bio 204 - biochem lecture

• Protein

  A naturally-occurring, unbranched polymer in which the monomer units are amino acids
• Proteins


  • They are the most abundant molecules in cells after water, accounting for about 15% of a cell's overall mass
  • They contain C, H, N, O, and often S
  • The average nitrogen content of proteins is 15.4% by mass
  • They also contain iron (Fe), phosphorus (P) and some other metals in some specialized proteins
• Amino acid


  An organic compound that contains both an amino (-NH2) and carboxyl (-COOH) groups attached to the same carbon atom
• Amino acids


  • The alpha carbon atom is the position of the carbon atom
  • The -NH2 group is attached at the alpha carbon atom
  • The -COOH group is attached at the alpha carbon atom
  • The R-group is the side chain, which varies in size, shape, charge, acidity, functional groups, hydrogen-bonding ability, and chemical reactivity
  • There are over 700 known amino acids, but the standard amino acids are divided into 20 based on the properties of the R-groups
• Types of amino acids based on R-group properties


  • Non-polar (hydrophobic)
  • Polar neutral
  • Polar acidic
  • Polar basic
• Chirality


  • 19 of the 20 standard amino acids contain a chiral center, exhibiting left-handed (L) and right-handed (D) forms
  • The amino acids found in nature and in proteins are the L isomers
• Zwitterion


  An ion with both positive and negative charges on the same molecule, resulting in a net zero charge
• Isoelectric point (pI)


  The pH at which the concentration of the zwitterion is maximum and the net charge is zero
• Cysteine


  The only standard amino acid with a sulfhydryl (-SH) group, which allows it to form covalent disulfide bonds (cystine)
• Peptide


  An unbranched chain of covalently-linked amino acids
• Types of peptides based on length


  • Dipeptide (2 amino acids)
  • Oligopeptide (10-20 amino acids)
  • Polypeptide (large number of amino acids)
• Peptide nomenclature


  • The C-terminal amino acid keeps its full name, while the other amino acids have names ending in -yl
  • The naming sequence begins at the N-terminal amino acid
• Peptides with the same amino acids but in different order are different molecules (constitutional isomers) with different properties
• Biochemically important small peptides


  • Hormones
  • Neurotransmitters
  • Antioxidants
• Protein structure


  • Primary structure: the order of amino acids
  • Secondary structure: alpha-helix and beta-pleated sheet
  • Tertiary structure
  • Quaternary structure
• Frederick Sanger sequenced and determined the primary structure of the first protein - insulin
• Alpha-helix


  A single protein chain adopts a coiled spring shape, with hydrogen bonding between the same amino acid chains
• Beta-pleated sheet


  A completely extended amino acid chain, with hydrogen bonding between different chains
• Arrangement of atoms of backbone in space


  • The two most common types: alpha-helix (a-helix) and the beta-pleated sheet (b-pleated sheet)
• Peptide linkages


  1. Essentially planar

  2. Allow only two possible arrangements for the peptide bond

  3. Six atoms lie in the same plane

  4. Planar peptide linkage structure has considerable rigidity, therefore rotation of groups about the C-N bond is hindered

  5. Cis-trans isomerism is possible about C-N bond

  6. The trans isomer is the preferred orientation
• Alpha-helix (a-helix)


  • A single protein chain adopts a shape that resembles a coiled spring (helix)
  • H-bonding between same amino acids chains – intra molecular
  • Coiled helical spring
  • R-group outside of the helix – not enough room for them to stay inside
• Beta-pleated sheets


  • Completely extended amino acid chain
  • H-bonding between two different chains-interior and/or intramolecular
  • Side chains below or above the axis
• Tertiary structure of proteins


  • The overall three-dimensional shape of a protein
  • Results from the interactions between amino acid side chains (R groups) that are widely separated from each other
• Four types of interactions in tertiary structure


  • Disulfide bond: covalent, strong, between two cysteine groups
  • Electrostatic interactions: salt bridge between charged side chains of acidic and basic amino acids
  • H-Bonding between polar, acidic and/or basic R groups
  • Hydrophobic interactions: Between non-polar side chains
• Quaternary structure of proteins


  • Refers to the organization among the various peptide chain in a multimeric protein
  • Highest level of protein organization
  • Present only in proteins that have 2 or more polypeptide chains (subunits)
  • Subunits are generally independent of each other – not covalently bonded
  • Proteins with quartenary structure are often referred to as oligomeric proteins
  • Contain even number of subunits
• Protein classification based on shape


  • Fibrous
  • Globular
  • Membrane
• Fibrous proteins


  • Protein molecules with elongated shape
  • Generally insoluble in water
  • Single type of secondary structure
  • Tend to have simple, regular, linear structures
  • Tend to aggregate together to form macromolecular structures (hair, nails)
• Globular proteins


  • Protein molecules with peptide chains folded into spherical or globular shapes
  • Generally water soluble – hydrophobic amino acid residues in the protein core
  • Function as enzymes and intracellular signalling molecules
• Membrane proteins


  • Associated with cell membranes
  • Insoluble in water – hydrophobic amin acid residues on the surface
  • Help in transport of molecules across the membrane
• Alpha-keratin


  • Provide protective coating for organs
  • Major protein constituent of hair, feather, nails, horns and turtle shells
  • Mainly made of hydrophobic amin acid residues
  • Hardness of keratin depends upon -S-S- bonds
  • More -S-S- bonds make nail and bones hard
• Collagen


  • Most abundant proteins in humans (30% of total body protein)
  • Major structural material in tendons, ligaments, blood vessels, and skin
  • Organic component of bones and teeth
  • Predominant structure – triple helix
  • Rich in proline (up to 20%) – important to maintain structure
• Myoglobins


  • An oxygen storage molecule in muscles
  • Monomer- single peptide chain with one heme unit
  • Binds one O2 molecule
  • Has a higher affinity for oxygen than hemoglobin
  • Oxygen stored in myoglobin molecules serves as a reserve oxygen source for working muscles
• Hemoglobin


  • An oxygen carrier molecule in blood
  • Transports oxygen from lungs to tissues
  • Tetramer (four peptide chains) – each subunit has a heme group
  • Can transport up to 4 oxygen molecules at time
  • Iron atom in heme interacts with oxygen
• Major categories of proteins based on function


  • Catalytic proteins (enzymes)
  • Defense proteins (immunoglobulins or antibodies)
  • Transport proteins
  • Messenger proteins
  • Contractile proteins
  • Structural proteins
  • Transmembrane proteins
  • Storage proteins
  • Regulatory proteins
  • Nutrient proteins
• Protein hydrolysis


  1. Reverse of peptide bond formation

  2. Results in the generation of an amine and a carboxylic acid functional groups

  3. Digestion of ingested protein is enzyme-catalyzed hydrolysis

  4. Free amino acids produced are absorbed into the bloodstream and transported to the liver for the synthesis of new proteins

  5. Hydrolysis of cellular proteins and their resynthesis is a continuous process
• Protein denaturation


  Partial or complete disorganization of proteins's tertiary structure
• Protein denaturation


  • Cooking food
  • Coagulation: precipitation (denaturation of proteins)
  • Egg white- a concentrated solution of protein albumin – forms a jelly when heated because the albumin is denatures
  • Cooking denatures proteins- makes it easy for enzymes in our body to hydrolyze/digest proteins
  • Cooking kills microorganisms by denaturation of proteins
  • Fever: >104F – the critical enzymes of the body start getting denatured
• Glycoproteins


  • Conjugated proteins with carbohydrates linked to them
  • Many of plasma membrane protein are glycoprotein
  • Blood group markers of the ABO system are also glycoproteins
  • Collagen and mmunoglobulins are glycoproteins
  • Collagen – glycoprotein
  • Most abundant protein in human body (30% of total body protein)
  • Triple helix structure
  • Rich in 4-hydroxyproline (5%) and 5-hydroxylysine (1%) – derivatives
  • Some hydroxylysine are linked to glucose, galactose, and their disaccharides – help in aggregation of collagen fibrils
• Immunoglobulins


  • Glycoproteins produced as a protective response to the invasion of microorganisms or foreign molecules- antibodies against antigens
  • Immunoglobin bonding to an antigen via variable region of an immunoglobin occurs through hydrophobic interactions, dipole – dipole interactions, and hydrogen bonds
• Lipoproteins


  • A conjugated protein that contains lipids in addition to amino acids
  • Major function: help suspend lipids and transport them through the blood stream
  • Four major classes of plasma lipoproteins: Chylomicrons, Very-low-density lipoproteins (VLDL), Low-density lipoproteins (LDL), High-density lipoproteins (HDL)