Biochemistry Module 3 Exam 2025

List the 5 functions of proteins - -Transport, hormones, catalysis, structure, protection Define transport function of proteins and example - -helps to move molecules around the cell and organism, ex: Hemoglobin is a blood-based protein that carries oxygen from the lungs to tissue Define hormone function of proteins and example - -Hormones communicate messages between cells, ex: relaxin is a protein hormone that helps women relax pelvic ligaments during childbirth Define catalysis function of proteins and example - -Enzymes speed up or catalyze chemical rxns, ex: protease enzyme breaks down proteins in cells to help organisms recycle unneeded proteins Define structure function of proteins and example - -Proteins give strength to cells, organelles and tissues, ex: collagen is the structural protein in cartilage, skin and tendons Define amino acids - -building blocks of proteins What functional groups do amino acids contain? - -amine and carboxylic acid What permits all amino acids to link together in a protein? - -Each amino acid having the same groups What is the R group in an amino acid and how are they grouped? - -Side chain of the amino acid; there are 20 different side chains that differ in composition/size/charge so side chains are grouped by charge, size and polarity What pH do amino acids exist at? - -7.4 What do amino acids lose and gain at pH of 7.4? - -Lose the carboxylic acid H group and gain an extra proton (NH3+) Name the 5 sets of amino acids - -Non-polar aliphatic, non-polar aromatic, polar neutral, acidic, basic Define non-polar aliphatic amino acids - -Straight chain amino acids Name the 7 nonpolar, aliphatic amino acids - -glycine (Gly, G), alanine (Ala, A), proline (Pro, P), valine (Val, V), leucine (Leu, L), isoleucine (Ile, I), methionine (Met, M) Biochemistry Biochemistry Name the 7 nonpolar, aliphatic amino acids in abbreviations - -Gly, Ala, Val, Pro, Leu, Ile, Met Describe aliphatic amino acids and their location in proteins - -Relatively small which allows them to interact with other groups, found in interior of protein away from water with other aliphatic groups (fold together) Why is proline unique? - -its side chain makes a ring by bonding with its main chain nitrogen How do non-polar aromatic groups compare to aliphatic? (5 reasons) - -similar to aliphatic in that they are non-polar, but the side chains of these compounds contain a ring of carbons as an aromatic functional group, not as small as the aliphatic, but they are more rigid, aromatic ring structures have unique physical and chemical properties Why are the benzene rings important in aromatic groups? - -The double bonds (conjugated system) absorb light well for proteins Name the 3 non-polar aromatic groups - -Phenylalanine (Phe,F), Tryptophan (Trp,W), Tyrosine (Tyr,Y) Describe the polar neutral amino acids and location in proteins - -side chains that have a dipole, and most can hydrogen bond, permits these amino acids to interact strongly with water, found on the outside of the protein and in contact with water Name the 5 polar neutral amino acids - -Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Asparagine (Asn, N), Glutamine (Gln, Q) Describe the acidic amino acids - -side chains with pKa values smaller than 7, which indicates they lose their proton in the acidic pH range, at physiological pH (7.4) that these amino acids are negatively charged Name the 2 acidic amino acids - -aspartic acid (Asp, D), glutamic acid (Glu, E) Describe basic amino acids - -pKa that is near or greater than pH = 7, which means their side chains are normally positively charged, found in contact with water because they hydrogen bond, located near acidic residues in proteins to take advantage of favorable interactions between positive and negative charges Name the 3 basic amino acids - -lysine (Lys, K), arginine (Arg, R), histidine (His, H) Why is Histidine unique? - -Does not have a charged group on its side chain, but can be charged under certain circumstances, also has lower pKa of 6 Biochemistry Biochemistry Why is Cysteine unique? - -its side chain is uncharged, but two cysteines can react together and can form a disulfide bond by their sulfur atoms which forms a covalent bond What are the functions of disulfide bonds? Where are they found? - -Stabilize a protein structure when present, found in proteins that exist outside of the cell (keratin in hair) Define polypeptides - -long chains of amino acids What does DNA do for amino acids? - -Dictates the exact sequence of amino acids Where does the synthesis of all proteins begin? - -Ribosomes Describe ribosome synthesis - -Amino acids are covalently linked together to form protein How is a dipeptide formed? - -The amino functional group of one amino acid reacts with the carboxylic acid functional group of a second, resulting in two monomers joined together with release of water Define condensation reaction - -A reaction that releases a molecule of water (one oxygen from carboxylic acid and two Hs from amine) when it links molecules together Define peptide bond - -Rigid amide bond that links two amino acids together into dipeptide What's special about the ends of the dipeptide? - -The ends have reactive amine and carboxy groups which permit them to form additional peptide bonds Define oligopeptide - -Short chain of amino acids from two to twenty amino acids, has an amino-terminal end (N-terminal end) and a carboxy-terminal end (C-terminal end) Define protein backbone - -All peptide bonds in protein form this which links all amino acids together, highlighted by ribbon diagrams What is the other name for amino acids and why? - -Residues to reflect the molecule remaining after condensation reaction takes place Compare polypeptide and protein classification - -When the number of residues is 99 or less, we say that it is a polypeptide, After 100 residues have been added together, it is said that the molecule is a protein What is albumin? - -Blood soluble protein that regulates osmotic pressure of blood and bonds ions and fatty acids and carries them in bloodstream When a protein has 100 amino acids protein mass is about... - -10,000 g/mol Biochemistry Biochemistry Define Dalton (Da) - -Unit to replace g/mol for protein mass (kilodaltons used as well) Conversion of kilodalton to Dalton - -1kDa = 1,000 Da Define supramolecular chemistry - -Chemistry of large compounds Examples of supramolecular chemistry in biochemistry - -Proteins folding into specific shapes or conformers, interaction of more than one protein, DNA double helix formation Define conformation - -3D structure of a protein that can be either fibrous or globular Define intrinsically disordered - -Random conformation of proteins Name the four standard levels of protein structure - -Primary, secondary, tertiary, quaternary Define primary structure of protein - -Order of amino acids covalently bonded together, including disulfide bonds, in a polypeptide chain How do you write an amino acid sequence? - -Start with N-terminal amino acid residue on left, continue to right towards C-terminal Define secondary structure - -Used to examine local 3D structure of amino acid residues close in linear sequence Name the 3 types of secondary structure - -Alpha-helices, beta-sheets, beta-turns Define alpha helices - -Coiled structures of amino acids where backbone atoms form hydrogen bonds to stabilize sequence Describe a standard helix structure - -3.6 amino acids per each turn while rising 5.4 angstroms per turn Angstrom conversion - -1 angstrom = 1 x 10-10m What amino acids are common in a helix and which are not? - -alanine, arginine, and leucine, are more common in a helix; proline and glycine are much less likely to be found in this secondary structure What do ribbon diagrams highlight about secondary structure? - -The ribbon follows the path of the backbone What do the R groups to in the helix? - -Point out from