Structure and Function of Amino Acids, Proteins, and Nucleic Acids, Exams of Nursing

Download Structure and Function of Amino Acids, Proteins, and Nucleic Acids and more Exams Nursing in PDF only on Docsity! WGU C785 2023/2024 What is the basic structure of an amino acid? What do they look like? - ansamino 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? - ansNon-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? - ansionic, hydrophobic/non-polar, charged What are the 4 levels of protein structure? - ansPrimary - 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? - anshydrophobic - 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? - anshydrophobic bonds how do environmental changes affect protein folding? - ansExtreme temp can cause hydrogen bonds to break apart = malformation of protein folding how do mutations affect protein structure? - ansCan cause structure to change. Protein loses form = loses function. May form a different protein. What is an electron? - ansNegatively charged atom on outer ring for bonding What is energy: - ansPower derived fro chemical interaction what are covalent bonds? - anschemical bond, atoms share 1+ valence electrons what is an ionic bond? - ansbond between positive and negative what is a hydrogen bond? - answeak bond between positive and negative with an amino? - anspiece of amino acid, NH2 or NH3 what is a carboyxl? - anspiece of amino acid, COO or COOH What is hydrophobic? - ansDoesn't like water, end with CH what is hydrophilic? - ansWater Lovering, end with OH, NH, or SH what is disulfide bond? - ansstrongest bond between reduction agents, formed between SH's. what are zwitterions? - ansamino with positive and negative charges = overall charge of zero what is a polypeptide - anspolymer of amino acids What is dehydration synthesis? - ansProcess of forming peptide bonds what is hydrolysis? - ansadding water to destroy bonds what is an alpha helix? - anstwisted secondary structure, formed by hydrogen bonds what is a beta sheet? - ansfolded second structure shape, formed by hydrogen bonds what is denaturation? - ansloss of shape duet o interruption of chemical bonds; occurs via extreme salt, temp, pH what is aggregation? - ansclumping of inner or outer cellular proteins caused by misfolded proteins leading to diseases such as Alzheimers, ALS, Parkinson's how do enzymes catalyze reactions? - ansbind with substrates to decrease activation energy required and decrease reaction rate how do enzymes affect reaction rate and activation energy? - ansdecrease activation energy and decrease reaction rate what are the 4 steps of the enzymatic cycle? - ansenzyme 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? - ansHigh heat, pH change, high salt concentration, and reducing agents can cause an enzyme to lose its form/lose function what is a competitive inhibitor? - ansMimics substrate and takes its place on the active binding site what is a noncompetitive inhibitor? - ansBinds 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. - ansInhibitor would cause a build up for product B, decrease product C. Enzyme 3 and product D would not be created. how do we anneal DNA? - ansprimers base pair with DNA strands how do we elongation/extend DNA? - ansDNA polymerase attach primers and synthesize new DNA strands what are the components of PCR? - anstarget DNA, heat stable DNA polymerase, nucelotides (dNTP), primers how are primers used to assist in a PCR reaction? - ansPrimers 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? - ansEach cycle produces doubles the amount of DNA how does PCR compare to normal DNA replication in the cell? - ansRNA 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? - ansprocess by which info coded in DNA creates proteins and RNAs What are nucleotides? - ansbuilding blocks of nucleic acids what is antiparallel? - ansrefers to arrangement of DNA double helix (run in opposite directions) what is complementary? - anspredictable counterparts what is template DNA? - ansDNA strand, provides pattern for ordering via complementary base pairing in RNA transcript what is coding DNA? - ansnontemplate strand of DNA, same sequence as mRNA except has T instead of U what is replication? - ansprocessing of copying DNA molecules via DNA synthesis what is transcription? - anscreation of RNA using info from DNA What is RNA polymerase? - ansenzyme, links ribonucleotides to growing RNA chain during transcription what is a promoter? - anssequence of DNA that binds with RNA, encourages RNA transcription what is a transcription factor? - ansproteins that bind to promoter regions, help initiate transcription what is mRNA? - anstype of RNA, created via DNA template, specifies primary structure of protein what is translation? - anscreation of polypeptide using info in the mRNA what is tRNA? - ansRNA that brings amino acids to ribosomes during creation of polypeptide what are ribosomes? - ansmolecular complex, assist with orderly linking of amino acids/polypeptide chains what are codons? - ansnucleotide triplet of DNA or RNA. Basic genetic code. Specifies type of amino acid or termination signal what are anticodons? - ansnucleotide triplet at one end of tRNA. Base pairs with complementary codon on mRNA what is splicing? - ansparts of transcript are removed and others are reconncected what are introns? - anspieces of noncoding that are removed during RNA processing what are exons? - anspieces of coding that stay with RNA during processing - ARE NOT DISCARDED what are histones? - ansProtein; high proportion and charged amino acid that binds with DNA. Plays key role in chromatin structure. what is a nucleosome? - ansbasic bead like unit of DNA. what is methylation? - anspresence of methyl groups on DNA bases, adding of methyl groups to DNA bases what is acetylation? - ansattachment of acetyl groups to certain amino acids of proteins (mainly histones) what is the structural difference between myoglobin and hemoglobin? - ansmyoglobin - 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? - ansmyoglobin - found in muscle, stores O2 in muscle, higher affinity for O2. hemoglobin - found in blood, delivers O2 to tissues in need, decreased affinity for O2 what are the structural properties of the tense state of hemoglobin? - ansdeoxygenated 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? - ansBright red color. Heme is planar with subunits moved closer, increased affinity of O2 binding what causes hemoglobin to change between relaxed and tense state? - ansO2 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? - anslocks HgB in R- state, and takes up space on HgB for binding to O2 how does it cause carbon monoxide poisoning? - anskeeps 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? - ansDNA -> transcribed -> mRNA -> translation -> protein what is an okazaki fragment? - ansOkazaki 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? - ansreduces hemoglobin's affinity for O2 what is the natural function of 2,3-BPG? - ansincreases release of O2 in atmosphere with decreased oxygen. efficiently deliver oxygen to fetus. what are we measuring when we measure pH? - ansnumber of H+ protons in blood what level of pH is blood considered acidic? - ansBelow 7.2 what level of pH is blood considered basic? - ansabove 7.4 what factors change pH in blood? - ansIncreased or decreased CO2, increased or decreased H+ how to do changes in pH affect hemoglobin's structure? - ansIncreased CO2/Increased pH = T-state, Decreased CO2/Decreased pH = R-state what is a heme? - anssubunit of hemoglobin/myoglobin what is affinity - ansstickiness of oxygen binding what is cooperativity? - ansbinding of O2 to deoxygenated blood what is bicarbonate? - anscarbon dioxide in disguise, outcome of CO2/H2O + carbonic anhydrase what is carbonic anhydrase? - ansenzyme; converts CO2 into bicarb and proton what do chaperones do? - ansassist with protein folding what is gluconeogensis? - ansformation of glucose from non-carbohydrate sources what is the cori cycle? - ansfermentation + gluconeogenesis, way to make 2 ATP in muscle what is metformin? - ansdiabetic medication for Type 2 DM. Decreased gluceoneogensis in liver/increases glucose uptake by muscle what is glycation? - anscolvalent bond of a sugar to a protein What are advanced glycation end products (AGEs)? - anssugars bonded with proteins; effects collagen by decreasing elasticity of blood vessels = damage to nerves, kidneys, and eyes what are the roles of NADH and FADH2? - anstransport electrons from CAC to ETC how is NADH generated in glycolysis? - ansglycolysis consumes 2 NAD to create 2 NADH how are NADH and FADH2 generated in the citric acid cycle? - anseach turn of CAC creates 3 NADH molecules and 1 FADH2 how does the ETC use NADH and FADH2? - ansNADH and FADH2 bring high energy electrons to complex 1 and 2; ETC uses their energy to power the proton pump which complexes accept NAHD and FADH2? - ansNADH -> complex 1, FADH2 -> complex 2 what is the role of the electrons in the ETC? - ansprovide energy to pump protons from mitochondrinal space to intermembrane space what is the role of protons in atp product? - ansprotons provide energy to make atp as they cross the inner membrane what enyme ultimately makes atp? - ansatp synthase what is the role of oxygen in the ETC? - ansoxygen binds with exhausted electrons from complex 4 to create water how do fats and proteins enter aerobic metabolism? - ansproteins -> amino acids -> pyruvate or acteyl CoA or CAC. fats -> fatty acids -> acetyl CoA what are the two different fates of pyruvate? - anspyruvate can be convereted to ethyl alcohol or lactic acid in fermenttaion or acetyl CoA in aerobic metabolism what factors affect the use of pyruvate by the cell? - anspresence of oxygen in the catabolism how are aerobic and anaerobic metabolism the same? - ansboth use glucose, both create ATP and CO2, both use glycolysis in the cytoplasm how are anaerobic and aerobic metabolism the different? - ansaerobic metabolism utilizes oxygen and can produce more ATP (36). Anaerobic metabolism does not use oxygen and creates 2 ATP which aeroboic and anaerobic pathways are controlled by insulin? - ansInsulin inhibits: gluconeogensis, glycogenolysis Insulin promotes: Glycolysis, glycogenesis which aerobic and anarobic pathways are controlled by glucagon? - ansGlugcagon promtes: gluconeogensis, glycogenolysis Glucagon inhibits: glycolysis, glycogensis what are the differences between type 1 and types 2 diabetes? - ansType 1 is an autoimmune disorder effeting beta cells in pancreas, unable to produce insulin. Type 2 is when target cells are not responding to insulin; insulin is produced, but cells aren't receptive/glucose remains elevated how does metformin treat diabetes? - ansdecreases glucogenesis in the liver and increases glucose uptake by the muscle cells how does metformin relate to glut4 and gluconeogensis? - ansglut4 enables glucose to pass from blood to cell in presence of insulin. metformin increases presence of glut4 or makes it more responsive; decreases gluconeogensis in liver. how does length of a fatty acid affect its melting point and physical state at room temp? - ansshorter the fatty acid = lower melting point, liquid at room temp. longer the fatty acid = higher melting point, solid at room temp how do we label the different carbons and bonds in fatty acid? - ansalpha, beta, or omega carbons/bonds and single or double bonds. *alpha bond links with carboxyl group, beta joins alpha and beta together* how do we count the carbons in a full structure of a fatty acid? - ansfrom the omega end how do we count carbons in a structure formula? - ansstart at end, work your way with smalle groups to write mathematical equation counting carbons in a zig-zag struture? - ansmore simplified; carbons at the points (or bends) of zig-zag structure what are the structural differences between saturated and unsaturated fats? - anssaturated fats do not have double bonds between carbons while unsaturated fats do how does affect melting point and physical state at room temp of unsaturated/saturated fats? - anssaturated fats are mostly solid at room temp while unsaturated fats are mostly liquid at room temp how can I recognize structure of triglycerides, cholesterol, and phospholipids? - anstriglycerides - 3 fatty acid chains and 1 glycerol. phospholipids - 2 fatty acid tails and 1 phosphate head. cholesterol - 4 member ring Functions of cholesterol, phospholipid, and triglycerides? - anscholesterol - membrane buffer/maintain integrity of membrane. phospholipid - major component of cell membrane. triglyceride - ATP storage how do we break down a triglyceride? - ansdigested by stomach and small intestine by enzumes such as lipases by using hydrolysis where in the cell does fatty acid breakdown occur? - ansmatrix of mitochondria what happens to the different components of the triglyceride? - ansbroken into glycerol and fatty acids. picked up by epithelial cells. how do we break down a fatty acid? - ansbeta oxidation where in the cell does beta oxidation take place? - ansFatt acetyl CoA molecules enter mitochondrial matrix and begin beta oxidation cycle what are the 3 products of beta oxidation? - ans1 acetylCoA, 1 NADH, 1 FADH2 how do we calculate the number of acetylCoA produced from a fatty acid? - ansnumber of carbons in a fatty acid divided by 2 how do we calculate the number of rounds it takes to break it down completely? - ansone less than the number of acetylCoA moleules produced how do we calculate the amount fo ATP produced? - ansnumber of acetylCoA molecules mulitplied by 14 what happens to the products of beta oxidation after they are produced? - ansenter ETC for further ATP production how and why are ketone bodies produced? - ansproduced by breaking down fatty acids in liver cell's mitochondria; produced when body has decreased carbs or increased fatty acids for energy needs. Ketones make 22 ATP each. **alternative energy form** ***Seen with Type 1 DM, starvation, alcoholism*** what is the molecule use for fatty acid synthesis? - ansacetyl-COA how is acetyl-COA exported from the mitochondria to the cytosol? - ansmust pair with oxaloacetate to make citrate, cross into cystol, break apart to become acetylCOA again what is a micelle? - ansspherical single layer of phospholipids; transport fatty acids, vitamins, and cholesterol what is an adipocytes? - ansfat cells what is lipase? - ansenzyme that catalyzes triglyceride breakdown what is lipolysis? - ansbreakdown of lipids what is beta oxidation? - ansfatty acid breakdown in mitochondria to 1 acetyle COA, 1 NADH, and 1 FADH2 what are ketone bodies? - ansalternative energy form; comes from fatty acid breakdown what is ketoacidosis? - ansaccumulation of too many ketones within the body what is MCADD? - ansdefect in enzyme used for beta oxidation; need to avoid fasting, eat slow release carbs what is fatty acid synthesis? - anslinking of acetylCOA repeatedly to make new fatty acids in the cytoplasm what is oxaloacetate? - ansIntermediate that couples with acetyl Co-A to form citrate what is citrate? - ansBridge between carb and fatty acid metabolism; important for fatty acid synthesis what is amphipathic? - ansmolecules that are hydrophilic and hydrophobic what is the phospholipid bilayer? - anspolar heads interact with watery environment; nonpolar tails remain inside to avoid water. controls in/out of cell. what is the plasma membrane? - ansboundary of every cell, acts as selective barrier, regulates chemical composition what is a glycolipid? - anslipid + sugar; bases for A, B, and O blood types what is a glycoprotein? - anssugar + protein; basis for A, B, and O blood types what is an essential fatty acid? - ansomega 3 and omega 6 fatty acids, must be eat thru diet what is an eicosanoid? - ansclass of lipids derived from essential fatty acids; act as local hormones generated as needed; control fever/pain/BP/reproduction/blood coagulation what is an arachidonic acid? - ansprecursor to ecosanoids what is chylomicron? - ansLipid transport globule composed of fats mixed with cholesterol and coated with proteins what is a cis fat? - anshave both hydrogen atoms on the same side of the double bond; have a kind or bend in the carbon chain, make it difficult for the fatty acids to pack together what is a trans fat? - anshydrogen atoms are on opposite sides of the double bond; trans fatty acids can pack tightly like saturated fats = higher melting point example of cis fat? - ansunsaturated natural oils example of trans fat? - ansmargarine; raises blood cholesterol levels and increases risk of heart disease what makes LDL? - anshigh cholesterol what is cholesterol needed for? - anssynthesize vitamin D in the skin, cholic acid, steroid hormones what don't RBCs have? - ansmitochondria what supplies glucose to RBCs? - anscori cycle why does a runner eat high carbs a day before a race? day of? - ansday before - gluconeogensis building up for race day; day of - glycolysis because its burned right away