IB Biology --> Topic 2 (Molecular Biology)

Reductionist approach

Usual approach of Molecular Biology.
Molecular biologists identify the steps in a metabolic pathway and break down each one into its components

Carbohydrate

Organic compound consisting of one or more simple sugars.

Lipid

Non-polar, hydrophobic molecule made of glycerol and fatty acids

Nucleic acid

Macromolecule made of nucleotides (phosphate, pentose, and nitrogenous base). Contains the genetic information of an organism

Protein

Large organic compound made of amino acids arranged into one or more linear chains.

Carbon, hydrogen, and oxygen

Elements that are contained in carbohydrates and lipids

Carbon, hydrogen, oxygen, nitrogen

Elements that are contained in all proteins.
(Note: sulfur is contained only by some of them)

Carbon, hydrogen, oxygen, nitrogen, and phosphorus

Elements contained in nucleic acids

Monosaccharide

Monomer of a carbohydrate

Glycerol and fatty acids

Components of a lipid

Amino acid

Monomer of proteins

Nucleotide

Monomer of nucleic acids

Glycosidic bond

Type of covalent bond in carbohydrates

Peptide bond

Type of covalent bond in proteins

Phosphodiester bond

Type of covalent bond that joins nucleotides of nucleic acid

Saturated fat

Type of lipid
None of the carbons has arms to bond with other elements.
Solid

Unsaturated fat

Type of lipid
A double bond of carbon can be broken to make 2 new bonds
Liquid

Simple / neutral fat

Type of lipid
Esters of fatty acids and alcohol
Examples: triglycerides and waxes

Compound fat

Type of lipid
Esters of fatty acids, alcohol, and additional groups
Examples: phospholipids and glycolipids

Derived fat

Type of lipid
Substances derived from simple or compound lipids
Examples: steroids and carotenoids

Functions of carbohydrates

- Short-term energy storage
- Recognition molecule (glycoproteins)
- Structural component (part of DNA and RNA)

Functions of lipids

- Major component of cell membranes
- Long-term energy storage
- Signaling molecule (steroids)

Ribose

Sugar in RNA

Deoxyribose

Sugar in DNA

Nitrogenous bases

Adenine, Thymine, Guanine, Cytosine, and Uracil

Functions of nucleic acids

- Genetic material of all cells. Determines the inherited features of an organism

Functions of proteins

- Major regulatory molecules involved in catalysis
- Structural molecules in the plasma membrane
- Cellular signaling
- Hormones
- Gas transport (hemoglobin)
- Immune response (antibodies)

Urea

By synthesizing this organic molecule in a lab, Frederik Woehler disproved vitalism as a theory

Metabolism

Totality of an organism's chemical reactions, consisting of catabolic and anabolic pathways. Manage the material and energy sources of an organism.
It is an emergent property of life

Functions of metabolism

- Provide a source of energy for cellular processes
- Enable the synthesis and assimilation of new materials for use within the cell

Anabolism

Set of metabolic reactions that build up complex molecules from simpler ones.
Biosynthetic pathways.
Endergonic (uses energy)

Condensation

Type of reaction most common for anabolism
Monomers are covalently joined and water is produced as a byproduct

Catabolism

Set of metabolic reactions that break down complex molecules into simpler ones.
Releases energy when bonds are broken

Hydrolisis

Most common type of reaction of catabolism.
Water is consumed to break the bonds within a polymer

Covalent bond

Sharing of a pair of valence electrosn by two atoms.

Molecule

Two or more atoms held together by a covalent bond

Electronegativity

Attraction of a particular kind of atom for the electrons of a covalent bond.

Nonpolar

Covalent bond where electrons are shared equally between 2 atoms of similar electronegativity

Polar

Covalent bond between atoms with different electronegativity. One side of the molecule is slightly negative and the other is slightly positive

Ionic bond

Chemical bond resulting from the attraction between oppositely charged atoms

Hydrogen bond

Weak chemical bonds formed when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom.
Bonds complementary bases in DNA.
Also present in lipids

Vander Waals interactions

Weak attraction between molecules or part of molecules that result from localized charge fluctuation
Present in lipids
Responsible for the gecko's ability to walk up walls

Inorganic compounds

Compounds that are not produced by living things.
Include all compounds that don't contain carbon

Trace elements

Elements required by an organism in minimum quantities.
Examples: sulfur, phosphorus, iron, sodium, calcium, and nitrogen

Organic compounds

Compounds produced by living things.
Include all compounds including carbon (except hydro-carbonates, carbonates, carbon oxides, and cyanides).

Alkane

Hydrocarbon that only has single bonds
Suffix: - ane
Formula: CnH2n+2

Alkene

Hydrocarbon that has single and double bonds
Suffix: - ene
Formula: CnH2n

Alkyne

Hydrocarbon that has triple bonds
Suffix: -yne
Formula: CnH2n-2

Isomers

Compounds that have the same elements but different properties
Can be structural, geometrical, or enantiomers

Hydroxyl

Functional group
- OH
Compounds are named alcohols

Carbonyl

Functional group
>C=O
Compounds can be ketones or aldehydes

Carboxyl

Functional group
- COOH
Compounds are organic acids.
When combined with an amino group, amino acids result

Amino

Functional group
-NH2
Compounds are amines
When combined with a carboxyl group, amino acids result

Sulfhydryl

Functional group
- SH
Compounds are called thiols

Phosphate

Functional group
- PO4
Compounds are called organic phosphates

Methyl

CH3
Compounds are called Methilated compounds

Functional group

Specific configuration of atoms commonly attached to the carbon skeleton of organic molecules and often involved in chemical reactions