BCH 101 Protein PDF

BCH 101 Amino acids/Proteins BY ADEYEMO, ADESEGUN GIDEON  Protein - More than an Energy Source Proteins / polypeptides - chains formed by the condensation/combination of 20 different  - amino acids. Polypeptides - may be di-, tri -, etc; up to 10...

BCH 101 Amino acids/Proteins BY ADEYEMO, ADESEGUN GIDEON  Protein - More than an Energy Source Proteins / polypeptides - chains formed by the condensation/combination of 20 different  - amino acids. Polypeptides - may be di-, tri -, etc; up to 10 a.a. Proteins - longer than 10 a.a. units; ie. MW>10,000  Amino Acids - Protein building blocks An amino acid is a compound having both a carboxyl group(-COOH) and an amino group(-NH2). H All amino acids from protein H2N C COOH have R the -NH2 attached at the C  to the –COOH (as well as the H- & R-). All naturally occurring -amino acids, except glycine (R=H), are chiral and the ‘L’ stereoisomer.  H H2N C COOH There are 20 -amino acids R in naturally occurring protein. By convention the -NH2 is placed ‘to the left’. Each aa has a ‘common’ name often ending in ‘- ine’. There are ~150 other physiologically important amino acids, GABA (a neurotransmitter). Amino Acids - 1 Amino Acids - 2  Amino acids Contain both an acidic functional group (COOH) and a basic one (-NH2), NH or N Thus reactions are highly pH dependent Condensation and Hydrolytic Reactions Figure 6.3  pH dependent properties Zwitterionic structures contain both N-H+ and COO-. At low pH, protonate COO-. At higher pH : lose H on N Isoelectric pH: differs for each amino acid (due to structural differences)  Peptides – Buildup/Breakdown O O H dehydration H2N CH C OH + H N CH C OH hydrolysis CH3 H alanine (ala) glycine (gly) Peptide or amide linkage O O H H2N CH C N CH C OH + H2 O CH3 H carboxylic acid amine end end alanylglycine (ala-gly) -a dipeptide  Essential, Nonessential, and Conditional Essential – must be consumed in the diet Nonessential – can be synthesized in the body Conditionally essential – cannot be synthesized due to illness or lack of necessary precursors – Premature infants lack sufficient enzymes needed to create arginine  Dipeptides Consider the 2 amino acids glycine (G) and alanine (A). How many dipeptides can be made if these are randomly mixed? GG, AA, GA and AG N terminal on LHS; C terminal on RHS  Tripeptides Consider amino acids Glycine (G), Alanine (A) and Phenylalanine (P) How many different tripeptides are possible if each amino acid must be present?  Possible tripeptides 3 choices for the N-terminal amino acid 2 choices for middle 1 choice for the C terminal amino acid Thus 3 x2 x1 =6 choices if each aa must be present. But total number possible is 3 x3x3 =27; includes AAA, PPP, GGG etc  Levels of Protein Structure Primary structure - the sequence of amino acids in the peptide chain and the location of the disulfide bridges. Secondary structure - a description of the conformation/ shape of the backbone of the protein. Tertiary structure - a description of the 3D structure of the entire polypeptide. If the protein has more than one chain it can have a quaternary structure.  Val-Ile-Gly Insulin (21 + 30) Glu Gln Cys Cys-Ser-Leu-Tyr-Gln-Leu-Glu-Asn-Tyr-Cys-Asn Cys-Thr-Ser-Ile Cys-Gly-Ser-His-Leu-Val-Glu-Ala-Leu-Tyr-Leu-Val-Cys-Gly Leu Glu His Arg Gln- Asn-Val-Phe Gly Thr-Lys-Pro-Thr-Tyr-Phe- Phe Secondary (20) Structure - sheets O R H N N H O H – bond O H N N H R O sheets/strands, eg. fingernails, silk Secondary Structure(20) - the -Helix H-bonding - intramolecular  Tertiary Structure of Proteins Arises from weaker attractive forces (non polar dispersion forces) between hydrophobic parts of the same chain that are widely separated in the primary structure, but close in space “intramolecular” Results in chain twisting and folding  Tertiary structure of protein: braids and globs Collagen-a fibrous protein (precursor of gelatin) has a triple helix structure-some elasticity due to interchain interactions Hemoglobin (a globular protein) Tertiary Structure (30) - braids & globs collagen hemoglobin Hemoglobin(H) and Myoglobin (M) H has 4 polypeptide chains : carries O , CO 2 2 and H+ in the blood, and possesses quaternary structure M has a single chain of 153 amino acids: carries O2 from the blood vessels to the muscles and stores it until needed. Both have Fe II containing heme unit in each chain that binds O2. Myoglobin Structure  To summarize Myoglobin cannot have quaternary structure since it has only one polypeptide chain Hemoglobin has 4 polypeptide chains and possesses quaternary structure  Enzyme structure Many enzymes are proteins and their specific binding properties to a substrate depend on their overall molecular shape or “conformation” Lock and key mechanism for activity Active Site of Enzymes Denaturation - any physical or chemical process that changes the protein structure and makes it incapable of performing its normal function. Whether denaturation is reversible depends on the protein and the extent of denaturation. Examples:  heating egg whites (irreversible)  ‘permanent’ waving of hair (reversible)  Proteins by Structure Proteins Simple Conjugated Fibrous Globular Lipo- Glyco- Hemo- insoluble soluble ‘structural’ ‘reactive’ hair, horn enzymes HDL, interferon hemo- LDL globin  Proteins by Structure Fibrous Collagens Elastins Keratins Myosins bones lungs hair/feathers muscles tendons ligaments horn/nails cartilage  Proteins by Structure Globular Albumins Globulins egg whites antibodies(- globulin) enzymes  Proteins by Function Enzymes - the biological catalysts Contractile - muscle Hormones - insulin, growth hormone Neurotransmitters - endorphins Storage - store nutrients, eg. seeds, casein in milk Transport - hemoglobin Structural - collagen, keratins Protective - antibodies Toxins - snake venom, botulinum  (Non)Essential Amino Acids The essential amino acids (10) are those that our bodies cannot synthesize. We must obtain them from our dietary intake. They are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine (and arginine in infants). The non-essential a.a.(10) can be synthesized in our bodies from breakdown products of metabolism.  Vegetarian Diets Main challenge is to get enough high quality protein with the correct balance of essential amino acids Protein Content (approx.%) of Foods cheese 30 peanuts 27 chicken 21 fish 18 beef 18 soy 17 wheat 13 beans 7 rice 8 peas 7 milk 6 corn 4 cassava 3 potatoes 2  Malnourished - the inability to obtain sufficient complete protein, ie. essential amino acids, for the body to function properly. Symptoms - extreme emaciation, bloated abdomen, lack of pigmentation, mental apathy, eventual death, eg. no antibodies, muscle breakdown, capacity of brain diminished ( increases from ~350g at birth to full size(~1200g) by 2 yrs). 1 of every 8 people on Earth suffers malnutrition severe enough to stunt physical and mental growth.