Lecture 6 Amino acids and sugars MCQ PDF

Introduction to Amino Acids and Sugars 4BICH001W Biochemistry Dr Sarah K Coleman Any questions: You can type in the chat function box during this live session (synchronous)? Or onto the Question Board in the Biochemistry Blackboard module and I will look at them later (asynchronous)....

Introduction to Amino Acids and Sugars 4BICH001W Biochemistry Dr Sarah K Coleman Any questions: You can type in the chat function box during this live session (synchronous)? Or onto the Question Board in the Biochemistry Blackboard module and I will look at them later (asynchronous). Learning Outcomes To define the structural features of amino acids and sugars To be able to classify amino acids and sugars To be able define the term isoelectric point (pI) for an amino acid To be able to state some types of bonding in bio-polymers To be able to explain chirality Side Chains and Functional Groups A functional groups is a specific combination of atoms which make up part of a larger molecule Functional groups will determine activity and polarity of larger molecules Ones of BIOLOGICAL importance are: Carbonyl Carboxyl X Aldehyde Ketone Phosphate Hydroxyl Amino Sulfhydryl  Basic Amino Acid Structure Amino acids have a general structure of two carbon atoms, one in the carboxylic acid group; other has amine group attached. The side chain (R) usually has carbon atoms The central carbon is the alpha-carbon  Functions of Amino Acids Used to make proteins Energy sources from nutrients Pre-cursors to make other molecules (L-DOPA) Important signalling molecules e.g. L-glutamate, GABA, Histidine There are many more than are used to make proteins via universal code GABA Glu L-Dopa from Tyr Amino Acids and basic Molecular Geometry Amino acids have a central carbon atom. That carbon atom has TETRAHEDRAL molecular geometry  Amino Acids and Side Chains Human proteins built from 20 α-amino acids α-amino acids because amino groups is next to α-carbon R groups will determine amino acid identity and properties Naming the atoms: the Greek alphabet is used Lysine Glutamate Lys (Glutamic acid) K Glu E Acid / Base properties of Amino Acids Amino acids have both a BASIC amine group and an ACIDIC carboxylic acid group At physiological pH (7.4) the carboxyl group is dissociated (deprotonated) forming a negative carboxylate ion (COO-) and the amino group is protonated giving a positive ion (NH3+) This forms a ZWITTERION (hybrid ion)  Zwitterions Degree of ionisation of an amino acid depends on surrounding pH values Every amino acid has a specific pH value where the positive and negative charges are equal Thus, the amino acid has no NET charge This is the isoelectric point, known as pI If the pH value of a solution is HIGH (e.g. pH 10) does that mean there is a high or low concentration of Hydrogen ions present? Answer in the chat box  Isoelectric Point, pI The pH at which the majority of molecules in a compound in solution have no net charge. All amino acids have an isoelectric point – influenced by the side chains THUS, all proteins also have an isoelectric point  Amino Acid Side Chains (R groups) Differing chemical properties of amino acids are due to differing side chains Amino acids are sub-classified on the properties of their side chains and functional groups Side chains can vary by: 1) Size 2) Shape and structure 3) Polarity 4) Charge 5) Hydrophobicity 6) Ability to hydrogen bond These will determine properties, structure, shape, functionality of proteins THIS YEAR You will need to know names and matching: Three letter codes Single letter codes By your final year will be expected to be familiar with structure / property of these amino acids and side chains START NOW!  Non-polar side chains Size ranges from small (glycine) to larger (methionine) Shapes from carbon chains (isoleucine) to rings (phenylalanine) R groups do not bind or donate protons R groups do not participate in ionic or hydrogen bonding Alanine, Valine, Leucine and Isoleucine have saturated hydrocarbon R groups Alanine; Ala: A Valine; Val; V Leucine; Leu; L Isoleucine; Ile; I  Non-polar side chains Tryptophan and Phenylalanine have a ring system (see aromatic side chain slide) Methionine has a sulphur atom in the R group Glycine is only non-chiral amino acid; R group is hydrogen Glycine gives flexibility to polypeptides Proline has cyclic ring R group, forms imino group * not an amino group Proline ring makes it structurally restrictive in polypeptides * Methionine; Met; M Glycine; Gly; G Proline; Pro; P  Non-polar side chains R groups are ‘oily’ or hydrophobic (water-hating) Water is a polar molecule R groups will pack together rather than interact with water If in proteins in aqueous solution the R groups will cluster in interior of protein If in membrane embedded proteins the R groups will be outside interacting with lipid environment  Non-charged polar side chains These are the amino acids; serine, threonine, asparagine, glutamine, cysteine and tyrosine Serine and threonine have hydroxyl groups attached which allow phosphorylation secondary modification in proteins Asparagine and glutamine R groups have both a carbonyl and amide group allowing hydrogen bonding Serine; Ser; S Threonine; Thr; T Asparagine; Asn; N Glutamine; Gln; Q  Non-charged polar side chains Tyrosine has a ring system (see aromatic side chain slide) Cysteine R group contains a sulfhydryl group Thiols are reactive – so Cys R group important in many enzyme active sites Cysteine R group allows intramolecular covalent cross-linking in proteins, via the disulphide bond (-S-S-) Cysteine; Cys; C Reduced form Oxidised form  Acidic side chains Aspartic acid and glutamic acid are proton donors At physiological pH 7.4 the R groups fully ionised, so have a negative carboxylate group (COO-) They are called aspartate and glutamate to emphasise they are negatively charged at pH7.4 Aspartic acid; Asp; D Glutamic acid; Glu; E  Basic side chains The R-groups of basic amino acids accept protons At physiological pH lysine and arginine are fully ionised, thus positively charged Histidine is weakly basic, thus its R group may positive or neutral depending upon surrounding environment Lysine; Lys; K Arginine; Arg; R Histidine; His; H  Aromatic side chains Tryptophan has indole ring Phenylalanine and Tyrosine have benzene ring Tyrosine is also a polar amino acid All three are large and bulky amino acids Tyrosine –OH group site of phosphorylation in proteins and hydrogen bonding Tryptophan; Trp; W Phenylalanine; Phe; F Tyrosine; Tyr; Y  Polypeptides formed by linking Amino Acids Glycine Alanine Water Glycyl-alanine The amine group of one amino acid reacts with the carboxyl group of another amino acid. The bond linking two amino acids is called a peptide bond. Condensation reaction – water released. Mathews, van Holde, and Ahern Biochemistry 3rd ed Polypeptide chains cannot branch Hexapeptide (6 amino acids) Biological roles of amino acids The 20 standard amino acids can undergo chemical transformation to make other required compounds Are precursors of many complex nitrogen containing molecules e.g. nucleotides Many non-standard amino acids are synthesised for other functions Over 1000 identified in various plants, fungi and bacteria Other biological roles : Chemical messengers / Neurotransmitters Precursor compounds Metabolic intermediates (often feed into the Citric acid cycle) Toxins  Basic Structure of Carbohydrates Carbohydrates general formula is (CH2O)n , (where n is  3). Monosaccharides are named according to number of carbon atoms present: NAME Carbon Biological examples atoms Triose 3 Glyceraldehyde Tetrose 4 Erythrose (plant metabolite) Pentose 5 Ribose Hexose 6 Glucose Heptose 7 Sedoheptulose (plant metabolite) Other aspects of simple carbohydrate structure (n-1) carbons have a hydroxyl group (-OH) attached. A carbon has EITHER an aldehyde group OR a ketone group attached. Aldose sugars have aldehyde group. Ketose sugars have a ketone group. Aldehyde group is located on C1 carbon; ketone group on C2 carbon. Aldose Ketose  Simple Mono-Saccharide Structures Simple sugars are mono- or di-saccharides Glucose Fructose Haworth projections Glucose Fructose Fischer Projections Glycosidic bond formation: linking saccharides Condensation reaction Water is lost when bond formed Sucrose is a di-saccharide + H2O Glycosidic bond formation: linking saccharides Disaccharides have two monosaccharides e.g. sucrose or maltose or lactose Oligosaccharides have ‘several’ monosaccharides e.g. raffinose or stachyose Polysaccharides MANY (over 10-20) monosaccharides e.g. cellulose, starch, glycogen Polysaccharides can form BRANCHING structures as well as chains Glycosidic bonds can form on multiple carbons in a monomer ring Glycosidic bonds can form with non-saccharide molecules Cellulose is a long, non- branching chain of glucose subunits Glycogen is a long BRANCHING chain of glucose monomers olysaccharides on proteins Many proteins also have carbohydrate components Called glycoproteins O-linked saccharides are via - OH group of serine or threonine N-linked saccharides are via amide nitrogen of asparagine Mathews, van Holde, and Ahern Biochemistry 3rd ed Glycosylation of proteins… Often important for targeting protein to correct location in cell Affects how glycosylated protein will interact with other molecules Incorrect glycosylation plays a role in various diseases and cancers https://rarediseases.org/rare-diseases/congenital-disorders-of-glycosylation/ Human blood antigens – vary due to the complex glycans (polysaccharides) attached Figs. Mathews, van Holde, and Ahern Biochemistry 3rd ed.  Biological roles of carbohydrates (sugars) Simple sugars are energy sources for living organisms Some simple sugars are part of more complex molecules e.g. nucleotides Some complex sugars are energy ‘stores’ for living organisms Some complex carbohydrates have structural roles e.g. cellulose, bacterial cell wall Complex and branching glycans (sugars) label proteins and are used for quality control in cells Other biological roles : Precursor compounds Metabolic intermediates Part of some plant toxins e.g. oleandrin  Isomerism and Chirality Isomers: different molecules but same atomic composition Stereo-isomers: molecules with same groups and bonding, but different spatial organisation Chirality is due to stereo-isomers ; this is the ‘handedness of molecules’ In biological molecules due to the carbon atom bonding or its tetrahedral molecular geometry These occur in sugars and amino acids and has biological relevance  Isomerism and Chirality Isomers: different molecules but same atomic composition Butane, C4H10 Methyl-propane, C4H10  Isomerism and Chirality Isomers: different molecules but same atomic composition Stereo-isomers: molecules with same groups and bonding, but different spatial organisation Cis-butene Trans-butene C4H8 C4H8 Double bonds do not allow rotation in carbon chains.  Chirality is the ‘handedness of molecules’ Chiral molecules exist in 2 forms: The mirror images cannot be superimposed on each other They have a ‘handedness’ All amino acids (except glycine) are chiral Amino Acids and Chirality Chiral molecules have the same MOLECULAR formula They have left- and right-handed isomers called enantiomers All the amino acids used to make your proteins are L-isomers Enzymes and receptors will recognise a specific enantiomer of a chiral molecule GluR respond to L-glutamate but not D-glutamate C3H6NO2 C3H6NO2 Sugars and Chirality Majority of biological mono-saccharides are D-isomers Molecules can have multiple chiral centres Fig. Mathews, van Holde, and Ahern Biochemistry 3rd edition.  Biological Relevance: Chirality in nature To exert an effect a molecular interacts with a receptor or enzyme Proteins are chiral (as amino acids are chiral) Receptors are specific for a particular enantiomer Humans have over 400 olfactory receptors L-Limonene smells of turpentine (possibly lemony) D-Limonene smells of oranges C10H16 (found in oranges) L (-)Limonene D (+)Limonene  Stereochemistry: A tragic case study Thalidomide is a chiral molecule: has (R)- and (S)- enantiomers (R)-enantiomer (R)-enantiomer acts as a sedative and was used to treat morning sickness. (S)-enantiomer acts as a teratogen causing birth defects. It is estimated that worldwide 10000 infants were born with limb malformation and other problems. The enantiomers can inter-convert in vivo. This tragedy led to more stringent drug testing and approval regulations.  Summary Chemical properties and structure of amino acids depends on side chain. Only a small number of amino acids are used to make proteins; they have many other roles. Polypeptides are linear chains of amino acids. Protein structure and properties are influenced by the amino acid side chains. Sugars can be simple (mono- or di-saccharides) or complex (poly-saccharides) Sugars have multiple roles: energy; structural; quality control Sugars can be parts of other molecules Poly-saccharides can form either linear chains or branched chains. Due to the nature of the carbon atom most biological molecules have chirality. Chirality will affect a molecules biological properties. https://web.mit.edu/jmorzins/www/greek-alphabet.html For your interest you do NOT have to memorise MCQ quiz for Lecture 6: Introduction to Amino Acids and Sugars Answers will be given in your Seminar sessions – with further discussion. You must attempt before your seminar session. These quizzes are part of your learning for the Biochemistry module They will aid your on-going studies at the University of Westminster Q1)Which of the following statements about amino acids is correct? a) All amino acids are used to form proteins. b) All amino acids contain a carboxyl group and an amine group. c) All amino acids are chiral. d) Amino acids may be polar or non-poplar but never electrically charged. e) All amino acids are considered as acidic. Q2) Which of the following statements about amino acids is incorrect? a) The amino acid side chain (R group) has an influence on the overall protein structure. b) Amino acids can form zwitterions (hybrid ions both positively and negatively charged). c) The pI of an amino acids is the specific and individual pH where it has no net charge. d) Tryptophan, Tyr, T, all refer to the same amino acid. e) Amino acids can form linear chains only. Q3) Which group of carbohydrates cannot be hydrolysed to give smaller sugars? a) Monosaccharides b) Disaccharides c) Trisaccharides d) Oligosaccharides e) Polysaccharides Q4) Which of the following statements about sugars is incorrect? a) Polysaccharides can form branching or linear chains. b) Monosaccharides can have between 3 to 7 carbon atoms. c) Polysaccharides can attach to proteins. d) Some sugars can have the same atomic composition but different structures. e) Sugars only have biological roles as energy sources and stores or as structural molecules. Q5) Which of the following statements is correct? a) Isomers, stereo-isomers and chirality all refer to the same property of molecules. b) Chiral molecules can be superimposed on each other. c) Chirality has no biological relevance. d) Chirality in organic molecules is due to the tetrahedral molecular geometry of the carbon atom. e) Molecules can have only one chiral centre present.