Biochemistry

Looking at the logic of the living system

Life observes levels of organization.

Atoms and molecules as fundamental building blocks

Life performs various metabolic processes

Set of chemical reactions

Gas exchange in the alveoli involves the formation and dissociation of the complex between hemoglobin and
oxygen or carbon dioxide gases
Life engages in energy transformation

Forms energized biomolecules: ATP & NADPH

Life has the capacity for self-replication.

DNA as the genetic material

Life’s origin may be explained chemically

 With the idea of the Big Bang, we had established the formation of elements and, later on, common
gases like water, carbon dioxide, ammonia, methane, etc. These gases occupied the primitive Earth which were
believed to be the ingredients needed to form biomolecules

In 1953, one of the most known evidences in the formation of biomolecules was presented by Stanley Miller and
Harold Urey. They simulated the conditions of the primitive Earth in the laboratory to observe the formation of
these biomolecules

Biochemistry: Chemical Foundations

The wonders of carbon

The presence of elements other than carbon and hydrogen modifies the orientation and function of the entire
molecule.

Hydrocarbons are considered non-polar but with the addition of new elements, their shape and properties change.

The functional group

Polarity matters!

Polarity plays a role in forming the structure of life and how it interacts to its environment.

Molecules have to keep in SHAPE!

 For every molecule to perform its designated function in the system, forming the appropriate shape
based on how its atoms are arranged must be followed.

Models of atomic structure

The Human Body

Three types of Bonding

Covalent Bonds and polarity

Covalen Bonds

– Form between atoms that share electrons rather than donating or receiving them

– Single covalent bonds share a pair of electrons (H2)

– Double covalent bonds share two pairs of electrons and are more rigid than single bonds (O2)

Polar Molecule
  Results when a molecule is formed between two atoms that have different electronegativity, or ability to
attract electrons

Non Polar Molecule

 Molecules formed when atoms have similar electronegativity

Ionic Bonds: Electron Transfer

Ionic Bonds:

 Formed when electrons are transferred completely from one atom to another and
are not shared

Ionization: Formation of charged Particles

Ionization:

 The formation of charged particles when a molecule formed by ionic

bonds dissolves in a solvent

Cations: positively charged ions

Anions: negatively charged ions

Electrolytes: substances such as salts, acids, and bases that release ions when
dissolved in water
Hydrogen Bonding

Hydrogen bonds:

 Formed due to attractive forces between nearby atoms or molecules

 A weak type of bond that forms between a hydrogen covalently bonded to
one molecule and an oxygen or nitrogen atom on the same molecule or on
a different molecule
 This bond is temporary and easily disrupted

van der Waals forces:

 Weak attractions between molecules that show polarity

 Neighboring groups with slight attractions will interact and remain
associated

Chemical Reactions

Synthesis Reaction:

 Reactants bond together in a manner that produces an entirely new molecule

 SO  SO
2 2
Decomposition Reaction
 Bonds on a single reactant molecule are permanently broken to release two or more product molecules
 2H O 2H O+O
2 2 2
Exchange Reactions:
 Reactants trade portions with each other and release products that are combinations of the two
 AB + XY ⇄ AX + BY
Catalysts
 Substances that increase the rate of a reaction without being consumed in the process
 Enzymes are catalysts in cells

Solutions

Hydrophilic:
 Molecules such as salt or sugar that attract water to their surface
Hydrophobic:
 Nonpolar molecules such as benzeze that repel water
Amphipathic:
 Molecules such as phospholipids that have both hydrophilic and hydrophobic properties
Acidity, Alkalinity, and the pH scale

Acidic Solution:

 Occurs when a component dissolved in water releases excess hydrogen ions (H+)

Basic Solution:
 Occurs when a component dissolved in water releases excess hydroxyl ions (OH-)

Hydrogen ion and Hydroxide Ion

Concentrations at a given pH

The pH Scale
The chemistry of Carbon

Inorganic chemicals:

 Molecules that do not contain both carbon and hydrogen

 NaCl
 Mg3(PO4)2
 CaCO3
 CO2

Organic chemicals:

 Molecules with a basic framework of the element of carbon

bonded to other atoms
 Simplest: CH4
 Complex: antibody molecules with a molecular weight of
1,000,000

• Carbon is the fundamental element of life:

– Ideal atomic building block to form the backbone of organic

molecules

– Four electrons in outer orbital can be shared with four other

atoms, including other carbons

Functional Groups
 Molecular groups or accessory molecules that bind to organic compounds

 Help define the chemical class of organic compounds

 Confer unique reactive properties on the whole molecule
 Reactions of an organic compound can be predicted by knowing its functional group

Representative functional groups and

classes of organic compounds

Macromolecules

Functions of macromolecules:

 Structural components
 Molecular messengers
 Energy sources
 Enzymes (biochemical catalysts)
 Nutrient stores
 Sources of genetic information

Biochemistry:

 Scientific field that explores the compounds of life

Four main families of biochemical:

 Carbohydrates
 Lipids
 Proteins
 Nucleic Acid

Carbohydrates: Sugars and polysaccharides

Saccharide: a sugar

Monosaccharide: a simple sugar containing three to seven carbons

Disaccharide: combination of two monosaccharides

Polysaccharide: polymer of five or more monosaccharides

Monosaccharides and disaccharides are named with the suffix –ose

Hexose: composed of six carbons

Pentose: composed of five carbons

Macromolecules and their functions: Carbohydrates

Examples of polysaccharides

 Cellulose:
- Long, fibrous polymer
- Gives strength and rigidity to plants and microscopic algae
- One of the most common organic substances on earth
- Digestible only by bacteria, fungi, and protozoa
 Agar:
- Important in preparing solid culture media
- Natural component of seaweed
- Polymer of galactose and sulfur-containing carbohydrates
 Chitin:
- Polymer of glucosamine
- Found in the exoskeletons of certain fungi
 Peptidoglycan:
- Polysaccharides are linked to peptide fragments
- Provides the main source of structural support to bacterial cell walls
 Lipopolysaccharide:
- Complex of lipid and polysaccharide found in the outer membrane of gram-negative bacteria
- Responsible for symptoms of fever and shock

 Glycocalyx:
 - Composed of polysaccharides bounds in various ways to proteins
- Functions in attachment to other cells or as a site for receptors
 Glucose polymers starch and glycogen:
- Storage molecules in cells
- Must be broken down by appropriate enzymes for use by the cell
- Hydrolysis: digestion or breakdown of polysaccharides that requires the addition of water

Lipids: Fats, Phospholipids, and waxes

Lipid:

- Operational term for substances that are not soluble in polar solvents such as water but are
soluble in nonpolar solvents such as benzene and chloroform
- Long or complex hydrocarbon chains that are hydrophobic

Triglycerides

- Storage lipids
- Fats and oils
- Composed of a single molecule of glycerol bound to three fatty acids
- Glycerol: 3-carbon alcohol with three OH groups that serve as binding sites
- Fatty acids: long chain hydrocarbons with a carboxyl group at the end

Synthesis and structure of a triglyceride

Fatty Acids

 Saturated fatty acid:

All carbons in the fatty acid chain are single-bonded to two other carbons and two hydrogens

 Unsaturated fatty acid:

A fatty acid in which at least one double bond exists between carbon atoms

Phospholipids

• Phospholipids:

– Contain only two fatty acids attached to a glycerol

– Third binding site holds a phosphate group bound to an alcohol

– Have a hydrophilic region and a hydrophobic region

– Allows the molecule to form bilayers and membranes

Membrane Lipids

• Membrane formation in an aqueous solution:

• Polar heads of phospholipids attracted to the water phase

• Nonpolar tails repelled from the water phase

• Membranes and lipid bilayers:

– Hydrophilic face orients itself toward the solution

– Hydrophobic tails immerse themselves in the bilayer

– These characteristics allow selective permeability and

fluidity

Steroid and Waxes

• Steroids:

– Ringed compounds commonly found in cell membranes and animal hormones

– Cholesterol: reinforces cell membranes in animal cells and cell- wall-deficient bacteria
(mycoplasmas)

– Ergosterol: found in the cell membranes of fungi

• Wax:

– Ester formed between a long-chain alcohol and a fatty acid

– Soft and pliable when warmed, water resistant when cold

– Natural waterproofing of skin, fur, feathers, etc.

– Bacteria that cause tuberculosis and leprosy produce a wax that repels ordinary laboratory
stains and contributes to their damaging effects on the body

Macromolecules and their functions: Lipids

Proteins: Shapers of life

• Predominant organic macromolecule in cells

– Determine structure, behavior, and unique qualities of organisms

• Amino acids:

– Building blocks of proteins

– Exist in 20 different naturally occurring forms

– Linked by peptide bonds

Basic structure of amino acids

• α (alpha) carbon

• Amino group (NH2)

• Carboxyl group (COOH)

• Hydrogen atom (H)

• R group: imparts unique characteristics to the amino acid

Peptides
• Peptide:

– Molecule composed of short chains of amino acids

• Polypeptide:

– Has more than 20 amino acids

– Not all polypeptides are large enough to be considered proteins

Protein Structure

• Primary (1°) structure:

– The type, number, and order of amino acids

• Secondary (2°) structure:

– Arises when functional groups on the outer surface

of the molecule interact with each other

α helix

β pleated sheet

• Tertiary (3°) structure:

– Torsion caused by interaction between functional

groups

– Covalent disulfide bonds

• Quaternary (4°) structure:

– Large multiunit proteins formed by more than one

polyprotein

Enzymes and Antibodies

• Enzymes:
– Catalysts for chemical reactions in cells

– Specificity comes from the unique patterns in enzyme binding sites

• Antibodies:

– Complex glycoproteins with specific attachment regions for bacteria, viruses, and other
microorganisms

Nucleic Acids

• Deoxyribonucleic Acid (DNA):

– Contains a special coded genetic program with detailed

and specific instructions for each organism’s heredity

• Ribonucleic Acid (RNA):

– Helper molecules responsible for translating and carrying out the instructions of DNA

Nucleic Acid Structure

• DNA and RNA are composed of repeating nucleotide subunits

• Nitrogen base

• Pentose (5-carbon) sugar

• Phosphate

Purines and Pyrimidines

• Purines:
– Nitrogen bases composed of two rings

– Adenine and Guanine

• Pyrimidines:

– Nitrogen bases composed of one ring

– Thymine, Cytosine, and Uracil

DNA vs. RNA

• DNA:

– Contains all of the nitrogen bases except uracil

– Nitrogen bases are covalently bonded to deoxyribose

• RNA:

– Contains all of the nitrogen bases except thymine

– Nitrogen bases are covalently bonded to ribose

RNA: Protein Synthesis and Regulation

• Long, single strand of nucleotides

• Three major types of RNA:

– mRNA: copy of a gene

– tRNA: carrier that transports the correct amino acids to the ribosome for protein assembly

– rRNA: major component of ribosome

Macromolecules and Their Functions: Nucleic Acids

ATP : Energy Molecule

• Adenosine Triphosphate (ATP):

– Adenine

– Ribose

– Three phosphates

• Releases energy when the bond is broken between the second and third phosphates