Chemical Bonds • The interaction between 2 atoms may result in the formation of a chemical bond whereby 2 atoms are chemically linked to one another – 2 major types • Ionic • Covalent • Atoms bond with one another to become stable – an atom is stable when the valence shell is completely full (satisfying the “octet rule”) • Groups of atoms that are associated with each other through bonds are called molecules – chemicals that are LARGER and structurally more

CoMpLe

X

than individual atoms

Molecules • Molecules – two or more atoms bonded together • carbon dioxide (CO2), Glucose (C6H12O6), water (H2O), sodium chloride (NaCl)…

Nonpolar and Polar Molecules • Nonpolar molecules include those containing a high number of nonpolar covalent bonds and few polar covalent bonds (very little or no O and/or N) – lipids (fats) • uncharged (neutral) molecules • Polar molecules include those containing a moderate number of polar covalent bonds (moderate amounts of O and/or N) • include every other substance: – carbohydrates, proteins, nucleic acids, water… – ions (cations and anions) • charged molecules

Hydrogen Bonds • Electrical attraction between a polar covalently bound H (has a partial positive charge) and a covalently bound electronegative atom (O/N) (has a partial negative charge) • Too weak to bind atoms together – serve as intramolecular (within molecule) bonds • aids in the stabilization of very large molecules • observed in proteins and nucleic acids – serve as intermolecular (between molecules) bonds • holds 2 or more molecules in close proximity to one another • observed in between water molecules

Hydrogen Bonds in Water (intermolecular)

Water

• The most abundant molecule of the human body – 70% of body mass (weight) is attributed to water • Polar substances mix easily with other polar substances, but do not mix with nonpolar substances (REMEMBER THIS) • Nonpolar substances mix easily with other nonpolar substances, but do not mix with polar substances (REMEMBER THIS) – like dissolves like • The majority of the chemicals found in the body are polar, however lipids are molecules essential for proper functioning of the body

Polarity (Water vs Lipids) • All polar chemicals mix with water and are considered to be hydrophilic (water loving) – polar chemicals that mix with water will not mix with lipids and are considered to be lipophobic (lipid fearing) • All nonpolar chemicals mix with lipids and are considered to be lipophilic (lipid loving) – Nonpolar chemicals that associate with lipids will not mix with water and are considered to be hydrophobic (water fearing) • Polar = hydrophilic = lipophobic • Non-polar = hydrophobic = lipophilic

Properties of Water • Solvency – ability to dissolve matter • because water is the most abundant compound in the body it is the universal solvent • environment for all metabolic reactions • provides a means for the transport of substances from one location in the body to another • Adhesion and Cohesion – molecules of water “stick” to themselves and other types of molecules • due to hydrogen bonds • High heat capacity • prevents rapid increases or decreases in temperature

Biochemical Reactions • The functioning of the body (physiology) occurs as the organic molecules of the body react with one another • Written symbolically with chemical equations – relative amounts of reactants (starting chemicals) and products (finishing chemicals) – number and type of reacting substances, and products produced • C6H12O6 + 6O2  6H2O + 6CO2 • Chemical reactions occur when covalent bonds in a molecule are formed or broken – the formation of a covalent bond uses energy – the breaking of a covalent bond releases energy • All chemical reactions are theoretically reversible A + B ↔ AB CO2 + H2O ↔ H2CO3 ↔ HCO3- + H+

Work and Energy • Energy – capacity to do work • Kinetic energy – energy of motion • Potential energy – energy due to object’s position

Energy Sources • Energy sources that the body uses includes: – Chemical • stored in the covalent bonds of energy-rich molecules (potential) – Electrical • the movement of ions (potential and kinetic) – Heat • causes molecules to move (kinetic) – Mechanical • moving molecules collide with one another which transfers energy between the two molecules (kinetic) • Energy sources can be converted from one form to another

Metabolism and Biochemical Reactions • All of the collective biochemical reactions of the body are grouped into two general classes: – Catabolic (exergonic) reactions • decomposition reactions that release energy (due to bonds breaking) in the form of HEAT into the environment of the reaction • reactants contain more energy than the products – Anabolic (endergonic) reactions • synthesis reactions that remove (store) energy (HEAT) from the environment of the reaction to create bonds • products contain more energy than the reactants • All reactions must overcome the activation energy before the reaction takes place – energy required to bring reactants together

Energy Flow in an Exergonic Reaction

Organic Molecules • Molecules unique to living systems contain carbon and are referred to as organic molecules • Most of the anatomy and physiology of the body is provided by the interaction between 4 different classes of organic macromolecules • Each class consists of small molecular subunits called monomers (one unit) – smallest subunits of macromolecules that exhibit chemical properties of the macromolecule • Monosaccharide (carbohydrates) • Fatty acid (lipids) • Amino acid (proteins) • Nucleotide (nucleic acids) – able to function individually or in covalently bound groups

Biologically Important Organic Molecules • Monosaccharides – basic (smallest) unit of carbohydrates (sugars) • Amino acids – basic (smallest) unit of proteins • Fatty acids – basic (smallest) unit of lipids (fats) • Nucleotides – basic (smallest) unit of nucleic acids

Synthesis Reactions of Macromolecules • Monomers can be covalently bound to one another to create a molecule gets progressively larger resulting in a polymer (many units) • Two or more small molecules combine to form a larger one • A+B  AB+C  ABC+D  ABCD…

Dehydration Synthesis • 2 monomers are covalently bonded together to form a a new molecule that is larger and structurally more complex by the removal of a water molecule (dehydration)

Decomposition Reactions • Large polymer molecules can be reduced down to the individual monomers by breaking the covalent bond between monomers through a decomposition reaction • ABC  AB+C  A+B+C

Hydrolysis • Splitting a polymer by the addition of a water molecule

Exchange Reactions • Two molecules collide and exchange atoms or group of atoms • AB+CD  ABCD  AC + BD

Oxidation-Reduction (Redox) Reactions • Involves the transfer of electrons from one atom/molecule to another – eg. formation of an ionic bond • Reactants losing electrons are become oxidized (Loss Electron(s) Oxidation = LEO) • Reactants gaining electrons are become reduced (Gain Electron(s) Reduction = GER) • Na + Cl → Na+ + Cl– Na is oxidized and Cl is reduced

Reaction Rates • The rate of chemical reactions are determined by molecular motion and collisions between chemicals • The speed at which a chemical reaction proceeds is affected by: – the concentration of reactants • more concentrated = more collisions = faster rate – the temperature • higher temperature = faster molecular movement = more collisions = faster rate – the presence of catalysts • “molecular matchmakers” –bring reactants together faster • biological catalysts are proteins called enzymes

Macromolecules

Carbohydrates • “hydrated (H2O) carbon” • Contain carbon, hydrogen, and oxygen • Carbohydrate names end in the suffix “-ose” – glucose, maltose, amylose, fructose, sucrose • The monomer of carbohydrates is the monosaccharide (one sugar) of which there are a number of types – glucose is the most biologically important • Carbon:Hydrogen:Oxygen in a 1:2:1 atomic ratio – glucose = C6H12O6 • Because they contain oxygen, they are polar molecules (hydrophilic or lipophobic)

Monosaccharides • Simplest molecular form of carbohydrates • Three major monosaccharides – obtained by the digestion (hydrolysis) of dietary polysaccharides – major function is to supply a source of cellular fuel for the creation of chemical energy (adenosine triphosphate ATP) • Structural isomers (same formula (C6H12O6), different structure

Disaccharides • Pairs of monosaccharides covalently bonded together • Three major disaccharides – sucrose • glucose + fructose – lactose • glucose + galactose – maltose • glucose + glucose

Polysaccharides • Long chains of glucose form polysaccharides • Starch (amylose) – form of stored carbohydrates produced by plants – the main source of dietary carbohydrates – hydrolyzed to glucose molecules in the digestive tract then distributed to all cells of the body

Polysaccharides • Excess glucose in the body following the hydrolysis of dietary carbohydrates is taken up by the liver and is used to synthesize the polysaccharide glycogen – the liver gradually hydrolyzes glycogen to glucose between meals and releases it into the bloodstream for distribution to all cells of the body

Lipids • Nonpolar organic molecules made mostly of carbon and hydrogen • Energy rich molecules that can be used for energy – typically occurs when there is an absence of usable carbohydrates in the body • Major molecule that provides structure to biological membranes • Used as signaling molecules for communication between cells (steroid hormones)

Fatty Acids

• Hydrocarbon chains of 4 to 24 carbon atoms (always an even number) bound to hydrogen atoms • Has more energy per molecule than glucose • 2 different functional groups are at each end – carboxylic acid group • provides acidic properties to the molecule – methyl group • 2 different types exist – Saturated • solid at room or body temperature (RT/BT) – Unsaturated • some are solid but most are liquid at RT/BT

Fatty Acids

• Hydrocarbon chains of 4 to 24 carbon atoms (always an even number) bound to hydrogen atoms • Has more energy per molecule than glucose • 2 different functional groups are at each end – carboxylic acid group • provides acidic properties to the molecule – methyl group

Fatty Acids • 2 different types – Saturated • solid at room or body temperature (RT/BT) – Unsaturated • some are solid but most are liquid at RT/BT • Saturated fatty acid – each carbon in the hydrocarbon chain is saturated with hydrogen (bonded to 2 hydrogens) • no double bonds between carbons (C=C) • Unsaturated fatty acid – each carbon in the hydrocarbon chain is not saturated with hydrogen • contains at least one C=C

Types of Lipids • The fatty acids (1, 2 or 3) may be found in the body bound to a molecule of glycerol (glucose derived molecule) – monoglyceride – diglyceride – triglyceride

• Functions – energy storage in adipose (fat) tissue • each fatty acid of a triglyceride contains approximately 4 times more energy than a single molecule of a monosaccharide (glucose) – insulation • prevents excessive heat loss from the body – protection • provides shock absorption for organs that are surrounded by adipose tissue

Phospholipids • Similar in structure to a triglyceride consisting of: – 1 glycerol – 2 fatty acids – 1 phosphate group (PO4-) with attached nitrogencontaining group • Amphiphilic (both loving) molecule – has BOTH polar and nonpolar portions • Hydrophobic “tails” consist of two fatty acids • Hydrophilic “head” consists of a negatively charged phosphate and nitrogen-containing groups • Found in a liquid state at body temperature • Predominant molecule in cellular membranes

Phospholipid Structure

Lipid Related Molecules • The hydrocarbons in a molecule of cholesterol are arranged in a 4 ringed structure • Cholesterol is used to make steroid hormones including: – cortisol – aldosterone – estrogen – testosterone • Cholesterol is an important component in cellular membranes to keep them in a fluid state

Proteins (Peptides) • Polymer (chain) of amino acids which are bonded together through covalent bonds called peptide bonds • 20 different amino acids are used to create proteins by the body – 11 of the 20 amino acids (nonessential) can be synthesized within the body and therefore do not need to be supplied by the diet – 9 of the 20 amino acids (essential) cannot by can synthesized by the body and therefore need to be obtained through hydrolysis of dietary proteins during the digestive process

Amino Acids • Each of the 20 different amino acids have similar structural components – a central carbon atom with an attached: • an amino (NH2) group • a carboxyl (COOH) group • a hydrogen atom • Each amino acid unique due to the functional group located at the R position attached to the central carbon atom

Amino Acids • The 20 amino acids can also be divided into 2 groups based on their solubility in water • The molecular composition of the R group determines whether an amino acid is – polar – nonpolar • The polarity of amino acids play a crucial role in determining the overall 3 dimensional structure of proteins which in turn determines its biological function

Protein Structure • The 20 different amino acids can be joined by peptide bonds with an almost infinite number of combinations • Proteins vary greatly in size – some are as small as 3 amino acids in length – some are as large as 34350 amino acids in length • 4 levels of structural complexity in proteins • Primary structure – the amino acid sequence of the protein – glutamic acid – histidine – proline is the amino acid sequence of thyrotropic releasing hormone – determined genetically and is required for proper protein function • a single amino acid deletion or substitution could lead to a completely dysfunctional protein – since each protein has a unique amino acid sequence, each protein is structurally and functionally unique

Protein Structure

• Secondary structure – simple shapes that segments of amino acids make within the protein • α helix (coiled), β-pleated sheet (folded) shapes are held together by intramolecular hydrogen bonds between nearby amino acids • Tertiary structure – the overall 3 dimensional shape of the protein – determined by polar and nonpolar interactions between the amino acids of the protein and the surrounding water – stabilized by intramolecular hydrogen bonds and disulfide bridges • Quaternary structure – two or more separate polypeptide chains interacting with one another to create a functional unit

Protein Conformation and Denaturation • Conformation – overall 3 dimensional shape (tertiary/quaternary) that is required for function (activity) – the function of some proteins requires an ability to change their conformation • Denaturation – drastic conformational change in a protein caused by the breaking of hydrogen bonds within a protein • increases in temperature • increases or decreases in pH – can be partial or complete • when a protein is partially denatured, its function is impaired • when a protein is completely denatured, its function is lost

Protein Types and Functions PROTEINS PERFORM ALL BODY FUNCTIONS Proteins are categorized into 2 groups • Globular proteins are water soluble and function in: – Catalysis • enzymes speed up biochemical reactions – Communication • hormones and neurotransmitters act as signaling molecules between cells – Cell Membrane Transport • channels allow substances to enter/exit cells • Fibrous proteins are insoluble in water and function in: – Structural integrity • collagen and elastin hold body parts together – Movement • actin and myosin allow for muscle contraction

Characteristics of Enzymes • Enzymes are chemically specific for a particular substrate (chemical on which an enzyme acts upon) – each enzyme can only act upon one substrate • Enzymes are unchanged by reactions that they catalyze and are able to repeat the process many times over • Enzymes increase the rate of a chemical reaction by lowering the activation energy of the reaction • Enzymes are frequently named for the type of reaction they catalyze or by their substrate • Enzyme names usually end in the suffix -ase

Enzymes and Activation Energy

Enzyme Structure and Action • The region of an enzyme that recognizes a substrate is called the active site – recognizes the specific molecular structure of a substrate • An enzyme temporarily binds its substrate(s) and allows the appropriate chemical reaction proceed – Synthesis – Decomposition – Exchange – RedOx

Enzymatic Catalysis of a Biochemical Reaction

Nucleic Acids • Largest molecules in the body • Molecules of instruction and heredity • Two major classes – deoxyribonucleic acid (DNA) – ribonucleic acid (RNA) • The monomers of nucleic acids are nucleotides

Nucleotides

• A nucleotide has 3 parts – a nitrogen containing base (arranged in a ring(s)) – a sugar – a phosphate group • 5 different nucleotides are used to make nucleic acids – Each nucleotide is different based on 2 criteria: • the identity of the nitrogen base –double ringed bases are called purines • adenine (A) and guanine (G) –single ringed bases are called pyrimidines • cytosine (C), thymine (T) and uracil (U) • the identity of the sugar (DNA uses deoxyribose while RNA uses ribose) • Nucleotides are covalently bound to one another between the sugar of one nucleotide and the phosphate of another nucleotide to make long straight (linear) molecules referred to as nucleic acid strands

Nucleotides

DNA • Double-stranded helical molecule – looks like a ladder that has been twisted – each strand is between 100 million to 1 billion nucleotides in length – 2 strands are held together by H-bonds between complimentary nucleotides on opposite strands • H-bonds can only be made between a purine on one strand and a pyramidine on the other strand –A can only bind with T –G can only bind with C –U is NOT part of DNA (only found in RNA) • The sequence of nucleotides in one of the strands contains the genetic code • the amino acid sequence of all proteins

Structure of DNA

RNA • Single-stranded molecule – made from the nucleotides A, U, G and C • Three varieties of RNA: – messenger RNA – transfer RNA – ribosomal RNA

Adenosine Triphosphate (ATP) • Source of immediately usable energy for the cell • Nucleotide derivative bound to 3 phosphate groups – second and third phosphate groups are attached by high energy covalent bonds • phosphate groups are negatively charged and naturally repel each other • Enzymes that hydrolyze the high energy bond of ATP produces releases chemical energy – ATP → ADP + P + energy • the body can convert the ADP and P back into ATP using the energy stored in the covalent bonds of carbohydrates and lipids as a fuel

ATP