AP Bio: Unit 1 - The Chemistry of Life

What are the major chemical elements that make up life? (Topic 1)

• Carbon

• hydrogen

• oxygen

• phosphorus

• sulfur

What are isotopes and how are they used in biology? (Topic 1)

• Isotopes - atoms of the same element with different amounts of neutrons

• Can be used to track compounds, determine ages of atoms, create images of biological processes

Why and how is carbon used in organic molecules? (Topic 1)

• Can bond to up to four other molecules

• Allows for the creation of unique/complex molecules

• Used in organic molecules as the backbone

What types of organic molecules contain nitrogen? (Topic 1)

• Amino acids

• proteins

• nucleic acids

• ATP

What types of organic molecules contain phosphorus? (Topic 1)

• nucleic acids (mainly)

• lipids

How does carbon, nitrogen and phosphorus cycle between living and non-living reservoirs and what factors affect these cycles? (Topic 1)

Carbon cycle processes

• photosynthesis

• cellular respiration

• decomposition → carbon released into atmosphere or soil

• carbon reserves (ocean, atmosphere, fossel fuels)

Nitrogen cycle processes

• nitrogen fixation - converting atmospheric nitrogen into biologically available forms (ammonia, NH3) by ntrogen-fixing bacteria (rhizobium) or lightning

  nitrogen-fixing bacteria in soil forming symbiotic relationships with plants

• nitrification - process where ammonia (NH3) is oxidized into nitrite (NO2-) and then nitrate (NO3-) by nitrifying bacteria for plant uptake

• denitrification - reducing nitrate back into atmospheriic nitrogen by denitrifying bacteria

Phosphorus cycle processes

• weathering - physical/chemical breakdown of rocks and minerals → phosphorus released as PO4- into soil and water

• erosion - weathered materials transported by wind, water, ice to other places

• when plants and microorganisms absorb PO4- from soil or water and incorporate them into biomass

• sedimentation - phosphorus-containing particles settle at the bottom of aquatic systems to form sedimentary layers

Factors affecting these cycles

• natural forces

• human-driven forces

What functional group determines an amino acid? (Topic 2)

R group

What are common chemical function groups that are part of biological molecules? (Topic 2)

• Hydroxl (-OH)

• amino (-NH2)

• carbonyl (C=O)

• phosphate (-PO4)

• sulfhydrl (-SH)

• methyl (CH3)

How do the subcomponents of biological molecules and their sequence determine the properties of that molecule? (Topic 2)

The subcomponents and their sequence determine the structure and thus function of biological molecules

• Monomers of macromolecules

  • Proteins - amino acids (bond together with peptide bonds)

  • Nucleic acids - nucleotides

  • Carbohydrates - monosaccharides

  • Lipids - fatty acids

    • Saturated - solid at room temp. due to no double bonds

    • unsaturated - liquid at room temp. due to double bonds

What is a polymer? (Topic 2)

Large molecules made up of repeatiing small units called monomers that are linked through chemical bonds

What are hydrolysis and condensation reactions? (Topic 2)

• Hydrolysis - when a hydrogen atom is added into a large molecule causing it to break apart into smaller molecules

• Condensation - when a hydrogen atom is taken away in order to bond smaller molecules together to create a larger molecule (used to create macromolecules from monomers)

What is the chemical make-up of carbohydrates, and why do different carbohydrates like starch and cellulose have unique structures and functions? (Topic 2)

• Carbohydrates are made up of carbon, hydrogen, and oxygen in a 1:2:1 ratio (think glucose

• The differences in linkage lends to differences in structure and function

  • Starch stores glucose in plants

  • Cellolose provides structure and support in plants (cannot be digested by humans)

What is the general structure of lipids? (Topic 2)

Lipids are made up of a glycerol backbone, 2 fatty acid tails (hydrophobic), and a phosphate group (hydrophilic) (used to create phospholipid bilayer/cell membrane)

How does the different parts of a phospholipid’s structure interact with other molecules to produce its function properties? (Topic 2)

• Phosphate head interacts with/is attracted to water (hydrophilic)

• Fatty acid tails repel water (hydrophobic)

  • Creates bilayer

What is hydrophobicity and polarity? (Topic 2)

• Hydrophobicity - aversion to water

• Polarity - measure of how electrically charged a molecule is

• Small, nonpolar molecules can easily pass through phospholipid bilayer through osmosis

What does it mean that an amino acid chain has directionality? (Topic 2)

It has two ends that are chemically distinct from one another

• A free amino group (amino terminus/N-terminus)

• A free carboxyl group (carboxyl terminus/C-terminus)

What are the four levels of protein structure? (Topic 2)

1. Primary - the sequence of amino acids in a polypeptide chain (straight line, no folding

2. Secondary - Folded structure that form within a polypeptide due to interactions between atoms of the backbone

   1. Does not involve R group atoms

   2. Most common - a helix and b pleated sheet held in shape by hydrogen bond

3. Tertiary - overal three-dimensional structure of a polypeptide

   1. Due to interactions between r groups of the amino acids like hydrogen bonding, ionic bonding, non-covalent bonds in general

   2. Disulfide bonds = strongeset bonds that contribute to tertiary structure (covalent linkages between sulfur-containing side chains)

4. Quaternary structure - When proteins are made up of multiple polypeptide chains (subunits), and these chains come together

   1. Basically consists of more than one amino acid chain

What makes up a nucleotide? (Topic 2)

• A phosphate group

• A sugar molecule (pentose)

• A nitrogenous base

How do nucleotides link together to form nucleic acids? (Topic 2)

Through covalent bonds between the phosphate group of one nucleotide and the sugar of another

What determines directionality of a nucleic acid chain? (Topic 2)

The two ends of a polynucleotide chain are different from each other

• 5’ end (the beginning) is where the 5’ phosphate group of the first nucleotide sticks other

• 3’ end (the end) is where he 3’ hydroxyl of the last nucleotide is exposed

• DNA sequences run from 5’ to 3’

• New nucleotides are added to a strand of DNA/RNA

  • strand grows from 3’ end allowing the 5’ phosphate of incoming nucleotides to attach

What chemical interactions occur to create a DNA double-helix? (Topic 2)

Hydrogen bonds between complementary nitrogenous base pairs and covalent bonds within each strand

What are the structural similarities and differences between DNA and RNA? (Topic 2)

Similarities

• Both composed of nucleotides

• Both share adenine, guanine, and cytosine

• Both are composed of long chains of nucleotide monomers linked together

• A pairs with T/U and G pairs with C in both

Differences

• The sugar in DNA is deoxyribose

• The sugar in RNA is ribose

• DNA has thymine

• RNA has uracil

• DNA is typically double stranded

• RNA is typically single stranded

• DNA is more stable

• RNA is less stable and more susceptible to degradation

Why is water a polar molecule, and what are hydrogen bonds? (Topic 3)

• It is polar because of the uneven distrbution of elections within the molecule which creates a partial positive charge on the hydrogen atoms and a partial negativec charge on the oxygen atoms

• Hydrogen bonds are attraction between a hydrogen atom and an electronegative atom (oxygen, nitrogen, or fluoriine) in another or within the same molecule

What are the properties of water? (Topic 3)

• Universal solvent

• High specific heat

• Hight surface tension

• less dense in solid form than in liquid form due to expansion

• Polarity gives way to cohesive and adhesive properties

What is osmosis and water potential? (Topic 3)

• Osmosis - the flow of a solvent from high solute concentration to low solute concentration through a semipermeable membrane

• Water potential - the likelihood of water flowing from one place to another

What is transpiration, and what are the environmental factors that influence it? (Topic 3)

• Transpiration - evaporation of water from plants through stomata

  • Temperature can increase rate

  • Humidity can lower rate

  • Air movement can increase rate

  • Light intensity can increase rate