Biological Chemistry Lecture 5 PDF

BIOLOGICAL CHEMISTRY BLM 11221 Lecture 5 Proteins  Learning Outcomes At the end of this lesson, you’ll be able to; 1. Classify proteins according to the structure, function, composition, and solubility. 2. Identify the common amino acids. 3. Understand about the o...

BIOLOGICAL CHEMISTRY BLM 11221 Lecture 5 Proteins  Learning Outcomes At the end of this lesson, you’ll be able to; 1. Classify proteins according to the structure, function, composition, and solubility. 2. Identify the common amino acids. 3. Understand about the optical activity of the common amino acids. 4. Classify the common amino acids based on the R group. 5. Identify the amphoteric nature of common amino acids.  Classification of Proteins Proteins can be classified in several ways. Classification based on structure Classification based on function Classification based on composition Classification based on solubility  Classification of Proteins – Based on Structure Fibrous proteins These are elongated and insoluble proteins that provide structural support. E.g. collagen, keratin, and elastin Globular proteins These are more compact, generally soluble in water, and have complex shapes. E.g. enzymes, antibodies, haemoglobin Membrane proteins These are found embedded in cell membranes and help with transport, signaling, and communication. E.g. ion channels and receptors  Classification of Proteins – Based on Function Class of protein Function Examples Urease, amylase, catalase, Enzymatic proteins Biological catalysts alcohol dehydrogenase Collagen, elastin, keratin, Strengthening or protecting Structural proteins fibroin biological structures Myoglobin, haemoglobin, Transport or carrier Transport of ions or molecules in lipoproteins proteins the body Nutrient or storage Provide nutrition to growing Ovalbumin, casein, ferritin proteins embryos and store ions  Classification of Proteins – Based on Function Class of protein Function Examples Contractile and mobile Function in the contractile system Actin, myosin, tubulin proteins Antibodies, fibrinogen, Defence proteins Defending against other organisms thrombin Regulate cellular or metabolic Insulin, G protein, growth Regulatory proteins activities hormone Toxic proteins Hydrolyse enzymes Snake venom, ricin  Classification of Proteins – Based on Composition Simple proteins Yield only amino acids when hydrolysed E.g., albumins, globulins Conjugated proteins Consist of a protein part (apoprotein) and a non-protein component (prosthetic group). E.g. glycoproteins (with carbohydrate), lipoproteins (with lipid), and metalloproteins (with metal ions). Derived proteins Proteins that have been modified or degraded from their original form through chemical or physical processes, such as hydrolysis or denaturation. Important in food processing, pharmaceuticals, and biochemistry. E.g. proteans, metaproteins, coagulated proteins, and peptones  Classification of Proteins – Based on Solubility Albumins are water-soluble proteins that coagulate when heated, commonly found in blood plasma. Globulins are insoluble in pure water but soluble in dilute salt solutions, found in blood and milk. Prolamins are soluble in alcohol and commonly found in seeds, e.g., gliadin in wheat. Glutelins are soluble in acids or bases, found in wheat and rice. Amino Acids  Amino Acids Proteins are polymers of amino acids. Twenty different amino acids are commonly found in proteins. The first to be discovered was asparagine, in 1806. All 20 of the common amino acids are α-amino acids. A carboxyl group and an amino group bonded to the same carbon atom known as the α carbon. They differ from each other in their side chains, or R groups.  The Common Amino Acids The common amino acids of proteins have been assigned three-letter abbreviations and one-letter symbols which are used as shorthand to indicate the composition and sequence of amino acids polymerized in proteins.  Identifying the Carbons in an Amino Acid Two conventions are used to identify the carbons in an amino acid. 1. The additional carbons in an R group are commonly designated β, γ, δ, ε, and so forth, proceeding out from the α carbon. 2. Carbon atoms are numbered from one end, giving highest priority (C-1) to the carbon with the substituent containing the atom of highest atomic number.  Amino Acids – Optical Activity For all the common amino acids except glycine, the α carbon is bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom. The α-carbon atom is thus a chiral center. Amino acids have two possible stereoisomers called enantiomers. All molecules with a chiral center are also optically active. The amino acid residues in protein molecules are exclusively L stereoisomers.  Amino Acids Can be Classified by R Group Amino acids can be classified into five main classes based on the properties of their R groups. 1. Non polar, aliphatic R groups 2. Aromatic R groups 3. Polar, uncharged R groups 4. Positively charged (basic) R groups 5. Negatively charged (acidic) R groups  Amino Acids Can be Classified by R Group Non polar, aliphatic R groups – R groups in this class of amino acids are non polar and hydrophobic.  Amino Acids Can be Classified by R Group Aromatic R groups – the aromatic side chains are relatively nonpolar (hydrophobic). Amino Acids Can be Classified by R Group Polar uncharged R groups – R groups of these amino acids are hydrophilic.  Amino Acids Can be Classified by R Group Positively charged (basic) R groups – R groups of these amino acids hydrophilic and contain net positive charge at pH 7.0.  Amino Acids Can be Classified by R Group Negatively charged (acidic) R groups – R groups of these amino acids hydrophilic and contain net negative charge at pH 7.0.  Question Below is a list of uncommon amino acids. Indicate the function(s) of each uncommon amino acid. 4-hydroxyproline 5-hydroxylysine 6-N-Methyllysine γ-carboxyglutamate Desmosine Selenocysteine Ornithine Citrulline  Amino Acids Can Act as Acids and Bases When an amino acid is dissolved in water, it exists in solution as the dipolar ion known as zwitterion. A zwitterion can act as either an acid (proton donor) or a base (proton acceptor). acts as an acid (proton donor) acts as a base (proton acceptor) Substances having this dual nature are amphoteric and are often called ampholytes  Amino Acids Can Act as Acids and Bases A simple monoamino monocarboxylic α- amino acid, such as alanine, is a diprotic acid when fully protonated—it has two groups, the -COOH group and the -NH3+ group, that can yield protons.