Chemistry Comes Alive - Biochemistry

Biochemistry

• Biochemistry is the study of the chemical composition and reactions of living matter.
• All chemicals are either organic or inorganic.
  • Inorganic compounds:
    • Water, salts, and many acids and bases.
    • Do not contain carbon.
  • Organic compounds:
    • Carbohydrates, fats, proteins, and nucleic acids.
    • Contain carbon, are usually large, and are covalently bonded.
• Both organic and inorganic compounds are equally essential for life.

Inorganic Compounds

Water

• Most abundant inorganic compound, accounting for 60-80% of the volume of living cells.
• Most important inorganic compound because of its properties:
  • High heat capacity: ability to absorb and release heat with little temperature change, preventing sudden changes in temperature.
  • High heat of vaporization: evaporation requires large amounts of heat, making it a useful cooling mechanism.
  • Polar solvent properties: dissolves and dissociates ionic substances, forming hydration (water) layers around large charged molecules (e.g., proteins). It's the body’s major transport medium.
  • Reactivity: necessary part of hydrolysis and dehydration synthesis reactions.
  • Cushioning: protects certain organs from physical trauma (e.g., cerebrospinal fluid cushions nervous system organs).

Salts

• Salts are ionic compounds that dissociate into separate ions in water.
  • Separate into cations (positively charged molecules) and anions (negatively charged), not including $H+$ and $OH-$
• All ions are called electrolytes because they can conduct electrical currents in solution.
• Ions play specialized roles in body functions (e.g., sodium, potassium, calcium, and iron).
• Ionic balance is vital for homeostasis.
• Common salts in the body: $NaCl$, $CaCO3$, $KCl$, calcium phosphates.

Acids and Bases

• Acids and bases are both electrolytes that ionize and dissociate in water.

Acids

• Are proton donors: they release hydrogen ions $(H+)$, bare protons (have no electrons) in solution.
  • Important acids: $HCl$ (hydrochloric acid), $HC2H3O2$ (acetic acid, abbreviated $HAc$), and $H2CO3$ (carbonic acid).

Bases

• Are proton acceptors: they pick up $H+$ ions in solution.
  • When a base dissolves in solution, it releases a hydroxyl ion $(OH-)$.
  • Important bases: bicarbonate ion $(HCO3-)$ and ammonia $(NH3)$.

pH: Acid-Base Concentration

• pH scale is the measurement of the concentration of hydrogen ions $[H+]$ in a solution.
• The more hydrogen ions in a solution, the more acidic that solution is.
• pH is the negative logarithm of $[H+]$ in moles per liter that ranges from 0–14.
• The pH scale is logarithmic, so each pH unit represents a 10-fold difference.
  • Example: a pH 5 solution is 10 times more acidic than a pH 6 solution.
• Acidic solutions have high $[H+]$ but low pH; acidic pH range is 0–6.99.
• Neutral solutions have equal numbers of $H+$ and $OH-$ ions; all neutral solutions are pH 7; pure water is pH neutral.
  • pH of pure water = pH 7: $[H+] = 10^{-7} m$
• Alkaline (basic) solutions have low $[H+]$ but high pH; alkaline pH range is 7.01–14.

Neutralization

• Neutralization reaction: acids and bases are mixed together.
  • Displacement reactions occur, forming water and a salt.

Buffers

• Acidity involves only free $H+$ in solution, not $H+$ bound to anions.
• Buffers resist abrupt and large swings in pH.
  • Can release hydrogen ions if pH rises.
  • Can bind hydrogen ions if pH falls.
• Convert strong acids or bases (completely dissociated) into weak ones (slightly dissociated).
  • Carbonic acid–bicarbonate system (important buffer system of blood).

Clinical Homeostatic Imbalance

• Enzymes in the body work within a very narrow pH range.
• An arterial pH of 7.0 during cardiopulmonary resuscitation predicts a poor outcome.
• Patients presenting with an arterial pH of less than 6.85 rarely survive.

Organic Compounds: Synthesis and Hydrolysis

• Organic molecules contain carbon.
  • Exceptions: $CO2$ and $CO$, which are inorganic.
• Carbon is electroneutral.
  • Shares electrons; never gains or loses them.
  • Forms four covalent bonds with other elements.
  • Carbon is unique to living systems.
• Major organic compounds: carbohydrates, lipids, proteins, and nucleic acids.
• Many organic compounds are polymers, which are chains of similar units called monomers (building blocks).
• Synthesized by dehydration synthesis.
• Broken down by hydrolysis reactions.

Carbohydrates

• Carbohydrates include sugars and starches.
• Contain C, H, and O, with hydrogen and oxygen in a 2:1 ratio.
• Three classes:
  • Monosaccharides: one single sugar (monomers: smallest unit of carbohydrate).
  • Disaccharides: two sugars.
  • Polysaccharides: many sugars (polymers are made up of monomers of monosaccharides).

Monosaccharides

• Simple sugars containing three to seven carbon atoms. General formula: $(CH2O)n$, where $n$ = number of carbon atoms.
• Monomers of carbohydrates.
• Important monosaccharides:
  • Pentose sugars: ribose and deoxyribose.
  • Hexose sugars: glucose (blood sugar).

Disaccharides

• Double sugars.
• Too large to pass through cell membranes.
• Important disaccharides: sucrose, maltose, lactose.
• Formed by dehydration synthesis of two monosaccharides: glucose + fructose → sucrose + water.

Polysaccharides

• Polymers of monosaccharides, formed by dehydration synthesis of many monomers.
• Important polysaccharides:
  • Starch: carbohydrate storage form used by plants.
  • Glycogen: carbohydrate storage form used by animals.
• Not very soluble.

Lipids

• Contain C, H, O, but less than in carbohydrates, and sometimes contain P.
• Insoluble in water.
• Main types: triglycerides, phospholipids, steroids, eicosanoids.

Triglycerides

• Called fats when solid and oils when liquid.
• Composed of three fatty acids (linear hydrocarbons) bonded to a glycerol molecule (sugar alcohol) by dehydration synthesis.
• Main functions: energy storage, insulation, protection.
• Can be constructed of:
  • Saturated fatty acids:
    • All carbons are linked via single covalent bonds, resulting in a molecule with the maximum number of H atoms it can hold (saturated with H).
    • These create linear molecules which can pack closely together forming a solid at room temperature (Example: animal fats, butter).
  • Unsaturated fatty acids:
    • One or more carbons are linked via double bonds, resulting in reduced H atoms (unsaturated).
    • Double bonds cause a kink in the fatty acid so they cannot pack together closely, resulting in unsaturated fatty acids being liquid at room temperature (Example: plant oils, such as olive oil).
    • Trans fats: modified unsaturated fatty oils that resemble the structure of saturated fats and are considered unhealthy.
    • Omega-3 fatty acids: “heart healthy”.

Phospholipids

• Modified triglycerides: glycerol and two fatty acids plus a phosphorus-containing group.
• “Head” and “tail” regions have different properties.
  • Head is polar and hydrophilic (attracted to water).
  • Tails are nonpolar and hydrophobic (repelled by water).
• Important in cell membrane structure.

Steroids

• Consist of four interlocking ring structures.
• Most important steroid is cholesterol.
  • Made by the liver and also found in animal products (ex: cheese, eggs, meat).
  • Starting material for synthesis of vitamin D, steroid hormones, and bile salts.
  • Important in cell plasma membrane structure.

Eicosanoids

• Derived from a fatty acid (arachidonic acid) found in cell membranes.
• Most important eicosanoids are prostaglandins.
  • Play a role in blood clotting, control of blood pressure, inflammation, and labor contractions.
  • Inflammatory actions are blocked by NSAIDs (non-steroidal anti-inflammatory drugs, such as aspirin or ibuprofen).

Proteins

• Comprise 20–30% of cell mass.
• Have the most varied functions of any molecules: structural, chemical (enzymes), contraction (muscles).
• Contain C, H, O, N, and sometimes S and P.
• Polymers of amino acid monomers held together by peptide bonds.
• Shape and function are due to four structural levels.

Amino Acids and Peptide Bonds

• All proteins are made from 20 types of amino acids, joined by covalent bonds called peptide bonds.
• Contain both an amine group and acid group.
• Can act as either an acid or base.
• Differ by which of 20 different “R groups” is present.

Structural Levels of Proteins

• Four levels of protein structure determine shape and function:
  • Primary: linear sequence of amino acids (order).
  • Secondary: how primary amino acids interact with each other.
    • Alpha ($\alpha$) helix coils resemble a spring.
    • Beta ($\beta$) pleated sheets resemble accordion ribbons.
  • Tertiary: how secondary structures interact.
  • Quaternary: how 2 or more different polypeptides interact with each other.

Fibrous and Globular Proteins

• Shapes of proteins fall into one of two categories: fibrous or globular.

Fibrous (structural) proteins

• Strandlike, water-insoluble, and stable.
• Most have tertiary or quaternary structure (3-D).
• Provide mechanical support and tensile strength.
• Examples: keratin, elastin, collagen (single most abundant protein in the body), and certain contractile fibers.

Globular (functional) proteins

• Compact, spherical, water-soluble, and sensitive to environmental changes.
• Tertiary or quaternary structure (3-D).
• Specific functional regions (active sites).
• Examples: antibodies, hormones, molecular chaperones, and enzymes.

Protein Denaturation

• Denaturation: globular proteins unfold and lose their functional 3-D shape.
  • Fibrous proteins are more stable.
  • Active sites become deactivated.
• Can be caused by decreased pH (increased acidity) or increased temperature.
• Usually reversible if normal conditions are restored.
• Irreversible if changes are extreme (e.g., cannot undo cooking an egg).

Enzymes and Enzyme Activity

• Enzymes: globular proteins that act as biological catalysts.
  • Catalysts regulate and increase the speed of chemical reactions without getting used up in the process.
  • Lower the energy needed to initiate a chemical reaction, leading to an increase in the speed of a reaction.
  • Allows for millions of reactions per minute!

Characteristics of enzymes

• Most functional enzymes, referred to as holoenzymes, consist of two parts:
  • Apoenzyme (protein portion).
  • Cofactor (metal ion) or coenzyme (organic molecule, often a vitamin).
• Enzymes are specific and act on a very specific substrate.
• Names usually end in -ase and are often named for the reaction they catalyze (e.g., hydrolases, oxidases).

Enzyme action

• Enzymes lower activation energy, which is the energy needed to initiate a chemical reaction.
  • Enzymes “prime” the reaction.
• Enzymes allow chemical reactions to proceed quickly at body temperatures.
• Three steps are involved in enzyme action:
  • Substrate binds to the enzyme’s active site, temporarily forming an enzyme-substrate complex.
  • The complex undergoes rearrangement of the substrate, resulting in a final product.
  • The product is released from the enzyme.

Nucleic Acids

• Nucleic acids, composed of C, H, O, N, and P, are the largest molecules in the body.
• Nucleic acid polymers are made up of monomers called nucleotides, composed of a nitrogen base, a pentose sugar, and a phosphate group.
• Two major classes: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

DNA

• Holds the genetic blueprint for the synthesis of all proteins.
• Double-stranded helical molecule (double helix) located in the cell nucleus.
• Nucleotides contain a deoxyribose sugar, phosphate group, and one of four nitrogen bases:
  • Purines: adenine (A), guanine (G).
  • Pyrimidines: cytosine (C) and thymine (T).
• Bonding of nitrogen base from strand to opposite strand is very specific and follows complementary base-pairing rules:
  • A always pairs with T.
  • G always pairs with C.

RNA

• Links DNA to protein synthesis and is slightly different from DNA.
• Single-stranded linear molecule is active mostly outside the nucleus.
• Contains a ribose sugar (not deoxyribose).
• Thymine is replaced with uracil.
• Three varieties of RNA carry out the DNA orders for protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).

ATP

• Chemical energy released when glucose is broken down is captured in ATP (adenosine triphosphate).
• ATP directly powers chemical reactions in cells and offers immediate, usable energy needed by body cells.
• Structure of ATP: adenine-containing RNA nucleotide with two additional phosphate groups.
• The terminal phosphate group of ATP can be transferred to other compounds that can use the energy stored in the phosphate bond to do work.
• Loss of phosphate group converts ATP to ADP.
• Loss of a second phosphate group converts ADP to AMP.