Exam #2

Biology

Selective permeability

the membrane lets some molecules cross easily (small + nonpolar C-H) while others have a harder time (large + polar O-H) (ex. the phospholipid bilayer)

Passive transport

(big umbrella category) large and polar molecule move through this. solutes move from high —> low concentration

Simple diffusion

(type of passive transport) small and nonpolar molecules move through this. solutes move from high —> low concentration directly through the membrane with no ATP (energy required)

Dynamic equilibrium

Both sides of the concentration gradient are equal; the molecules still move, but there is no net movement because movement is equal in both directions.

Osmosis

Diffusion of water; water follows the side with more solute.

Hypertonic

(In osmosis) Outside has more solute - water follows the solute - cell shrinks

Hypotonic

(In osmosis) Outside has less solute - water follows the solute - cell bursts

Isotonic

(In osmosis) Equal solute concentration - water moves both ways equally - no net change in cell size

Facilitated diffusion

(type of passive transport) solute moves from high —> low concentration with the help from a transport protein, no ATP

Channel protein

(used in facilitated diffusion) a type of transport protein that is a tunnel through the membrane that allows specific substances through Ex. Aquaporin (water channel)

Gated ion channel

(used in facilitated diffusion) a type of transport protein that is a channel that can open and close to allow specific substances through ( a revolving door)

Active transport

moves solutes from low —> high concentration, which is against the concentration gradient, so it requires energy ATP

Pump

(used in active transport) ATP powered protein that changes shape and moves substances against their gradient

Cotransporter

(used in active transport) it is a secondary active transport; use’s the gradient made by another active transport process to help transport another solute

Prokaryote

circular chromosome, no membrane-bound organelles, generally smaller

Eukaryote

linear chromosomes, membrane-bound organelles, generally larger

Molecular zip codes

are amino acid sequences that. tells the cell where a protein belongs (protein tag/signal tells the cell its destination with its uber info)

Nuclear transport

how molecules move through the nuclear envelope; in and out of the nucleus . 2 situations - small molecules and large molecules.

Nuclear pore complex

(type of nuclear transport) small molecules diffuse through these

Nuclear localization signal (NLS)

(type of nuclear transport) large molecules need a signal, NLS means send me into the nucleus

Nuclear export signal (NES)

(type of nuclear transport) large molecules need a signal, NES means send me out of the nucleus

Importin

recognizes the NLS, binds to it and transports the protein into the nucleus

Exportin

recognizes the NES, binds to it and transports the protein out of the nucleus

Endomembrane pathway

(proteins move from) Ribosome - rough ER - vesicle - golgi - vesicle - destination

Possible destinations

lysosome, plasma membrane or outside the cell

ER function

synthesizes, modifies and continues making the protein

Golgi function

sorts, modifies, packages and sends proteins to their destination (specific sorting becomes important with their tags)

ER signal sequence

about 20 amino acids, tells the ribsosome/protein “take me to the ER”

Mannose-6-phosphate (M6P)

protein tag saying “send me to the lysosome”

Lysosome pathway

Ribosome - ER- transport vesicle - golgi - M6P tag - vesicle - lysosome

Exocytotsis

Vesicle fuses with plasma membrane and releases material outside of the cell. Material exits.

Endocytosis

Material enters the cell, the plasma membrane surrounds it and forms a vesicle. the material can eventually be delivered to the lysosome. (the route that brings material there)

Lysosome

cells recycling bin, contains acid hydrolases that break down materials.

Hydrolysis

chemical reaction where water breaks down the bonds in a compound

Microfilaments

AKA actin filaments. smallest of the three, involved in muscle contraction, cell crawling, cytoplasmic streaming and cytokinesis. made of actin which mostly works with the motor protein Myosin

Intermediate filaments

involved in internal structural supports, maintain shape, resist tension, anchors structures like nucleus

Microtubules

the roads/tracks, involved in transport, resist compression, move chromosome/organelle and cilia/flagella. Motor proteins can walk on them while carrying vesicles/organelles

Myosin

motor protein that walks on actin towards the plus end

Kinesin

motor protein that walks on microtubules towards the plus end (outside)

Dynein

motor protein that walks on microtubules towards the neg end (nucleus)

Intracellular transport

connects endomembrane system to cytoskeleton. motor proteins carry vesicles along cytoskeleton tracks.

Kinetic energy

chemical reactions have this, it is energy of motion (heat)

Potential energy

chemical reactions have this, it is also known as chemical energy and is stored energy. (more potential energy = more nonpolar covalent bonds)

Exergonic reaction

“spontaneous”, happens on its own without energy, it releases energy. products have less potential energy than reactants - DG<0

Endergonic reaction

“non-spontaneous”, needs energy to occur. Products have more potential energy than reactants. DG>0

Gibbs free energy (G)

energy available to do work. DG = DH -TDS (T = temperature) (DG = product energy - reactant energy)

Enthalpy (H)

total energy in a molecule

Entropy (S)

amount of disorder

Energetic coupling

pairing an energy releasing exergonic reaction with an endergonic energy needing reaction (if there is no energy to preform the endergonic reaction, the exergonic can drive the endergonic)

3 ways reactions can be energetically coupled

1- transfer of electrons, 2- transfer of electrons and an H+, 3- transfer of a phosphate group

ATP Hydrolysis

Ex. of energetic coupling is ATP undergoing hydrolysis. It goes from ATP to ADP +Pi which releases energy as an exergonic reaction, providing energy for an endergonic reaction

Redox reaction

movement/transfer of electrons “LEO the tiger says GER”

Oxidation

“Leo” loses electrons, always occurs with GER

Reduction

“Ger” gains electrons, always occurs with LEO

Redox example

NAD+ —> NADH When NAD+ gains and e- and an H+, it becomes NADH = reduction.

Activation energy (Ea)

minimum amount of kinetic energy needed to sufficiently strain chemical bonds so a reaction can occur (energy needed to start the reaction) (transition state energy - reactant energy)

Transition state

Unstable state at the top of the Ea barrier (curve) where bonds are strained ( the more unstable transition state the higher the Ea)

Enzyme

a protein catalyst that decreases activation energy and speeds up a reaction by stabilizing and reducing the transition state(does not change DG)

Substrate

the molecule the enzyme acts on

Active site

area/pocket on the enzyme the substrate binds to

Induced fit

when the subtrate binds into the enzymes active site, the enzyme slightly changes its shape to correctly positions the substrate ( after reactions enzyme goes back to normal and can be reused)

Low enzyme saturation

lots of free enzymes with no substrate, adding substrate increasing the reaction rate

High substrate concentration

all enzymes active sites are occupied meaning, the enzyme is saturated (graph plateaus). adding substrate would not increace reactions rate because there are no more enzyme active sites to be filled, you would have to add more enzymes.

Optimal temperature

enzymes have an optimal temperature where activity is the highest. as temp rises toward the optimal temperature, reactions rate increases. but past the optimal temperature enzyme structure can change, changing its function.

Optimal pH

enzymes have optimal pH levels where activity is the highest. as pH rises towards optimal pH, reactions rate increases. but past or below the optimal pH enzyme shape can change, changing its function.

Cofactor

Inorganic molecule enzyme helper, interact near active site and help stabilize the transition state. Ex. Zn2+

Coenzyme

Organic molecule enzyme helper, interact near active site and help stabilize the transition state. Ex. vitamins, NADH

Competitive inhibition

(regulating enzyme’s activity) a regulatory molecule competes with the substrate for the active site (if inhibitor blocking the active site the substrate cant bind so less product is made)

Allosteric regulation

(regulating enzyme’s activity) a regulatory molecule binds somewhere other than the active site (allosteric site), changing the enzyme’s shape/activity

Phosphorylation

(regulating enzyme’s activity) a phosphate group is added to the enzyme acting like a molecular switch changing its shape/activity

Metabolic pathways

series of enzyme-controlled reactions, like an assembly line. Ex.

Feedback inhibition

one way to regulate an entire metabolic pathway. final product goes back and inhibits an earlier enzyme making the metabolic pathway stop. it does this to prevent the cell from wasting energy making a product it already has enough of