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Winter 2023 - Biology > Cycle 3: Thermodynamics & Membranes > Flashcards

Cycle 3: Thermodynamics & Membranes Flashcards

1
Q

what is kinetic energy?

A

energy possessed by an object because it is in motion

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2
Q

What is chemical energy?

A

energy stored in bond of atoms/molecules

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3
Q

What is potential energy?

A

stored energy due to its position or chemical structure

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4
Q

What is a covalent bond?

A

interaction between negatively charged electrons and positively charged nuclei of atoms in the molecule

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5
Q

What is an isolated system?

A

does not exchange matter or energy with its surroundings

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6
Q

What is a closed system?

A

can exchange energy but not matter with surroundings

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7
Q

What is an open system?

A

both energy and matter can be exchanged with surroundings ex ocean

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8
Q

What is the first law of thermodynamics?

A

energy can be transformed or transferred but it cannot be created or destroyed

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9
Q

What is the second law of thermodynamics?

A

the entropy of a system and the surroundings will increase – energy and matter will always become more spread out - everything breakdown

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10
Q

What is entropy?

A

tendency of energy to become dispersed or spread out - “energy spreading to become more disorderly”

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11
Q

What are the four potential levels of protein structures?

A

primary, secondary, tertiary, and quaternary structure

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12
Q

Why it is the less oxygen molecules = more oxidized state?

A

oxygen has a strong electron affinity so there is not much free energy because oxygen make electrons less accessible

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13
Q

What is the relationship between free energy and molecule state?

A

high free energy = reduced state (more hydrogen)

low free energy = oxidized state (more oxygen)

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14
Q

What are the reduced molecules?

A

sugars, fats, amino acids, nucleotides

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15
Q

what do autotrophs do?

A

uses sunlight energy and converted oxidized form of molecules to reduced form

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16
Q

what do heterotrophs do?

A

uses reduced form (takes in sugar) releases oxidized form (produces CO2)

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17
Q

What type of system are living things?

A

open systems – take in energy and matter from surroundings

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18
Q

what form of matter and energy are used by autotrophs?

A

energy - light from sun
matter - CO2

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19
Q

what form of matter and energy are used by heterotrophs?

A

carbon for sugar

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20
Q

Do cells have high or low entropy?

A

cells are islands of low entropy (they are more organized)

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21
Q

Does the system’s surroundings have high or low entropy?

A

very high entropy - disorganized, – heat and waste released from cell

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22
Q

What is free energy?

A

G, energy available to do work (and get low entropy)

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23
Q

What are endergonic reactions?

A

positive change in free energy (∆G) - not spontaneous reactions, requires energy to make reactions go

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24
Q

What are exergonic reactions?

A

negative change in free energy (-∆G) - SPONTANEOUS reactions - no energy needed for reaction to occur on its own

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25
Q

How do molecules show entropy?

A

more reduced form has more of the same atom in one molecule = low entropy (ex. C6H12O6 –> 6 carbons in one molecule)

more oxidized form has many of the same molecules = high entropy (ex. 6CO2 –> 6 carbons spread out)

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26
Q

How do states of matter show entropy?

A

solid = more organized = low entropy

gas = more disorder = high entropy

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27
Q

How does free energy, enthalpy, and entropy relate?

A

∆G=∆H-T∆S

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28
Q

what does spontaneous reaction mean?

A

reaction goes on its own, but not necessarily fast

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29
Q

How do enzymes work?

A

makes spontaneous and non spontaneous reaction go faster

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30
Q

How do enzymes work is exergonic reactions?

A

in exergonic (spontaneous) reactions (∆G <0) –> going from more free energy to less free energy

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31
Q

Hw do enzymes work in endergonic reactions?

A

goes from less free energy to more free energy, so energy input is needed because enzymes can’t make a substrate have more energy (they don’t give free energy)

32
Q

Why does life need enzymes?

A

increase rate of reaction without adding heat (no denaturation, so reaction proceeds at optimal temp)

33
Q

What is the activation energy?

A

kinetic barrier - certain amount of free energy that must be reached in order to transition from products to reactants

34
Q

What do enzymes do in a reaction? What does an enzyme not go

A

changes the part of reaction and lowers the activation energy
–> changes kinetics = how fast the reaction going
–> doesn’t change thermodynamics (amount of free energy) b/c reactants start at the same ∆G and products end at the same ∆G

35
Q

Do reactants or products have more free energy?

A

can be either. reactants for exergonic and products for endergonic

36
Q

how is the activation energy reached in terms of energy?

A

activate substrate through energy coming from system (ex motion/kinetic energy) NOT adding ATP

37
Q

At what point in the reaction is it spontaneous?

A

when activation energy is reached – at transition conformation the reaction goes by itself

38
Q

What is the result of having the EA barrier?

A

some spontaneous reactions take very long

39
Q

what do enzymes do to number of molecules in the reaction?

A

increases rate of # of molecules getting to transition state

40
Q

What does an enzyme do to the SUBSTRATE to lower the EA and reach transition state?

A

enzyme forces the substrate ion mimicking the transition state conformation

41
Q

What are the three interactions that the enzyme does to the substrate to reach transition state?

A

precise orientation of two substrate

charge interaction

conformational strain

42
Q

what type of reaction is protein folding?

A

exergonic - SPONTANEOUS reaction
–> proteins fold to correct conformation on its own without ATP

43
Q

What is Anfinsen’s dogma of protein folding? what experiment was done to prove it?

A

folded protein is 100% active

protein is unfolded by introducing urea which has hydrogens that compete to hydrogen bond with amino acid in proteins

causes protein to unfold = denatured

urea removed

protein refolds on its own = 100% active

shows that proteins don’t need additional energy – spontaneous

44
Q

how does free energy differ through protein folding?

A

polypeptides (unfolded proteins) have highest free energy

proteins have the lowest free energy (native)

45
Q

how can proteins be reversed and denatured?

A

adding other compounds (urea) or adding heat

46
Q

What do chaperone proteins do for protein folding?

A

slightly unfolds polypeptides that have been denatured so they can spontaneously refold (ex. HSP)

47
Q

what is a characteristic of the enzyme structure?

A

flexible –> change conformation to fit the substrate –> called INDUCED FIT

48
Q

what is the catalytic cycle of enzyme?

A

attaches to substrate

changes substrate conformation

releases product

enzyme picks up another molecule

49
Q

what is the active site?

A

where the enzyme binds with the substrate and is a pocket that is the product of protein folding

50
Q

how can you determine where the active site is?

A

cannot be determined from primary sequence –> must look at protein folding because active site is a “pocket”

51
Q

What is the phospholipid structure? Which parts are hydrophilic and hydrophobic? polar/nonpolar?

A

hydrophilic/polar: choline, phosphate group, glycerol

hydrophobic/nonpolar: lipid tails

52
Q

How are transmembrane proteins arranged on cell membrane?

A

non polar, hydrophobic AA are inside the chain so they end up in the lipid layer

polar, hydrophobic AA are on the outside of peptide chain, so they stick out of the membrane on each side

53
Q

Which molecules use simple or facilitated diffusion? Which need energy for active transport?

A

simple: non polar molecules (O2, CO2, N2) & small polar, uncharged molecules (H2O, glycerol)

facilitated: large, uncharged molecules (glucose) , ions

all need energy for active transport

54
Q

Which proteins go through secretory pathway?

A

proteins that leave cell or sit on plasma membrane (ie channelrhodopsin)

55
Q

What does the signal peptide do? Where does it come from? What does it’s sequence look like?

A

transcribed and translated sequence on N side of protein that tells the cell that it must go through the secretory pathway

sequence is highly conserved so it is something found in primary sequence

56
Q

What are the steps of signal peptide removal?

A
  1. signal recognition particle (SRP) protein recognizes signal peptide on the peptide chain forming from mRNA
  2. SRP takes the complex (ribosome, mRNA, peptide chain) to the ER

** protein stops being synthesized

  1. enzyme in ER that will cut the signal peptide
  2. protein continues translation and is released in ER lumen
57
Q

What does the transport protein on plasma membrane do for facilitated molecules?

A

shields molecules/ions from hydrophobic core

58
Q

What is the connection between ∆G, entropy, and transport across the membrane?

A

exergonic process from high to low concentration increases entropy (more disorder inside cell)

endergonic for active transport

59
Q

What are the components of the ABC transporter? What are the functions?

A

ATP-binding cassette transporter is an active transport protein

Transmembrane domain (within the membrane - specialized for different molecules to enter/leave)
ATP-binding domain (inside cell - not specialized)

60
Q

How can a pore/channel be specific for certain molecule?

A

PRIMARY SEQUENCE – transporters fold in a specific shape and protein’s amino acids interact with substrate differently

61
Q

Given the primary sequence of a protein how can you determine if its an Integral membrane protein?

A

hydrophobic: 7 transmembrane domains

62
Q

What is Cystic fibrosis and the function of CFTR?

A

CFTR mutation to ∆F508 which is a gene for ABC-transporter where the protein doesn’t fold correctly

63
Q

Fate of the deltaF508 form of CFTR?

A

∆F508 never goes to plasma membrane, it remains in ER at get degraded by proteosome

64
Q

What is the result of cystic fibrosis and disfunction of CFTR transporter?

A

mucus dries poor gas exchange and infection because CFTR can’t allow ABC transporter to pump chloride which will then pump water

65
Q

What was the experiment showing ∆f508 form is actually functional?

A

express ∆F508 on artificial membrane to see it it would be functional if it made it to the plasma membrane
-add ATP and Cl- inside artificial cell to see if Cl- would be pumped out

this showed that it was functional, just down regulated

66
Q

What is the role of the chaperone protein HSP90 in folding of ∆F508 form and WT?

A

detect misfiling which doesn’t allow ∆F508 to go to plasma membrane

67
Q

What is the Relationship of temperature on membrane fluidity?

A

high temp = more viscous = saturated hydrocarbon tails (all tail are lined up)

low temp = fluid = unsaturated hydrocarbons tails with kink (spaces for membranes to pass through)

68
Q

Why is it important to maintain proper fluidity for import/export, electron transport?

A

too fluid = fall apart

too rigid = no diffusion/transport nutrients

69
Q

What is the Role of desaturases in fatty acid biosynthesis?

A

when temperatures are low, enzyme is secreted to cause kinks in hydrocarbons with double binds

70
Q

What processes explain the shape of the growth vs temp curve?

A

increase temp = increase collisions = increase enzyme activity = increase growth rate

71
Q

How is the tertiary structure different in enzyme hexokinase different for extremophiles?

A

low temp: weaker tertiary structure = weak bonding interactions

high temp: strong bonding interactions to keep molecules together

** amino acids are different in the part that keeps the molecule tighter, not the active site

72
Q

What is primary protein structure?

A

AA sequence forming polypeptide

– AA subunits going covalently (peptide bond)

73
Q

What is secondary structure protein/

A

twists and turns of AA chain
- hydrogen bonds between hydrogen and electronegative atom - O, N, C

74
Q

What is Tertiary structure?

A

folding of AA chain into 3D shape
- ionic bonds
- hydrogen bonds
- hydrophobic interactions (aq endir forces together)
- disulphide bridges (2S)

allows conformational changes

75
Q

What is Quaternary structure?

A

sometimes present, arrangement of polypeptide chains in protein that is formed by more that one chain

Winter 2023 - Biology (11 decks)

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