UNIT 2 - Macromolecules and the Building Blocks of Cells

proteins

• catalysts (enzymes) that facilitate chemical reactions, structural support of the cell, and transport

  • monomer: amino acids, joined by peptide bonds

• a “protein” can be tertiary or quaternary

nucleic acids

encode and transmit genetic information

• monomer: nucleotides, joined by phosphodiester bond

• found in DNA/RNA, as well as mitchondria & chloroplasts

carbohydrates

provide energy and make up the cell wall

• monomer: monosaccharide, joined by glycosidic bonds

• 4C end of incoming monomer is added to 1C end

lipids

make up cell membranes, store energy, and act as signalling molecules

• do not polymerize in the same manner: monomers (fatty acid tails) are added to a head group

functional groups

specific clusters of atoms attached to carbon skeleton that determine the chemical behaviour, reactivity, and properties of biological molecules

nucleotide

5 carbon sugar (deoxyribose, ribose), 1 or more phosphate groups, base

• each adjacent air of nucleotides is connected by a phosphodiester bond

dehydration synthesis

reaction that joins monomers and creates H2O by removing water components from reactants

hydrolysis

reaction that breaks down polymers by adding a water molecule

pyrimidine bases

- single ring

- CUT

- cytosine, uracil, thymine

purine bases

- double ring

- adenine, guanine

3 key features of cells

- having a cell membrane

- ability to store and transmit info (DNA)

- ability to obtain energy from the environment and use it

metabolism

chemical reactions by which cells convert energy from one form to another

features of life

ability to reproduce, harness energy, respond to the environment, and evolve

integral membrane proteins

permanently associated with cell membranes, span the lipid bilayer

• includes transmembrane proteins

• includes channel and transporter proteins

• can pass signals from external side of membrane to internal side of membrane

peripheral membrane proteins

temporarily associated with the lipid bilayer thru weak covalent associations

• associated with bilayer on either side

passive transport

when molecules move across a cell membrane along the concentration gradient

• does not require an input of energy

• random movement of molecules

• diffusion

facilitated diffusion

• passive transport thru protein transporters

• helps polar molecules/ions move across the membrane (shielding them thru hydrophobic region of membrane)

• channels

• carrier proteins

osmosis

net movement of a solvent across a selectively permeable membrane

osmotic pressure

tendency of a solution to draw in water by osmosis

• higher solute concentration = higher osmotic pressure

primary active transport

“uphill” against a concentration gradient

• eg. Na-K pump

• uses ATP

• no random movement of molecules, very directional

antiporters

protein in cell membrane that moves different molecules/ions in opposite directions

symporters

protein in cell membrane that moves two different molecules in the same direction

secondary active transport

• uses potential energy of electrochemical gradient rather than ATP directly

• transporter proteins use movement of protons to drive molecules against their concentration gradient

• a transport protein couples the downhill movement on an ion with the uphill movement of another molecule

hypertonic solution

solute concentration higher than inside the cell

• causes cell to shrink

hypotonic solution

solute concentration lower than inside the cell

• causes water to move into the cell (lyses/bursts)

contractile vacuoles

organelles in some protists that take up excess water from inside the cell and expel it to external environment by contraction

turgor pressure

force that pushes plasma membrane against the cell wall (plants)

electronegativity

ability of atoms to attract electrons

polar covalent bond

when electrons are shared unequally between two atoms

hydrogen bond

interaction between a hydrogen atom with a partial positive charge and an electronegative atom of another molecule

polymers

complex molecules made up of repeated monomers connected by covalent bonds

what are the shapes formed by phospholipids determined by?

the bulkiness of the head group relative to the hydrophobic tails

micelles

• bulky heads and single hydrophobic fatty acid tails

• wedge shaped and packed into spherical structures

bilayer

liposomes

primary structure

linear sequence of amino acids in a protein

• dictates protein folding, which determines function

secondary structure

caused by hydrogen bonds forming between carbonyl group and amide group in another peptide bond (in polypeptide backbone)

• r groups are not involved

• alpha helix

  • stabilized by hydrogen bonds that form between each amino acid’s carbonyl group and amide group

  • R groups project outward

• beta sheet

  • pleated sheet

  • hydrogen bonds between carbonyl groups and amide groups in different chains

  • R groups project alternatively above and below

  • can be antiparallel or parallel

    • antiparallel more stable bc favourably aligned

tertiary structure

• 3d conformation of a single polypeptide chain

• determines function

• shape is determined by spatial distribution of the hydrophilic and hydrophobic R groups along the molecule

  • as well as diff types of chemical bonds and interactions (van der waals)

denaturation

molecules are unfolded and lose their structure

quaternary structures

• polypeptide subunits may either be identical or different

• subunits can influence each other in subtle ways

chaperones

help shield hydrophobic groups in protein from aggregation until they become 3d

how does pH affect the activity of enzymes?

1. can affect the way protein folds: pH affects charges of amino acids, which can affect how amino acids interact as they fold

2. affect the charges of the active site: charges of amino acid influences how well they bind to a substrate

• ionic and hydrogen bonds are often involved between enzyme & substrate

allosteric inhibitors

• decrease activity of enzyme

• prevents the substrate from binding to the active site

allosteric activators

• increase activity of enzyme

• promote substrate binding to the active site

diffusion

natural movement of particles from an area of higher concentration to an area of lower concentration until equilibrium

• small, nonpolar molecules can diffuse thru cell membrane without proteins

• small uncharged polar molecules like water can slowly diffuse too, but rely on aquaporins for fast diffusion

channel proteins

• can be “open” or “gated” (open/close due to a signal, usually binding of the molecule being transported)

• usually selective for a specific type of molecule (ions, small nonpolar molecules, small polar)

• molecules have to interact w protein channel to be transported

• provides hydrophilic passageway

• transport occurs at faster rate than carrier proteins

carrier proteins

• “gated”

• transport a specific type of molecule (more specific than channels)

• protein undergoes shape change (conformational change) to open and close the protein

amino acid

1. amino group

2. r group

3. central carbon atom - alpha carbon

4. carboxyl group

• structure and composition of the R group determines the identity of the amino acid

• proteins are polymerized N → C

polypeptide

chain greater than 50 amino acids in length

a peptide

short chain of less than 50 amino acids

why do phospholipids spontaneous form bilayers or lipsomes in water?

• it is energetically favourable

• ΔG is negative

• system moves from less stable to more stable state

allosteric enzyme

binds at a site that isnt the active site and changes shape of the active site

• activators/inhibitors

semi-permeable membrane

some molecules can pass through the membrane unassisted, while others cannot

hydrophobic effect

hydrophobic regions tend to aggregate in an aqueous solution, driven by the tendency of water to increase its own entropy (increases system stability)

fluid mosaic model

• proteins and lipids can freely laterally within the bilayer

• intermolecular non-covalent interactions/bonds that break and reform are required for the movement of molecules within the membrane

amino acid residue

specific chemical unit that remains in a polypeptide or protein chain after an indvidual amino acid loses a water molecule during peptide bond formation

polarity of polymers

polymer has two chemically distinct ends: directionality

macromolecular assembly

macromolecules (polymers) assemble into functional structures

• proteins (folded)

• DNA double helix

• lipid bilayers

intramolecular interaction

• within molecules

• covalent, ionic

intermolecular interaction

non-covalent

phospholipids

• amiphathic

• kink due to double bonds

what is the significance of water in biological chemistry?

enables formation of hydrogen bonds: leads to cohesive and solvent properies of water

purpose of poly A tail

• shields mRNA from being broken down in the cytoplasm

• required to transport mature mRNA out of nucleus

purpose of 5’ cap

• protects mRNA from degradation

• required for mature mRNA to leave nucleus