Lesson 6 - Biochemistry: The Chemistry of Life

Organic Chemistry

• Study of carbon-containing compounds

  • Not all carbon compounds are from living organisms

  • E.g., an E. coli cell contains over 6,000 organic compounds

    • Proteins (15%)

    • Nucleic acids (7%)

    • cPolysaccharides (3%)

    • Lipids (2%)

  • Impacts everyday items

    • E.g., fossil fuels, dyes, drugs, plastics, food, clothing

  • “chemistry of carbon and its covalent bonds”

  • focuses on carbon’s covalent bonds

Organic Compounds

• Compounds that contain carbon

  • Many are produced by or related to living organisms, some are not

  • Carbon containing compounds > non-carbon containing compounds

  • Some are very large and complex

  • Some contains thousands of atoms

Carbon

• Primary requisite for all living organisms

  • Valence: 4 (can bond to 4 elements)

Uniqueness of Carbon

Lies in the ability of its atom to bond to each other to form a multitude of compounds

Amorphous Carbon

• a type of carbon that is found in soot

  • Used in inks, paints, rubber products, cores of dry cell batteries

  • Black soot formed when a material containing carbon is burned with insufficient oxygen to burn completely

  • Aka lampblack, gas black, channel black, and carbon black

Graphite

a type of carbon that is soft, used as a lubricant (in a formed coke, used in steel production) and in pencil “lead”

Diamond

• a type of carbon that is hardest known material

  • Used in jewelry (natural) and tools (artificially produced)

Single Bond

a carbon bond where there is one pair of shared electrons

Double Bond

a carbon bond where there are two pairs of shared electrons

Triple Bond

a carbon bond where there are three pairs of shared electrons

Long Carbon Chains

lead to various molecular states

Cyclic Compounds

• Carbon atoms form rings

  • E.g., Benzene (C6H6) with six carbon and hydrogen atoms

Long Carbon Chains | Long Chain

a type of long carbon chain that is for liquids or solids

Long Carbon Chains | Short Chain

a type of long carbon chain that is for gases

Inorganic Chemistry

Non-carbon chemical reactions

Biochemistry

• Study of biology at the molecular level

  • A branch of organic chemistry

  • Focuses on biomolecules in living organisms

    • E.g., carbohydrates, lipids, proteins, and nucleic acids

  • Includes vitamins, enzymes, hormones, and energy molecules like ATP

  • Chemistry of living cells, chemistry of life, chemistry of living organisms

  • Involves study of the biomolecules that are present within living organisms

  • Cells function like a factory:

    • Machinery

    • Enzymes

    • Nutrients for energy

    • Manufacturing

Importance of Biochemistry

• Biochemical reactions are central to all cellular activities

• Biomolecules define living organisms:

  • Complex structure

  • Energy utilization

  • Self-replication

• Introduction to organic chemistry is necessary for understanding biomolecules

Nutrients and Cell Function | Humans

• Absorb nutrients from food (carbohydrates, fats, nucleic acids, proteins)

• Nutrients broken down, rearranged within cells to build necessary compounds

Nutrients and Cell Function | Microorganisms

Absorb nutrients directly, used in metabolic reactions for energy and structure

Carbohydrates

Made of carbon, hydrogen, and oxygen in a 1:2:1 ratio (CH2O)

Type of Carbohydrates | Monosaccharides

• a type of carbohydrates that is simple sugars

  • E.g., glucose (most important, hexose, C6H12O6), fructose, triose, pentoses, and hexoses

  • Sugars composed of only one ring

Type of Carbohydrates | Disaccharides

• a type of carbohydrates that is formed by two monosaccharides

  • E.g., sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (glucose + glucose)

  • Double-ringed sugars

  • Formed by dehydration synthesis

Type of Carbohydrates | Polysaccharides

• a type of carbohydrates that is composed of chains of monosaccharides

  • E.g., starch, glycogen (common storage molecules, found in liver and muscles), cellulose

  • Some are insoluble in water because they are so large

  • 2 main functions:

    • Store energy

    • 2Provide a “tough” molecule for structural support and protection

Glucose

a monosaccharide that may occur as a chain/alpha/beta ring and is the main source energy for body cells

Functions of Carbohydrates | Energy Storage

a function of carbohydrates that has glycogen (animals) and starch (plants)

Functions of Carbohydrates | Structural Support

a function of carbohydrates that has bacterial peptidoglycan in cell walls and cellulose in plant and algal cell walls (providing strength and protection)

Type of Carbohydrates by Size | Monosaccharides

• a type of carbohydrates by size that refers to simple-ring sugar

  • e.g., glucose, fructose

Type of Carbohydrates by Size | Disaccharides

• a type of carbohydrates by size that refers to double-ring sugar

  • formed by dehydration synthesis

Type of Carbohydrates by Size | Trisaccharides, Tetrasaccharides, and Polysaccharides

• a type of carbohydrates by size that refers to a composed of multiple monosaccharides

ATP and Energy

• Glucose serves as main energy source for cells, oxidized to produce ATP

• ATP contains high-energy phosphate bonds, fueling metabolic reactions

Complex Carbohydrates and Microbial Cell Walls | Polysaccharides

• a complex carbohydrate that provides storage function in cells as energy reserve

  • Provide structural strength and protection:

    • Bacterial capsules prevent phagocytosis by white blood cells

    • Cellulose in plants/algae aids in environmental resistance

Complex Carbohydrates and Microbial Cell Walls | Unique Polysaccharides

• Cellulose is indigestible for humans but provides structural support in plants

  • Decomposed by specialized microorganisms

  • E.g., protozoa in termites

Starch and Glycogen Structures

they are long, helical, or branched polymers of glucose

α-glycosidic bonds

enzymes break these bonds which enables animals to digest starch and glycogen

Use of Cellulose | Plant-based cellulose

cellulose fibers are used to make proper, cotton, linen, and rope

Use of Cellulose | Cellulose fibers

cellulose that are strong, rigid, and insoluble due to parallel strands

Complex Carbohydrates and Specialized Macromolecules | Polysaccharides + Other Groups

• Combine with amines, lipids, and amino acids to form complex macromolecules

• E.g.,

  • Glucosamine and galactosamine

    • Found in connective tissue, cartilage, and chitin

  • Chitin

    • Composes exoskeletons of insects, spiders, crabs, and fungal cell walls

Complex Carbohydrates and Specialized Macromolecules | Bacterial Cell Walls

• Composed of peptidoglycan layer

Peptidoglycan Layer

• Made of amino sugars and polypeptides

• Provides structural rigidity and protection for bacterial cells

• Consists of a repeating disaccharide, attached by polypeptides to form a lattice that surrounds and protects the entire bacterial cell

Lipids

• Essential biomolecules, insoluble in water but soluble in fat solvents (e.g., ether, chloroform, and benzene)

  • Functions:

    • Key components of cell membranes, energy storage, and signaling

Type of Fatty Acid | Saturated Fatty Acid

• a type of fatty acid that has single bonds, solid at room temperature

  • e.g., butter

Type of Fatty Acid | Monounsaturated Fatty Acids

• a type of fatty acid that has one double bond in the carbon chain

  • E.g., olive oil, peanuts

Type of Fatty Acid | Polyunsaturated Fatty Acid

• a type of fatty acid that has two or more double bonds, usually liquid at room temperature

  • e.g., corn oil, safflowers, sunflowers

Type of Fatty Acid | Essential Fatty Acids

• a type of fatty acid that cannot be synthesized by the body

  • Obtained from diet

  • E.g., Omega-3 fatty acid

Type of Fatty Acid | Trans Fat

• a type of fatty acid that is manufactured by the artificial addition of hydrogen atoms to unsaturated fats (hydrogeneration)

  • Solid or semisolid fats (often incorporated into food products)

  • Must be avoided because of their harmful effects on cholesterol levels and their link to heart disease

Fatty Acid

• Building blocks of lipids

  • Long-chain carboxylic acids that are insoluble in water

Classes of Lipids | Waxes

• a class of lipid that has long-chain alcohols + fatty acids

  • Waterproof coating on plants and animal fur

  • Mycobacterium tuberculosis uses waxes in cell walls for protection

Classes of Lipids | Fats and Oils (Triglycerides)

• a class of lipid that is composed of glycerol + three fatty acids

  • Fats are solid at room temperature

  • Oils are liquid at room temperature

  • Most common types of lipids

Classes of Lipids | Phospholipids

• a class of lipid that contains glycerol, fatty acids, and phosphate group

  • Lipid Bilayer in cell membranes

    • Hydrophilic heads

    • Hydrophobic tails

  • has 2 types

    • glycerophospolipids

    • sphingolipids

Classes of Lipids | Glycolipids

• a class of lipid that is found in brain and myelin sheaths

  • Define blood groups

  • Glycerol + 2 fatty acids + monosaccharide

  • E.g., cerebrosides and gangliosides

Classes of Lipids | Steroids

• a class of lipid that has four-ring structures, include cholesterol, bile salts, vitamins (A, D, E, K) and hormones (e.g., testosterone, estrogens)

Classes of Lipids | Prostaglandins and Leukotrienes

• a class of lipid that is derived from arachidonic acid

  • regulate inflammation, blood pressure, fever, and lung muscle contraction

Phospholipids | Glycerophospholipids

a type of phospholipid that is most abundant lipid in cell membranes

Phospholipids | Sphingolipids

a type of phospholipid that is found in brain and nerve tissues

Lipids’ Roles in Cell Membranes | Phospholipids

has a role in cell membrane where they form the cell membrane’s structure

Lipids’ Roles in Cell Membranes | Steroids and Glycolipids

has a role in cell membrane where they add rigidity and communication properties

Lipids’ Roles in Cell Membranes | Gram-negative bacteria

has a role in cell membrane where they are known to be a unique lipid in the outer membrane called lipopolysaccharide (LPS) which contains endotoxin (Lipid-A), linked to fever and septic shock

Proteins

• Essential biomolecules (most essential chemicals in all living cells), often called the substance of life

  • Polymers of amino acids

  • Functions

    • Structural roles (membranes, cells, tissues)

    • Biochemical regulation (enzymes, hormones)

  • Composition

    • Carbon, hydrogen, nitrogen, and sometimes sulfur

  • Amino Acids

    • 23 types (20 primary + 3 derived), with essential amino acids that must come from the diet

Essential Amino Acids

these cannot be synthesized and must be integrated with diet

General Structure of Amino Acids

it has a central carbon with an amino group, carboxyl group, hydrogen, and a variable “R” group

Peptide Bond

bond that forms between amino acids through dehydration synthesis

Type of Peptide | Dipeptide

a type of peptide that has 2 amino acids

Type of Peptide | Tripeptide

a type of peptide that has 3 amino acids

Type of Peptide | Polypeptide

a type of peptide that has a chain of multiple amino acids (more than 3 amino acids)

Level of Protein Structure | Primary Structure

a level of protein structure that refers to linear sequence of amino acids

Level of Protein Structure | Secondary Structure

• a level of protein structure that refers to helices or sheets formed by hydrogen bonding

  • Helices or sheets are result of charged side chains protruding from the carbon-nitrogen backbone of the molecule

  • e.g., fibrous proteins like keratin, collagen, myosin, and microtubules and microfilaments of cells

Level of Protein Structure | Tertiary Structure

• a level of protein structure that refers to three-dimensional folding (globular proteins) stabilized by disulfide bonds and hydrogen bonding between 2 sulfur groups

  • E.g., enzymes, insulin, albumin (eggs)

Level of Protein Structure | Quaternary Structure

• a level of protein structure that refers to multiple polypeptide chains linked

  • two or more polypeptide chains bonded together by hydrogen and disulfide bonds (results in 3D)

  • E.g., hemoglobin (consists of 4 globular myoglobins)

Example of Protein Type | Fibrous Proteins

• a type of protein that is insoluble, structure

  • e.g., keratin, collagen

Example of Protein Type | Globular Proteins

• a type of protein that is soluble, functional

  • e.g., enzymes, hormones, antibodies

Enzyme

• Proteins that accelerate biochemical reactions without being consumed

  • Protein molecules produced by living cells as “instructed” by genes on the chromosomes

  • Almost every reaction in the cell requires the presence of a specific enzyme

  • acts on a specific substrate (specific molecule on which an enzyme acts)

Structure of Enzyme | Apoenzyme

an enzyme structure that refers to the protein portion, inactive alone (can function as enzyme after linking up with a nonprotein cofactor)

Structure of Enzyme | Cofactor

an enzyme structure that refers to the non-protein component (metal ions or coenzymes like vitamins)

Structure of Enzyme | Holoenzymes

an enzyme structure that refers to the active enzyme formed by apoenzyme + cofactor

Functions of Enzyme | Catalysis

a function of enzyme which pertains to the enzymes lower activation energy, controlling reaction speed

Functions of Enzyme | Denaturation

a function of enzyme which pertains to heat or chemicals can disrupt protein structure, causing loss of function

Functions of Enzyme | Toxins and Enzyme Inhibition

a function of enzyme which pertains to certain toxins (e.g., cyanide) bind to enzyme cofactors, inhibiting ATP synthesis and energy production, leading to cellular death

Nucleic Acids

• Essential biomolecules, contains DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

  • Fourth major group of biomolecules in living cells

  • Critical to the proper functioning of a cell

Composition of Nucleic Acid

a macromolecule that is composed of elements carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and phosphorus (P)

Nucleic Acid Roles | DNA

a nucleic acid that has a role for storage of genetic information and instructions for cellular processes

Nucleic Acid Roles | RNA

a nucleic acid that has a role for converting genetic instructions into protein and other gene products

DNA’s Function

• Known as hereditary molecule

  • Contains genes

  • Forms the main component of chromosomes

  • Encodes instructions for the development, functioning, and reproduction of cells

RNA’s Function

• Acts as a messenger, transferring DNA instructions to the cellular machinery for protein synthesis

• has 3 types

  • mRNA

  • rRNA

  • tRNA

Type of RNA | Messenger RNA (mRNA)

a type of RNA that carries genetic instructions from DNA to ribosomes

Type of RNA | Ribosomal RNA (rRNA)

a type of RNA that is a structural component of ribosomes, facilitates protein synthesis

Type of RNA | Transfer RNA (tRNA)

a type of RNA that transport amino acids to ribosomes during protein synthesis

Nucleotides

• Basic units, the building blocks of nucleic acids

  • Each consists of 3 main components

    • Nitrogenous base (Adenine, Guanine, Cytosine, Thymine for DNA; Uracil for RNA)

    • Pentose sugar (Deoxyribose in DNA and ribose in RNA)

    • Phosphate group

Polymer Formation

• Nucleotides link together via covalent bonds between their sugar and phosphate groups

• Forms long strands of nucleic acids, with DNA strands being 100,000 + nucleotides long

Type of Nitrogenous Base | Purines

• a type of nitrogenous base that is double-ring structures

  • Adenine, Guanine

Type of Nitrogenous Base | Pyrimidines

• a type of nitrogenous base that is single-ring structures

  • Cytosine, Thymine, Uracil

Base Pairing Rules | DNA Base Pairs

a base pair rule that states Adenine pairs with Thymine (A-T) via 2 hydrogen bonds, and Guanine pairs with Cytosine (G-C) via 3 hydrogen bonds

Base Pairing Rules | RNA Base Pairs

a base pair rule that states Adenine pairs Uracil (A-U), and Guanine pairs with Cytosine (G-C)

DNA Structure | Double-Helix Formation

• DNA strands form a double helix (through bonding), resembling a twisted ladder

• Base pairs (A-T, G-C) are connected by hydrogen bonds, stabilizing the structure

DNA Structure | Helical Configuration

• The structure provides a compact, stable form that protects genetic information

• Allows for efficient storage and replication of DNA

DNA Replication

its purpose is to ensure that each daughter cell receives an identical copy of DNA

Key Enzyme in DNA Replication Process | DNA Helicase and DNA Toposiomerase

an enzyme during the DNA replication process which unzips the DNA double helix/separation of the two strands of the two DNA molecule

Key Enzyme in DNA Replication Process | Primase

an enzyme during the DNA replication process which synthesizes short RNA primers

Key Enzyme in DNA Replication Process | DNA Ligase

an enzyme during the DNA replication process which connects fragments of newly synthesized DNA

Replication Fork

refers to the point on the molecule where DNA replication starts

Process of DNA Replication | Strand Separation

• first step of DNA replication process where the DNA strands unwind and separate at the replication work

  • Addition of correct DNA nucleotides