Unit 1

Intro to Human Biochemistry : Intro to Human Biochemistry Who am I? Gum chewer Website Syllabus Lecture and Lab Texts Exams Grading Scantrons Structure of class First 5 units are chemistry and chemistry of Carbs, protein, fats, nucleotides Two units of enzymes and Kreb’s cycle 5 units of metabolism of the macromolecules

Unit 1: Introduction and Review of Organic Compounds : Unit 1: Introduction and Review of Organic Compounds H. Garrett Thompson, Ph.D.

Slide 3 : Biochemistry: the science of substances that occur in living tissue… and the metabolism, function and excretion of the metabolic wastes of these substances by the tissues Overall goal of Human Biochemistry: Understand how chemical structures, properties of substances and chemical processes are related to function in the human body Definition and scope of study

Slide 4 : What substances compose the human body What are the chemical structures and properties of them Where does the body obtain them (e.g. endogenous, diet) What chemical processes are involved in the digestion and absorption of substances derived from the diet How the body utilizes these compounds to synthesize new compounds What catalysts, enzymes and cofactors are What roles do they play in the body How they work Definition and scope of study

Slide 5 : How the body breaks down (catabolizes) compounds to release biochemically utilizable energy How the body stores and uses energy How anabolic and catabolic biochemical reactions are regulated How the body processes and excretes metabolic waste products How biochemical processes are related to heredity What is a gene How they dictate the biochemical processes of cells Definition and scope of study

Slide 6 : How fasting and exercise affect the biochemistry of the body How biochemical abnormalities are related to the pathological conditions of the body (and vice versa) And finally… How BIOCHEMISTRY is applied in clinical practice Definition and scope of study

Slide 7 : Review of Organic Compounds The human body is composed of both inorganic and organic compounds. Inorganic: occur as salts (e.g. hydroxyapatite), free ions or bound to organic molecules Organic: major part of biochemistry, often called biomolecules or biocompounds. Carbon compounds possessing at least one C-H or C-C bond (although there are exceptions: Urea O=C(NH2)2

Slide 8 : Review of Organic Compounds Functional groups: Unique part of the structure of a compound Several atoms arranged in a specific way Most reactive part of the molecule Organic compounds may possess more than one functional group Feature used in classification of the compound Some are prioritized by the IUPAC…determines classification

Slide 9 : Review of Organic Compounds Functional groups: Prioritization 1) –COOH Carboxyl 2) –CHO Aldehyde 3) >C=O Ketone 4) –OH Alcohol 5) –C=C— Alkyne 6) –C=C— Alkene

Slide 10 : Review of Organic Compounds Functional groups: Non-prioritized functional groups –NH2 Amine –ROR Ether –Ar Aryl –X Halogen –R Alkyl –C—H Alkane H Aryl: Simple aromatic ring

Slide 11 : Review of Organic Compounds Classification: Hydrocarbons (composed of only C and H) Alkanes (single covalent bond between carbons) Aliphatic alkanes (open-chain hydrocarbons) Pure alkanes ordinarily do not occur in living cells… but as side-chains of some biochemical compounds Example 1: Alanine (amino acid) COOH H2N –C—H CH3 Example 2: Triglyceride

Slide 12 : Classification: Hydrocarbons (composed of only C and H) Alkanes (single covalent bond between carbons) Aliphatic alkanes (open-chain hydrocarbons)

Slide 13 : Review of Organic Compounds Classification: Hydrocarbons (composed of only C and H) Alkanes (single covalent bond between carbons) Alicyclic or carbocyclic alkanes (cyclic carbon skeleton) Example: cyclobutane C4H8

Slide 14 : Review of Organic Compounds Classification: Hydrocarbons (composed of only C and H) Alkenes (double bond between carbons) Are found in living tissues (ex: ß-carotene) Nomenclature based on alkanes, but ‘ane’ changed to ‘ene’ Aliphatic alkenes (open-chain hydrocarbons) Carbocyclic alkenes Alicyclic : non-aromatic Aromatic: ‘conjugated’ ring (alternating double bonds)

Slide 15 : Review of Organic Compounds Classification: Hydrocarbons (composed of only C and H) Alkenes (double bond between carbons) Aliphatic alkenes (open-chain hydrocarbons)

Slide 16 : Review of Organic Compounds Classification: Hydrocarbons (composed of only C and H) Alkenes (double bond between carbons) Aromatic alkenes (conjugated/resonating/alternating double bonds) Examples: Benzene Phenylalanine CH COOH CH CH H2N—CH CH2 CH CH CH CH CH CH CH CH CH

Slide 17 : Review of Organic Compounds Structural Isomers: Two compounds with the same molecular formulas… but different structural formulas (and therefore different properties) Examples n-butane Isobutane CH3—CH2—CH2—CH3 CH3—CH—CH3 CH3 Cis- and Trans- isomers (a form of stereoisomerism): Two molecules have the same molecular and structural formulas… but different spatial arrangement (and therefore different properties) Examples cis-2-butene trans-2-butene CH—CH3 CH—CH3 CH—CH3 CH3—CH

Slide 18 : Review of Organic Compounds Classification: Hydrocarbons (composed of only C and H) Alkynes (triple bond between carbons) No alkynes are found in living tissue

Slide 19 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Carboxylic acids (–COOH) Fatty acids: Monocarboxylic acids with 3+ carbons usually occur in fats and oils

Slide 20 : BONUS ACTIVITY –3 points

Slide 21 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Aldehyde R–C=O H Methanal Ethanal 3,7-dimethyl-2,6-octadienal Formaldehyde Acetaldehyde Citral (lemon oil) Carbonyl group between alkyl group (or its derivative) and H

Slide 22 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Ketone R–C=O R’ Propanone Butanone poly-hydroxyketone Acetone Methylethyl ketone Fructose Carbonyl group between two alkyl groups (or derivatives)

Slide 23 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Alcohol R–OH Methanol Ethanol Isopropanol Wood alcohol ethyl/grain Rubbing/isopropyl alcohol Hydroxyl group attached to alkyl group (or its derivative) Some alcohols found in living tissues are glycerol, D-sorbitol, and cholesterol (Cholesterol is generally thought of as a lipid due to synthesis and metabolism)

Slide 24 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Phenol Ar–OH Phenol Catechol ?-naphthol Biocompounds with phenolic structure: Dopamine Tyrosine Hydroxyl group attached to cyclic aromatic structure “Catecholamine”

Slide 25 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Quinone Cyclic=O p-benzoquinone Ubiquinone Ubiquinone (or Coenzyme Q or CoQ) is a component of the ELECTRON TRANSPORT CHAIN in the mitochondria… important for generation of ATP

Slide 26 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Ester R1—C—O—R2 O Triglycerides (fats and oils) Triglycerides are formed from one glycerol (an alcohol) and three fatty acids Formed by condensation of acid and alcohol

Slide 27 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Amine R1—N—R2 R3 Histamine Choline Cyclic amines Pyrrole (heme) Indole (Trp, serotonin) nucleotides Formed by replacing one or more H of NH3 with an alkyl (or derivative)

Slide 28 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Amide R1—C—N—R2 O R3 L-glutamine L-asparagine Protein (polymer of amino acids) Formed by carboxylic acids and amines (or ammonia) Amide bond or Peptide bond

Slide 29 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Ether R1—O—R2 Ethyl methyl ether Dimethyl ether methoxyethane Diethyl ether Cyclic ethers of note: Tetrahydrofuran Tetrahydropyran Oxygen between alkyl groups (or derivatives) Medical anesthetic Structural skeletons of 5 and 6 carbon carbohydrates

Slide 30 : Review of Organic Compounds Classification: Derivatives of Hydrocarbons Other In addition to C, H, O, N, P, S… organic compounds may also possess other elements Example: Chloroform (trichloromethane) CHCl3

Slide 31 : Biochemical Organization of a Typical Eukaryotic Cell Cell membrane Phospholipid bilayer, embedded with proteins and cholesterol “Fluid mosaic model” Proteins: receptors, transporters, ion channels, cytoskeleton, etc Cholesterol: affects fluidity of membrane Outer cell membrane: Plasma membrane that protects the cell Intracellular membranes: ER, Golgi, nucleus, mitochondria

Slide 32 : Biochemical Organization of a Typical Eukaryotic Cell Cytoplasm Cytosol Mitochondrion Lysosome Golgi Apparatus Endoplasmic Reticulum Peroxisome Soluble part of cytoplasm. Contains water-soluble cellular substances such as amino acids, glucose, vitamins, ions, enzymes Double membrane structure: POWER PLANT of the cell (produce ATP), also aa deamination and urea synthesis Vesicles with hydrolytic enzymes to degrade intracellular organic compounds… some products can be recycled (eg aa) Contains enzymes for glycosylation of proteins; also membrane synthesis. Substances to be secreted from the cell are packed into vesicles Contains enzymes for phospholipid, steroid, proteoglycan synthesis. Rough ER with ribosomes for protein synthesis Vesicles structures containing oxidases, eg catalase, peroxidase, D-amino oxidase, etc

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Slide 34 : Biochemical Organization of a Typical Eukaryotic Cell Nucleus Surrounded by nuclear membrane Contains chromosomes, nucleolus, nucleoplasm Nucleolus Made of rRNA, when complexed with certain proteins form ribosomes Nucleoplasm Contains soluble substances and enzymes Chromosomes Composed of DNA and certain proteins Genes are segments of DNA

Classes of Biochemical Substances that occur in the Human Body : Classes of Biochemical Substances that occur in the Human Body 1. Amino acids, Peptides, Proteins 2. Carbohydrates 3. Lipids 4. Nucleic acids 5. Vitamins 6. Inorganic substances Primary functional group: COOH. Peptides and proteins are polymers of amino acids… which are amides (not carboxylic acids) Primary functional group: Aldehyde or Ketone Heterogenous: Fats / oils are Esters; Fatty acids are Carboxylic acids; Steroids are Alcohols or Ketones Primary functional group: Phosphoric acid. Polymers are Phosphodiesters Heterogeneous, eg Vitamin A: Retinol (alcohol), Retinal (aldehyde), Retinoic acid (Acid) Ca2+, Mg2+, Cl-, (PO4)3-

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