in DNA creates proteins and RNAs What are nucleotides? correct answers >> building blocks of nucleic acids what is antiparallel? correct answers >> refers to arrangement of DNA double helix (run in opposite directions) what is complementary? correct answers >> predictable counterparts what is template DNA? correct answers >> DNA strand, provides pattern for ordering via complementary base pairing in RNA transcript
what is coding DNA? correct answers >> nontemplate strand of DNA, same sequence as mRNA except has T instead of U what is replication? correct answers >> processing of copying DNA molecules via DNA synthesis what is transcription? correct answers >> creation of RNA using info from DNA What is RNA polymerase? correct answers >> enzyme, links ribonucleotides to growing RNA chain during transcription what is a promoter? correct answers >> sequence of DNA that binds with RNA, encourages RNA transcription what is a transcription factor? correct answers >> proteins that bind to promoter regions, help initiate transcription what is mRNA? correct answers >> type of RNA, created via DNA template, specifies primary structure of protein what is translation? correct answers >> creation of polypeptide using info in the mRNA what is tRNA? correct answers >> RNA that brings amino acids to ribosomes during creation of polypeptide
what is acetylation? correct answers >> attachment of acetyl groups to certain amino acids of proteins (mainly histones) what is the structural difference between myoglobin and hemoglobin? correct answers >> myoglobin - primary, secondary, tertiary, single subunit protein (1 heme, 1 iron, 1 O2). hemoglobin - primary, secondary, teriary, quaternary, 4 subunit protein (4 heme, 4 iron, 4 O2) what are the functional differences between myoglobin and hemoglobin? correct answers >> myoglobin - found in muscle, stores O2 in muscle, higher affinity for O2. hemoglobin - found in blood, delivers O2 to tissues in need, decreased affinity for O what are the structural properties of the tense state of hemoglobin? correct answers >> deoxygenated hemoglobin = deep purple color. heme is bent; subunits move farther apart. decreased affinity of O2 binding. what is the structural properties of hemoglobin in the relaxed state? correct answers >> Bright red color. Heme is planar with subunits moved closer, increased affinity of O2 binding what causes hemoglobin to change between relaxed and tense state? correct answers >> O2 binding with hemoglobin in tense state causing subunits to move in closer and change hemoglobin to relaxed state
how does carbon monoxide affect the structure of hemoglobin? correct answers >> locks HgB in R-state, and takes up space on HgB for binding to O how does it cause carbon monoxide poisoning? correct answers >> keeps HgB in R-state, HgB does not release O2. HgB has higher affinity for O2, but CO has higher affinity than HgB for O2. steps of DNA replication to protein? correct answers >> DNA -> transcribed -> mRNA -> translation -> protein what is an okazaki fragment? correct answers >> Okazaki fragments are short molecules of single-stranded DNA that are formed on the lagging strand during DNA replication. how does 2,3-BPG (2,3-DPG) affect structure of hemoglobin? correct answers >> reduces hemoglobin's affinity for O what is the natural function of 2,3-BPG? correct answers >> increases release of O2 in atmosphere with decreased oxygen. efficiently deliver oxygen to fetus. what are we measuring when we measure pH? correct answers
number of H+ protons in blood what level of pH is blood considered acidic? correct answers Below 7.
difference between fetal and adult hemoglobin? correct answers >> fetal hemoglobin has higher affinity for oxygen than maternal hemoglobin. fetal has alpha and gamma forms of hemoglobin while adults have alpha and beta Right left shift curve for decreased pH? increased pH? correct answers >> Decreased pH = right shift curve. Increased pH = left shift curve. what can show an MI? correct answers >> myoglobin - can show muscle damage Examples of monosaccharides correct answers >> glucose, fructose, galactose examples of disaccharides correct answers >> sucrose, lactose, maltose examples of polysaccharides correct answers >> starch, glycogen, cellulose, chitin how do the different linkages between monomers of polysaccharrides affect how they are digested? correct answers >> B linkages - enzymes that break down B linkages, unable to break down A linkages. A linkages - enzymes only able to break down A linkages. structure and function of ATP? correct answers >> 3 phosphate groups + adenosine. provide energy to cell
real-life scenarios that would like to insulin release from pancreas? correct answers >> eating carb rich meal, eating something excessively sugary how does insulin help reduce blood sugar level? correct answers >> promote glycogen formation from excess glucose, stimulates glucose uptake by cells how does glut4 aid in this process? correct answers >> protein channels open in presence of insulin, allow glucose to pass from bloodstream to cell what are some real life scenarios that would lead to glucagon release from the pancreas? correct answers >> blood glucose level getting too low due to fasting how can diabetes lead to glycation and AGEs? correct answers
diabetes is insulin resistance or lack of insulin production = increased blood sugar. glucose links with proteins when there is too much. glycated collagen has decreased elasticity of veins = damage to capillaries, eyes, kidneys, nerves What is catabolism? correct answers >> breaking down molecules what is anabolism? correct answers >> building up what is a carbohydrate? correct answers >> macromolecule. a type of sugar.
what is glycogenolysis? correct answers >> glycogen breakdown, release of glucose what is aerobic metabolism? correct answers >> ATP production using oxygen, breaks down fats and carbs. what is cellular respiratoin? correct answers >> cathbolic pathways of aerobic and anaerboic; break down molecules by using electron trainsport chain for ATP production what is glycolysis? correct answers >> breakdown of glucose, creates 2 new ATP and 2 pyruvate What is the citric acid cycle? correct answers >> creation of 3 NADH and 1 FADH2 and 2 CO2 molecules in each turn of the cycle what is ETC? correct answers >> electron transport chain; accepts electrons from FADH2 and NADH, uses their energy to pump protons to intermember space what does NAD/NADH do? correct answers >> transports electrons of the highest energy to and from complex 1 what does FAD/FADH2 do? correct answers >> transports electrons to/from complex 2
What is substrate level phosphorylation? correct answers >> ATP synthesis by direct transfer of phosphate group to ADP from an intermediate substrate What is oxidative phosphorylation? correct answers >> production of ATP using energy derived from ETC reactions; 3rd stage of cellular respiration what is anaerboic metabolism? correct answers >> atp production without oxygen what is fermentation? correct answers >> catabolic process; makes limited amounts of atp without ETC, produces lactic acid or eythl alcohol what is gluconeogensis? correct answers >> formation of glucose from non-carbohydrate sources what is the cori cycle? correct answers >> fermentation + gluconeogenesis, way to make 2 ATP in muscle what is metformin? correct answers >> diabetic medication for Type 2 DM. Decreased gluceoneogensis in liver/increases glucose uptake by muscle what is glycation? correct answers >> colvalent bond of a sugar to a protein
