AP Biology - Unit 1 - The Chemistry of Life

Atom (definition)

Smallest stable unit of matter that has the characteristics of it's specific element

Atom (structure)

Nucleus (protons + neutrons) surrounded by electron orbitals

Neutron

No charge, mass of 1, found in the nucleus

Proton

Positive charge, mass of 1, found in the nucleus

Electron

Negative charge, mass of 0, found in the electron orbital

Electron orbitals (energy)

Closer to the nucleus = less energy

Farther away from the nucleus = more energy

Valence electrons

found in the outermost orbital - most elements like to have 8 valence electrons in their valence shell (most stable)

Ions

Atoms that are non-neutral (have a charge)

Cations

Positively charged (protons>electrons)

Anions

Negatively charged (electrons>protons)

Main elements of life

CHON - carbon, hydrogen, oxygen, nitrogen

Trace elements

found in small amounts but critical to maintaining homeostasis, includes calcium, phosphorus, potassium, sodium, chlorine, magnesium, sulfur

Carbon cycle

Inorganic carbon is fixed from the atmosphere by plants (photosynthesis), decomposers recycle carbon back into the environment when organisms die

Importance of carbon

Used to make every biomolecule, main source of biomass in ecosystems

Nitrogen cycle

Inorganic nitrogen is fixed from the atmosphere by bacteria and other decomposers, and absorbed by plants to enter the food web, recycled back into the environment by decomposers

Importance of nitrogen

used to make proteins and nucleic acids

Importance of phosphorus

Used to make nucleic acids and certain lipids (phospholipids)

Electronegativity

The measurement of how strongly atoms attract bonding electrons. The closer to 8 valence electrons, the more electronegative the element

Electronegative elements

Fluorine (most negative), oxygen, nitrogen (less negative)

Electropositivity

A measurement of the ability of elements to donate electrons and form positive ions. Electropositive elements usually have 1 or 2 valence electrons

Covalent bonds

occurs when two atoms share electrons

energy is stored and released if the bond is broken

Ionic bonds

occurs when there is a transfer of valence electrons from a metal to a non-metal

weaker than covalent and will dissociate in water

Polar molecule

occurs when there is an unequal sharing of electrons across a covalent bond between a very electronegative and very small/electropositive element

Charges on a polar molecule

Overall neutral charge with partial positive and negative charges on the poles

electronegative element is partial negative (pulling electrons)

electropositive element is partial positive (less electron density)

Hydrogen bonds

weak attraction between a hydrogen atom and an oxygen, nitrogen or fluorine atom (only these elements because they are very electronegative)

How is the function of a molecule determined?

The structure, shape, and chemical properties of a molecule determines the function of that molecule

Laws of conservation

Energy, the amount and types of atoms, and the amount of bonds in a chem reaction are conserved

How does water support life?

Helps organisms maintain homeostasis, allows for the transport of materials in different organisms (ex. blood or sap)

Chemical properties of water

Polar molecule, allows it to hydrogen bond with other water and polar molecules

Important characteristics of water

cohesion, adhesion, surface tension, high specific heat capacity, evaporative cooling, great solvent, density (lighter as a solid)

Cohesion

Water molecules are attracted to and hydrogen bonded to other water molecules

Adhesion

Water molecules are attracted to and can hydrogen bond with other polar or charged molecules

Surface tension

caused by the cohesion of water molecules at the surface of a body of water - water is surround by air on one side, increasing the strength of h-bonds between other water molecules

Capillary action

water adheres to the side of tubes that are lined with polar/charged molecules and can crawl up - plants use it to transport nutrients from the roots to the vascular tissue

High specific heat capacity

h-bonds are collectively strong, therefore it takes a lot of energy to break all the hydrogen bonds an evaporate water, allowing it to resist temperature changes well

Excellent solvent

waters polar nature makes it an excellent solvent - polar compound is very good at seperating ionic compounds into ions, can also create a water shell around polar molecules

Organic molecule

carbon-based molecule

Biomolecules

organic, carbon-based macromolecules

carbohydrates - lipids - proteins - nucleic acids

Why is carbon important?

Has four valence electrons, always forms four covalent bonds, allowing it to form a variety of different structures

Hydrogen (number of bonds)

1 bond

Oxygen (number of bonds)

2 bonds

Nitrogen (number of bonds)

3 bonds

Monomer

individual subunit of a biomolecule

Dimer

two monomers covalently bonded together

Polymer

many monomers covalently bonded together

Biomolecular Metabolism

The combination of chemical reactions that synthesize and hydrolyze biomolecules for energy storage and release in an organism

Free energy

energy that is actually available for a cell to use for metabolic processes

Catabolic reaction

breaks down polymers into monomers to generate ATP, exergonic: net release of free energy (reactants > products)

Anabolic reaction

builds up monomers into polymers for energy storage, endergonic: net investment of free energy (products > reactants)

Dehydration synthesis

Anabolic process by which monomers are covalently bonded into polymers through the removal of water, requires enzymes

Hydrolysis

Catabolic process by which polymers are broken down into monomers through the addition of water, requires enzymes

Monomers of Carbohydrates

monosaccharides (glucose, fructose, galactose)

Polymers of Carbohydrates

polysaccharides (starch, glycogen, cellulose)

Structure of Carbohydrates

Hexamer rings

Elemental composition of Carbohydrates

CHO (carbon, hydrogen, oxygen) in a 1:2:1 ratio

Main function of carbohydrates

short term energy source, energy storage, structure for plants (cellulose) and certain animals (chitin in insects and crabs)

Energy storing carbohydrates

branched structure, allows more monomers to be broken off, increasing the rate of cellular respiration

Structural carbohydrates

linear structure, able to stack which provides stability and allows for the formation of tough structures

Monomers of Lipids

fatty acids (long hydrocarbon chains) and glycerol (three carbon alcohol)

Polymers of Lipids

lipids (triglycerides, phospholipids, steroids)

Triglycerides

One glycerol and three fatty acids linked by ester bonds, can be saturated or unsaturated

Phospholipids

One glycerol and two fatty acids with a phosphate group, form cell membranes with hydrophilic heads and hydrophobic tails

Elemental composition of lipids

CHO (P), 1:2 ratio, very little oxygen, sometimes contain phosphorus (phospholipids)

Main function of lipids

Long term energy storage, insulation and protection of body parts

Saturated fats

do not contain a double bond, therefore are linear and can stack, forming a solid at room temperature

Unsaturated fats

contain a double bond, cannot stack, therefore form a liquid at room temperature

Monomers of proteins

amino acids

Polymers of proteins

polypeptides

Structure of proteins

complex structure consisting of four levels: primary, secondary, tertiary, quaternary

Elemental composition of proteins

CHON(S), always contain CHON, sometime sulfur

Main function of proteins

Wounds and tissue repair, catalysing chemical reactions, cell signalling, antibodies, transport

Monomers of nucleic acids

nucleotides

Polymers of nucleic acids

nucleic acids

Structure of a nucleotide

phosphate group, sugar, nitrogenous base, linked by covalent bonds

Nucleic acids bonding

Phosphodiester linkages between the phosphate group of one nucleotide and the sugar of another

Elemental composition of nucleic acids

CHONP

Main function of nucleic acids

storage of genetic material, coding for an organism's physical characteristics determined by the order of nucleotides

Directionality of DNA and RNA

have a 5' end and a 3' end

DNA structure in eukaryotes

Linear, double strand helix located in the nucleus

DNA structure in prokaryotes

Circular, double strand helix found floating in the cytoplasm

DNA charcteristics

double stranded, stores the genetic code, nucleotides A, T, C and G, have deoxyribose sugar, more stable than RNA

RNA

single stranded, used for protein syntesis, 3 types: mRNA, tRNA, rRNA, nucleotides A, U, C and G, have ribose sugar, less stable than DNA, made in the nucleus and transported to the cytoplasm

How are biomolecules broken down?

Nucleic acids cannot be broken down for energy, Lipids have the most energy (9 cal per 1 gram), Proteins and Carbs have the same amount (4 cal per 1 gram)

What are the four levels of protein?

primary, secondary, tertiary, quaternary, each level builds on the others and is held together by different bonds

Directionality of proteins

N-terminus (amine group) located at the first amino acid to C-terminus (carboxyl group) located at the last amino acid

Amino acid variety

20 differnt types, all have the same peptide backbone with different R-groups

Amino acid structure

Central carbon surrounded by four groups:

Amine group - NH2 or NH3, if found in the side chain will be positively charged

Single Hydrogen

Carboxyl group - COOH or COO-, if found on the side chain will be negatively charged

R Side Chain - structure varies

R group properties

The chemical properties and bonding abilities of the amino acid side chains are determined by the elemental composition

Hydrophobic side chain

Long hydrocarbon chains with big hexamer rings

Hydrophilic side chain

oxygen/nitrogen with no charges

Acidic (hydrophilic)

carboxyl groups with negative charges

Basic (hydrophilic)

Amine groups with positive charges

Primary protein structure

sequence of amino acids, determines how the protein folds at all levels

Primary protein bonding

Amino acids are covalently bonded via dehydration synthesis - known as a peptide bond, made between the carboxyl group of the first AA and the amine group of the second

Secondary protein structure

occurs as the protein begins to fold (but is not active yet), two structures: alpha helixes and beta pleated sheets

Secondary protein bonding

Hydrogen bonding between the carboxyl and amine groups on the peptide backbone - no R-groups involved

Tertiary protein structure

occurs as the protein finished folding (active), controlled by the interactions between the R-side chains on the amino acids

Hydrophobic collapse

occurs as the hydrophobic amino acids collapse away from the water and into the interior of the tertiary structure of the protein

Tertiary hydrogen bonds

formed between side chains with electronegative atoms (O and N), charge attraction between acidic and basic charges, sensitive to changes in pH and temperature

Disulfide bridges

covalent bonds between the sulfur atoms in the side chains of two cysteine AAs, very strong and not sensitive to changes in pH and temperature