Carbon and the Molecular Diversity of Life | Chapter 4

• Chapter 4 discusses carbon and the molecular diversity of life.

Carbon: The Backbone of Life

• Living organisms are mainly composed of carbon-based compounds.
• Carbon has the unique ability to form large, complex, and diverse molecules.
• Organic molecules are carbon compounds.
• Graphene is a one-atom-thick planar sheet of carbon atoms.

Molecules of life

• Chemicals involved in or produced by metabolic reactions fall into two groups: inorganic and organic.
• Inorganic substances include water, oxygen, carbon dioxide, and inorganic salts.
• Organic substances are composed of what 3 elements?

Organic Compounds

• Organic compounds always contain carbon, oxygen, and hydrogen.

The Carbon Atom

• Carbon has 4 valence electrons.
• It completes its outer shell by sharing 4 electrons in 4 covalent bonds.

Carbon Bonds and Skeletons

• Carbon atoms can attach to each other which results in a diversity of carbon skeletons.
• Carbon's ability to bond in various ways makes large, complex molecules possible.
• Carbon skeletons can differ in length, branching, double bond location, and arrangement into rings.

Formation of Bonds with Carbon

• In molecules with multiple carbons each carbon atom bonded to 4 other atoms has a tetrahedral shape.
• When 2 carbon atoms are joined by a double bond the atoms connected to the carbons are in the same plane as the carbons.

Carbon and Partner Valences

• The valences of carbon, hydrogen, oxygen, and nitrogen influence the architecture of living molecules.

Hydrocarbons

• Hydrocarbons are the simplest organic compounds.
• The consist entirely of carbon and hydrogen atoms.
• They can undergo reactions that release a large amount of energy.
• The simplest hydrocarbon is methane.

Isomers

• Isomers have the same formula but different arrangements, resulting in different structures and properties.
• Structural isomers have different covalent arrangements of their atoms.
• Cis-trans isomers have the same covalent bonds, but different spatial arrangements.
• Enantiomers are mirror images of each other.
• Enantiomers effects demonstrate that organisms are sensitive to even subtle molecule variations.

Functional Groups

• Molecule properties depend on the carbon skeleton, functional groups and atoms.
• The number and arrangement of functional groups give each molecule its unique properties.

Modification of Hydrocarbons

• Modifying a hydrocarbon with functional groups can transform a non-polar hydrocarbon into a polar structure.
• Functional groups usually consist of O, N, P, or S.
• Functional groups usually contain O, N, P or S.

Important Functional Groups

• The most important 7 functional groups in chemistry of life are:
  • Hydroxyl group
  • Carbonyl group
  • Carboxyl group
  • Amino group
  • Sulfhydryl
  • Phosphate group
  • Methyl group

Functional Groups and Properties

• Hydroxyl functions such as Alcohols are polar because of the electronegative oxygen atom.
• Carbonyl groups such as Ketones occur within the carbon skeleton.
• Carboxyl groups such as carboxylic acids are acids; and can donate an H+.
• Amino groups such as Amines are bases.
• Sulfhydryl groups help stabilize protein structure.
• Phosphate groups contribute negative charge to the molecule. Methylated compounds effect the expression of genes.

Organic Macromolecules

• Organic macromolecules include carbohydrates, lipids, proteins, and nucleic acids.

Polymer Synthesis and Hydrolysis

• Polymers are synthesized through dehydration reactions.
• Polymers are broken down through hydrolysis.

Carbohydrates

• Carbohydrates consist of C, H and O, with the formula (CH₂O)ₙ.
• Carbohydrates are water soluble (hydrophilic).
• Functionally, they provide structural support, store energy, and act as quick fuel or long term storage.
• Carbohydrates are also classified by the location of the carbonyl group (aldose or ketose), the number of carbons in the carbon skeleton, and the number of subunits.

Carbohydrate Size Classes

• Monosaccharides contain 3-7 carbons (e.g., glucose, fructose, ribose, glyceraldehyde).
• Disaccharides consist of 2 sugars linked together (e.g., sucrose).
• Polysaccharides consist of 3 or more sugars linked together.

Simple Carbohydrates

• Aldose sugars have the carbonyl at the end, while ketose sugars have the cabonyl within the carbon skeleton. Aldose sugars have the carbonyl at the end, while Ketose sugars have the carbonyl at the end
• Glucose and Galactose are aldose sugars that only differ with arrangements of H and OH groups at one carbon.

Monosaccharides

• In aqueous solutions, monosaccharides form rings.

Disaccharides

• Disaccharides are made of 2 monosaccharides and form through a dehydration reaction to form a glycosidic linkage.
• Examples include lactose (glucose + galactose) and sucrose (glucose + fructose).

Polysaccharides

• Polysaccharides are long chains of sugar units.
• They are complex sugars (polymers of monosaccharides) made by dehydration.
• Functions include energy storage and structural support.
• Examples include starch (glucose storage in plants), glycogen (glucose storage in animals), and cellulose (plant cell walls).

Storage Polysaccharides

• Starch and glycogen are storage polysaccharides.

Starch

• Plants store these simple chains joined by 1-4 linkages (amylose) which can be helical and unbranched in conformation.
• Some starches are branch points (amylopectin) and stored within plastids (in chloroplast).
• This material can be hydrolyzed into glucose.

Glycogen

• Glycogen is a polysaccharide in animals.
• It is very highly branched form and is hydrolyzed into glucose.
• It is usually found in the Chloroplast Starch Granules.

Structural Polysaccharides: Cellulose

• Cellulose makes up plant cell walls.
• It is the most abundant organic molecule on Earth.
• It is a glucose polymer, but the glycosidic linkages differ.

Structural Polysaccharides

• In plants, the beta form glucoses link to form long straight molecules parallel to each other.
• These are joined by hydrogen bonds to form strong microfibrils.
• Enzymes that digest starch cannot break the beta linkages of cellulose, but prokaryotes possess cellulase.
• Human cellulose is unable to be hydrolyzed, therefore "insoluble fiber".
• Microfibrils - cellulose molecules parallel to one another due to hydrogen bonds between free OH of neighboring cellulose molecules resulting in Strong cable-like building material.

Cellulose vs. Starch

• Starch helical or unbranched, Cellulose is not.

Lipids

• There are many types of Lipid.

Lipid Types

• Other kinds of lipids are: fatty acids, carotenes, vitamin E, vitamin K, lipoproteins, and waxes and pigments.
• Types include: triglycerides (fats and oil), phospholipids, steroids, eicosanoids, and others.

Fats

• Contain only carbon, hydrogen, and oxygen.
• Hydrophobic, water insoluble.
• Function to supply energy.
• Contain only C, H, and is O in the formula.

Triglycerides

• Triglycerides are made of a glycerol molecule and 3 fatty acid chains (hydrocarbons, usually 16-18 carbons)

Fats

• Fats are formed through dehydration synthesis reactions to form an ester linkage.
• The -COOH (carboxylic acid) is the characterized fatty acid.

Fatty Acids

• Fatty acids differ in chain length and in location and number of double bonds.

Types of Fatty Acids

There are 2 types of fatty acids:

• Single C bonds - saturated, it is comprised of the maximum number of hydrogen atoms possible and no double bonds.
• Double C bonds - unsaturated, in can be either monounsaturated which is 1 double bond or polyunsaturated which is 2 or more double bonds.

Saturated vs Unsaturated Fats

• At room temperature, Saturated fat molecules are packed closely together.
• Unsaturated fat molecules the C=C bonds produce a "kink" in the fatty acid.
• Hydrogenated oils unsaturated chemically converted to saturated by adding hydrogens.
• This prevents their separation into an oil form - keeps them solid.

Importance of Fats

• Long-term energy storage is obtained (lighter than carbohydrates).
• 1g of fat stores 2x as much energy as 1g of a polysaccharide like starch.
• Adipose tissue evolved due to animal movement due to the energy requirements.
• This tissue is much less bulky than polysaccharides such as starch.
• Essential fatty acids cannot be made by the body and must be consumed through food such as omega-3 fatty acids.
• Polyunsaturated fatty acids are important in regulating cholesterol levels (lower LDL levels in the blood), increase calcium utilization by body, reduce inflammation (arthritis?) and promote wound healing.

Phospholipids

• Also similar to fat molecules: glycerol + 2 fatty acids.
• One FA replaced with a phosphate group (negative electrical charge) which is a phosphate gp → hydrophilic "head".
• Fatty acids gps → hydrophobic "tails".
• When added to water - self-assemble and form a phospholipid bilayer which is called hydrophilic heads/hydrophobic tails.
• This structure is a major component of the plasma membrane.
• The phosphate end is water soluble and the fatty acid end is water insoluble.

Steroids

• It is a carbon rings fused together with various functional groups.
• Cholesterol functions as a "base steroid" from which a body produces other steroids.
• Steroids include:
  • Sex hormones such as testosterone and estrogen.
  • Others steroids

Nucleic Acids (Proteins)

• Nearly every dynamic function of a living organism depends on proteins, from the Greek term proteios meaning "first place".
• Proteins make up > 50% of dry mass of most cells.
• Proteins have numerous roles.
• There are two types proteins Enzymatic and Defensive.
• Structural proteins provide Collagen in skin and keratin found in hair, While Transport Proteins, such as hemoglobin, are used for transferring substances.
• Movement proteins contain Actin and myosin in muscle.
• Defensive proteins utilize Antibodies to fight illness.

More Protein Functions

• Storage proteins are made with Albumin in egg white, to be used in the formation of signaling Growth hormone molecules and other important Enzymes.

Protein Functions

• Enzymatic proteins selective acceleration of chemical reactions EX: digestive enzymes.
• Defensive proteins- protection a gainst disease Antibodies.
• Storage proteins- Storage of amino acids EX: Casein, Ovalbumin.
• Transport proteins- Transport of substancesEX: Hemoglobin, membrane proteins (Cell Membrane).

Hormonal Proteins

• Hormonal proteins aid in coordination of an organism's activities for example such as insulin.
• Receptor proteins are also active in the response of a cell to chemical stimuli found in Receptors in nerve cell membrane.
• Contractile and Motor Proteins make Movement such as Motor protein in cilia and flagella, Actin and myosin in muscle.
• Structural proteins such as Keratin and Collagen connect between tissue found and webbed areas.

Proteins: Building Blocks

• The building blocks for proteins are amino acids.
• A central C, called alpha carbon bound to: an amino group, a carboxyl group, a hydrogen, and a R side group.
• There are 22 amino acids available for human protein synthesis.
• of which only 20 of them are coded for by our DNA.

Amino Acids

• Each side group is variable among all 20 amino acids.
• Gives its unique physical and chemical character.
• Side Chains are divided into polar aa, non-polar aa and electrically charged a (basic or acidic).

Amino Acid Diversity

• Amino acids are joined together by a dehydration synthesis reaction.
• A peptide bond = between the NH₂ of 1 aa and the COOH of the next aa.
• These bonds join to form chains of:
  • 2 a.a. linked bond, dipeptide
  • 3 a.a. linked bond tripeptide
  • 4 or more a.a. → polypeptide

Function Proteins - 3D Shape

• Proteins folding can be determined by sequence of amino acids, and the position of the polypeptide as they are spontaneously constructed.
• Changes such as in pH, salt, or temperature, can alter the shape of the protein and therefore its function.
• Denaturation.

Protein Conformation - Primary Structure

• Primary is the amino acid sequence of polypeptides e.g. Transthyretin – 127 a.a.
• is determined by genetic code found in DNA. Randomly created - then a 127 AA polypeptide could be made in the formula equation being 20 to the 127-th power.

Protein Conformation - Secondary Structure

• Protein structure has an effect determined through hydrogen bonding in specific folded patters often found in most proteins.

• In molecules with Oxygen and Nitrogen being negative atoms with Hydrogen the atoms have attraction to each other.

• alpha (α) helix: is produced by H bonding every 4th aa, as well as a beta (ß) pleated sheet: H bonding between 2 or more regions 2 adjacent polypeptides

Protein Conformation - Tertiary and Quaternary Structure

• Tertiary structure results from the folding of secondary structures into unique 3d shapes and functions.
• Hydrophobic interation and hydrogen bonds play a role in it's folding.
• While Quaternary is made from different polypeptide sub units coming together as one

Protein Conformation

There are different steps in the formation of protein:

• First one begins with amino acids in the Primary Structure.
• Secondary Structure is formed as Hydrogen and other elements combine with each other, Tertiary structure is bonded through it's R grouping.
• Quaternary is connected through individual polypeptide chains.

Medical Application Sickle-cell disease

• Sickle-cell disease is an inherited blood disorder, which results from a single amino acid substitution in the protein hemoglobin.
• Which replaces Acid Glutamic, with Valine.

Molecular Structure

Sickle Cell Diease and Proteins

• There are genetic conditions that can cause disease such as in Sickle-cell disease.
• Minor Structural change due to disorder causes the loss functionality of the components in hemoglobin.

Biotechnology Role

• Biotechnology has been used in a number of cures involving gene therapy of disorder and diseases.

Protein Folding In The Cell

• The process of creating each proteins folding is spontaneous one a basic level.
• Proteins must be folding properly other they are not constructed properly.
• More than 10,000 of proteins AA sequence are know
• Chaperonins are proteins that assist the proper folding of other proteins: and detect mis-folded protein and targets it for destruction

Protein Folding

• X-ray crystallography to determine 3D protein structure.
• NMR - does not require protein crystallization.

Nucleic Acids

Nucleic Acids

• There are two types of nucleic acids (DNA and RNA).
• Nucleic Acids are polymers of nucleotides.
• DNA = Deoxyribonucleic Acid.
• RNA = Ribonucleic acid.

Nucleotides

Nucleotide consists of the following:

• 1. Pentose is a 5-carbon sugar molecule.
• 2. Phosphate group.
• 3. Organic base located at 1'carbon.
• Sugar + base = nucleoside Types of sugars that can be formed that are located at
• 1. adenine (A) 2. cytosine (C) 3. guanine (G) 4. thymine (T) 5. uracil (U)

Nitrogenous Base Families

• There are 2 different families types
• Pyrimidines which cytosine, thymine,
• single 6-membered ring Purines

Which are 6-membered ring fused to a 5-membered ring

• Polynucleotide chain: formed by a phosphodiester bond phosphodiester a
• Is often comprised of phosphate group
• DNA/RNA chain "grows" in one direction only
• 5' to 3'

RNA

• Consist of a single polynucleotide chain and made with Sugar in Ribose
• Three majors types of RNA and also bases A,C,G,U.
• MRNA and also 3-7 Carbons
• C1 with
• MRNA MRNA MRNA MRNA

DNA and RNA

• DNA has double strand structure and RNA has singler structure.
• DNA has sugar that 5 HOCHH1 while oxygen is not bonded, and RNA structure contains one oxygen with OH OH combination..
• chains which bond the bases A, C, Gin a complementary
• 4 Types

A-T C-G

ATP

There are multiple nucleotide which preform a chemical bond called Adenosine Triphosphate. This combines ribose, adenine and 3 phosphate groups

• c. ATP individual nucleotide can have metabolic functions -g. adenosine = adenine + ribose adenine modified by adding three phosphates