biology exam unit 2

why does a concentration gradient form?

when solutes are unequally distributed within a solution, solutes naturally move from higher to lower concentration to achieve equilibrium

diffusion

the spontaneous movement of substances across a membrane

passive transport

diffusion without an energy source

osmosis

the diffusion of water across a selectively permeable membrane

what happens to water distribution when a cell has an unequal distribution of solutes relative to the cell's exterior? (assuming that the solute cannot pass through the membrane)

water will flow through the membrane toward the area of higher solute concentration to equalize concentrations

hypotonic

a solution with a lower concentration of solutes relative to another

hypertonic

a solution with a higher concentration of solutes relative to another

isotonic

a solution with the same concentration of solutes relative to another

what kinds of water molecules can pass through a selectively permeable membrane?

unbound water molecules

channel protein

a protein that forms a pore for molecules to pass through

active transport

the energy-intensive movement of molecules through a membrane that goes against the concentration gradient

aquaporins

gated channel proteins; let water through the membrane

integral proteins

proteins that span the entire membrane; also called transmembrane proteins

carrier proteins

transmembrane proteins that allow for membrane binding with the concentration gradient

facilitated diffusion

the transport of molecules with the help of channel or carrier proteins

passive transport

diffusion or facilitated diffusion; the movement of molecules across a membrane without the input of energy

what regulates the activity of channel proteins?

electrochemical signals that cause it to open or close

peripheral proteins

membrane proteins only found on the exterior of a membrane

secondary transport

when ATP is used to create an electrochemical gradient that allows a molecule to pass through

which molecules tend to form micelles?

free-floating fatty acids

liposomes

artificially-made vesicles

how does the amount of unsaturated fatty acid tails impact the permeability of a membrane?

when there are more unsaturated fatty tails, the reduction in van der vaals forces (due to greater gaps between molecules) increases permeability

it’s easier to get through when the molecules are less tightly packed

how does the presence of cholesterol impact the permeability of a membrane?

since cholesterol has a rigid, planar steroidal structure, it wedges between phospholipid fatty acid chains and decreases the permeability of a membrane. it’s bulky and acts as a physical barrier that often restricts the passive transport of molecules across a membrane

how does cholesterol affect the fluidity of a membrane?

how does fatty acid saturation affect the fluidity of a membrane?

in general, saturated fatty acids have a lower fluidity. this is because “straight” chains pack closely together, maximizing van der vaals forces and preventing lateral reshuffling

thus, unsaturated fatty acids—-with greater gaps between hydrophobic fatty acids—have a higher fluidity with a reduction in van der vaals forces

how does cholesterol impact membrane fluidity?

cholesterol is a bidirectional temperature buffer; it decreases membrane fluidity at high temperatures and increases fluidity at low temperatures

how do the membranes of organisms native to cold environments differ from that of organisms native to temperate environments?

organisms that have adapted to survive in the cold typically have membranes with a greater quantity of unsaturated fatty acids; this maintains selective permeability at low temperatures—-unsaturated fatty acids have very low freezing points

hormones

information-carrying molecules that are secreted by cells

signal receptor

a protein that undergoes conformational changes upon binding to a signalling molecule

G proteins

peripheral membrane proteins that are essential to signal transduction

signal transduction

the process by which a cell converts an external change to an intracellular response

second messengers

small, non-protein molecules that elicit an intracellular response

how does phosphorylation alter the function of proteins?

the addition of a phosphate group changes the structure of proteins, which in turn alters their function

cAMP

cyclic AMP; a second messenger that triggers an intracellular response by binding to protein kinases

what are the three stages of cell signalling?

1. reception — signal molecule binds to receptor

2. transduction — extracellular signal is converted to intracellular signal

3. response — changes in protein activity or gene expression

ligand

the first messenger; the molecule that binds to a receptor

G-protein-coupled receptor (GPCR)

an integral membrane protein (G protein) that is coupled with a receptor

what is the function of GTP in G proteins?

it acts as an on/off switch; off = GDP, on = GTP

what happens to the G protein when it binds to the ligand?

1. the G protein “kicks out” GDP, allowing GTP to bind—this activates the G protein

2. the GTP-binding subunit breaks apart from the receptor, which moves towards a membrane-bound enzyme

   1. the enzyme then produces an intracellular response!

how does cAMP differ from ATP?

cAMP only has one phosphate group, which allows it to form a ring with the sugar (hence the name cyclic adenosine monophosphate)

which processes regulate protein activity?

phosphorylation and dephosphorylation

phosphorylation cascade

signal amplification

when one initial signalling molecule facilitates the production of numerous second messengers

true or false: the same signalling molecule causes the same response in different cells

false; the same signalling molecule produces varied responses in different cells

what are the steps of signal transduction for epinephrine?

1. epinephrine binds to the GPCR outside the cell

2. the receptor changes shape; GDP is swapped for GTP

3. the activated G protein activates a nearby enzyme—adenylyl cyclase

4. adenylyl cyclase converts ATP to cAMP

5. cAMP activated protein kinase A (PKA)

6. PKA phosphorylates specific proteins and changes their activity

how do liver cells respond to epinephrine?

they break down glycogen into glucose

how does cell activity change upon signal transduction?

cytoplasmic protein activity changes; in the long-term, this can lead to changes in gene expression

how does signal transduction change when the ligand is lipid-soluble?

the ligand (signalling molecule) can pass through the membrane, binding to receptors directly in the cytosol

beta blockers

medication that binds to epinephrine’s receptors without activating them; decreases heartrate by inhibiting signal transduction

why is uninhibited signal transduction dangerous?

it can lead to certain cancers when cellular growth/division is uninhibited

what are the four ways in which GPCR transduction can be shut off?

1. the ligand leaves the receptor

2. the G protein hydrolyzes GTP back to GDP

3. phosphodiesterase breaks down cAMP

4. phosphotases remove the phosphates that PKA added

what is a high-energy bond?

a bond where electrons are equally shared — the electrons are further away from the nuclei of both atoms, which means they have higher potential energy

gibbs free energy

delta G = delta H - T * delta S

the change in free energy = the enthalpy (total energy) - temperature * the change in entropy

how do spontaneous chemical reactions occur?

in the direction that lowers the free energy of a system

exergonic reaction

spontaneous

endergonic reaction

non-spontaneous

what two things must happen for a reaction to proceed?

the substrates must collide and interact

how do polar bonds compare to nonpolar bonds?

nonpolar bonds are typically longer and weaker BUT they have higher energy

activation energy

the energy needed to reach transition state

transition state

the in-between phase between reactants and products

what does negative enthalpy mean?

exothermic — releases energy

what does positive enthalpy mean?

the reaction is endothermic; it consumes energy

energetic coupling

when endergonic reactions are facilitated by the energy produced in an exergonic reaction

reduction-oxidation reactions

reactions in which an electron is lost or gained

electron donor

a molecule that loses an electron in a reaction

what is a sign that entropy has increased during a reaction?

when the number of products is greater than the number of reactants

why does ATP have high potential energy?

because it has so many negative charges all pushed together

what leads to an increase in activation energy?

if the transition state is pretty unstable

when can activation energy be easily overcome?

when the kinetic activity of the reactants is high

when is an enzyme considered “saturated?”

when all available enzymes are being used

which molecules can reduce activation energy?

enzymes — they can place pressure on certain bonds, encouraging the transition state

what are the three states of catalysis?

1. binding

2. transition-state formation

3. termination

competitive inhibition

when a molecule binds to an enzyme’s active site to prevent substrate binding

allosteric regulation

when a regulatory molecule binds to a location other than the active site to prevent binding of a substrate

what is an example of how pH alters enzyme function?

if a solution is too basic (higher pH, lower number of protons) it can impact the R-groups of certain enzymes (it can protonate certain groups)

noncovalent regulation

when a molecule temporarily binds to an enzyme

covalent regulation

when an enzyme is chemically modified

feedback inhibiiton

when the product of a pathway is used to inhibit the enzymatic activity of the same pathway

catabolic pathway

breaks things down (i.e., cellular respiration)

anabolic pathway

builds things up (protein synthesis)

how does cellular respiration differ from fermentation in terms of the breakdown of glucose?

fermentation doesn’t fully oxidize glucose

what are the four steps of cellular respiration?

1. glycolysis

2. pyruvate processing

3. citric acid cycle

4. electron transport chain and oxidative phosphorylation

cytosolic

occurs in the cytosol

what is significant about the first five steps in glycolysis?

they are the energy-investment phases and require the input of ATP

substrate-level phosphorylation

when an enzyme catalyzes the transfer of a phosphate group from a phosphorylated substrate to ADP

where does glycolysis occur?

in the cytosol

where does pyruvate processing occur?

in the mitochondrial matrix

where does the citric acid cycle occur?

in the mitochondrial matrix

where does the ETC & oxidative phosphorylation occur?

the inner membrane of the mitochondria

what are the inputs and outputs of glycolysis?

1 glucose + 2 NAD⁺ + 2 ATP → 2 pyruvate + 2 NADH + 2ATP

what is phosphofructokinase and how does it engage in feedback inhibition?

PFK1 is a key enzyme in glycolysis; when ATP concentration is high, it binds to an allosteric site on the enzyme and blocks the enzyme from dephosphorylating ATP

inputs and outputs of pyruvate processing

2 pyruvate + 2 NAD⁺ → 2 acetyl-CoA + 2 CO₂ + 2 NADH

inputs and outputs of the krebs cycle

2 acetyl-CoA + 6 NAD⁺ + 2 FAD → 4 CO₂ + 6 NADH + 2 FADH₂

where is most of the energy stored throughout cellular respiration?

in the electron carriers

why do electron carriers have such high energy?

because they are holding the electrons pretty loosely, which means the kinetic energy of the molecule is pretty high

how can you generally track the movement of electrons?

through the movement of hydrogen ions

cristae

the folded inner sac compartments of the mitochondria

what is the first “step” in pyruvate processing?

the movement of pyruvate into the mitochondrial matrix

which steps use substrate-level phosphorylation?

glycolysis and the citric acid cycle

how do electrons move in terms of redox potential?

they move from molecules with lower redox potential to higher redox potential