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Lecture 2 Flashcards

1
Q

what are living creatures

A

chemical systems

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2
Q

name the 3 characteristics of cell chemistry

A

life depends on chemical reactions
most of carbons present are incorporated into macromolecules
cell chemistry is very complex

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3
Q

describe cell chemistry characteristics - number 1

A

chemical reactions = take place in aqueous solutions, based on carbon compounds mostly

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4
Q

describe cell chemistry characteristics - number 2

A

carbons present in macromolecules = allows cells to grow and function

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5
Q

describe cell chemistry characteristics - number 3

A

v complex = may interlink networks of chemical reactions

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6
Q

name a few types of interactions

A

covalent
non covalent
Hydrogen bonds

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7
Q

describe bond strength (properties of chemical bonds)

A

bond strength –> amount of energy needed to break bond

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8
Q

describe covalent bonds (properties of chemical bonds)

A

100x stronger than non covalent bonds - easier to break
forms macromolecules - so they won’t break
resist being pulled apart by thermal motions
only broken by biologically catalyzed chemical reactions

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9
Q

describe noncovalent bonds (properties of chemical bonds)

A

allow molecules to recognize each other and reversibly associate
ex = like ribosome, 2 subunits - large and small - together through noncovalent interactions, provides flexibility, splits after done with mrna

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10
Q

describe chemical components of cells

A

99% total number of atoms in cell = C,H,N,O
0.9% total number of atoms in the cell = P,S,Cl,Na, Mg, K, Ca - makes covalent bonds in water

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11
Q

what combos of atoms (chemical groups) are abundant in cells - 7

A

methyl - ch3
hydroxyl - oh
carboxyl - cooh
carbonyl - c=o
phosphate - po3 -2
sulfhydryl - sh
amino - nh2

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12
Q

describe cell compounds - 4 characteristics

A

carbons can form 4 covalent bonds with other atoms = high ability to form macromolecules
c-c stable bonds form chains and rings –> generate large complex molecules
many diff shapes = many diff functions
carbon compounds made by cells –> organic compounds
a few categories of molecules give rise to all extraordinary richness of form and function

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13
Q

describe organic compounds

A

carbon based ~30 carbons
found in free solution - aq
compounds in the cell are chemically related and classified in 4 major families of compounds

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14
Q

name major organic compounds families

A

sugar
amino acid
fatty acid
nucleotide

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15
Q

what are the uses of organic compounds

A

monomer subunits to construct polymeric macromolecules
energy sources = broken down and transformed into other small molecules - use in metabolic pathways
many have both functions = subunits and energy sources

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16
Q

describe organic molecules - breakdown and synthesis

A

synthesized of or broken down into the same set of simple compounds

sugars –> polysaccharides, glycogen and starch - in plants
fatty acids –> fats and membrane lipids
amino acids –> proteins (main functional unit in cells)
nucleotides –> nucleic acids (dna, rna)

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17
Q

describe macromolecules

A

stores energy by covalent bonds= break and make other chemicals or functions
most abundant carbon containing molecules
Principal building and functional blocks of cells
made by covalently linked organic molecules - monomers into chains

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18
Q

describe uses of macromolecules

A

Versatile and perform thousands of functions
enzymes = catalyze - reactions occur faster - formation and breaking of covalent bond s

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19
Q

name macromolecules

A

polysaccharides and proteins = versatile and catalyze
nucleic acids = dna, rna

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20
Q

describe assembly of macromolecules

A

not random but sequenced (aas)= subunits added in precise order (sequential chemical reactions), for gene to provide mrna, read in one direction
covalent bonds = allow rotation, gives flexibility = several conformations
non covalent bonds = many allow to assemble macromolecules and constrain the shape to one conformation = molecular machines in cells

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21
Q

describe catalysis and the use of energy by cells

A

living cells = create and maintain order, perform never ending stream of chemical reactions, product becomes starting material for next chem reaction
nonliving matter = universe tends to greater disorder

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22
Q

name and explain the 2 types of chemical reactions of cell metabolism

A

anabolic pathway = monomers, covalent, make macromolecules, condensation = energetically unfavourable, needs energy, does not produce energy, releases water
catabolic pathway = when ingest food = break macromolecules into monomers, hydrolysis, energetically favourable, releases energy

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23
Q

what is the second law of thermodynamics

A

in any isolated system the degree of disorder always increase

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24
Q

compare organic compound and macromolecules

A

organic compound = small organic building blocks of cells
Macromolecules = larger organic molecules of the cell

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25
describe the 2nd law of thermodynamics
the most probably arrangement is the most disorder - like a room
26
what is the amount of disorder in a system
expressed as entropy = s the greater the disorder the greater the entropy systems will change spontaneously towards arrangements with higher S
27
How is possible that cells generate order to function?
release of heat energy enables cell order cell is not an isolated system --> total S (cell plus surrounded environment) increases present in aq environment increased disorder outside and increased order inside more kinetic energy since heat release, warms up and creates disorder = molecules move more and more
28
Where does the cell heat come from?
catabolic pathways, get energy from food = lost heat, increase entropy of environment lost heat = released unless needed to create more order in the cell all animals and plants are powered by energy stored in chemical bonds of organic molecules organisms extract energy to live, grow, reproduce get monomers and energy and then make macromolecules extra energy liberated in form of heat
29
what is first law of thermodynamics
energy can be converted from one form to another but cannot be created or destroyed
30
describe photosynthesis and cellular respiration
photosynthesis = plants convert electromagnetic energy of sun into sugars = take h2o and use energy and create oxygen and sugars - polysaccharides cellular respiration = liberate water and co2, create chemical bonds in our body
31
describe energy in biological systems
store and managed within chemical bonds enthalpy H = energy that can released from chemical bonds negative enthalpy change (Hf-Hi) = spontaneously favourable reaction
32
describe gibbs free energy
ΔG = ΔH -TΔS ΔG change in free energy = Gf-Gi ΔH change in enthalpy = Hf-Hi ΔS change in entropy = Sf-Si t = temp in kelvin energetically favourable = ΔG <0 --> ΔH energetically favourable
33
describe energetically favourable reaction
Reaction can occur spontaneously free energy of y is greater than free energy of x, therefore ΔG <0 and disorder of universe increases during the reaction Y-->X
34
describe energetically unfavourable reaction
reaction can only occur if it is coupled to a second energetically favourable reaction if reaction x--> y occurred ΔG would be >0 and the universe becomes more ordered
35
describe chemical reactions and enzymes
catalyze reaction by lowering activation energy required for reaction to take place then takes less time for reactions to reach the required activation energy = speeds up reaction helps bring paper and lighter closer together, Y-->X need Ea
36
what can't enzymes do
cannot force energetically unfavourable reactions to occur cannot go uphill cannot make unfavourable favourable x cannot --> y
37
reactions in the cell areeeee
coupled
38
describe energy carriers - coupled reactions
borrow energy activated carriers catabolism provides energy for activated carrier molecule goes to anabolism reaction since needs energy ATP = shifts energy and then goes back and brings more energy sum of ΔG must be lower than 0 for reactions to happen, must always liberate energy
39
what is atp
most used activated carrier
40
describe atp
3 phosphates, gamma, alpha, beta ΔG* less greater than 0, energy from sunlight or from breakdown of food, adp --> atp, restore energetic bond using energy atp --> adp = energy available to drive energetically unfavourable reactions, break bond and take energy and help form macromolecule
41
what is driven by atp hydrolysis
synthesis of biological polymers
42
describe example of reaction driven by atp hydrolysis
one step, sometimes have sequential steps A-OH + B-H --> A-B step 1 = activation, activate A so has covalent bond with store energy, and then can interact with other molecule, adp liberated step 2 = condensation step, activated intermediate reacts with B-h to form product, net result = uses atp --> adp + pi, happens in cell to make glutamine and glutamic acid
43
describe making glutamine and glutamic acid
aa activated by atp and makes high energy intermediate with phosphoester bond and then interact with ammonia in condensation step = aa Multiple steps, many steps sometimes
44
describe acetyl coa
bigger higher energy thioester bond, modifications of proteins, sulfur group acetyl group post translational modifications handle = coa acetyl = acetyl group
45
describe coupled reactions in cells - X-->Y
x will become y overtime = no more c but cells manage through equilibrium (concentrations) energetically unfavourable x-->y is driven by energetically favourable reaction C-->D, net free energy of coupled reaction = less than zero=favourable
46
what are the steps to equilibrium
the reaction eventually at equilibrium
47
describe equilibrium - the reaction
Y---->X formation of x is energetically favoured in this example, ΔG is negative, X-->Y ΔG is positive bc of thermal bombardments, there will always be some x converting to y and vice versa
48
describe equilibrium - eventually
suppose we start with equal number of x and y molecules there will be a large enough excess of x over y to just compensate for the slow rate of x --> y, eq will be obtained conversion of y to x happens often conversion of x to y is less often since requires a more energetic collision than the transition y-->x ratio of x to y molecules will increase
49
describe equilibrium - at eq
the number of y molecules being converted to x molecules each second is exactly equal to the number of x molecules being converted to y molecules so there is no net change in the ratio of x to y
50
what is standard free energy equation
ΔG* = ΔG + RTLn ([X]/[Y]) ([X]/[Y]) = equilibrium constant (K)
51
what does oxidation and reduction involve
electron transfer
52
describe oxidation and reduction gen
partial pos charge -oxidized, e- closer to one atom and further from other partial neg charge - reduced, e- together = partial magnet charge, atom reduced
53
describe oxidation in the cells
catalyzed reaction refers to more than the addition of oxygen \ addition of oxygen rarely happens
54
describe oxidation - detail
removal of electrons from an atom partially + charge
55
describe reduction - detail
addition of electrons to an atom partially - charge if a molecule picks up an e-, it usually also picks up an h --> hydrogenation A + e- + H+ --> AH, hydrogenation is reduction if number of c-h bonds increases, molecule is reduced
56
what is NADH and NADPH
electron carriers, like adp and acetyl coa, reactions are coupled nadph = carries hydride ion (high energy)
57
what is NAD+
nicotinamide adenine dinucleotide
58
what is NADP+
nicotinamide adenine dinucleotide phosphate
59
name 6 activated carriers and the group carried in high energy linkage
atp = phosphate nadh, nadph, fadh2 = electrons and hydrogens acetyl coa = acetyl group carboxylated biotin = carboxyl group s-adenosylmethionine = methyl group uridine diphosphate glucose = glucose
60
describe enzymes - summary
speed reactions but cannot force energetically unfavorable reactions to occur (cannot go uphill)
61
describe equilibrium - summary
There is no net change between the number of Y (reactants) and X (product)
62
describe oxi/reduc - summary
Oxidation and Reduction in cells involve the transfer of electrons (NADP is a carrier)
63
what does life bring
life brings order
64
describe composition of living organisms
rich in carbon certain chemical groups are abundant four subunits - sugars, amino acids, nucleotides, fatty acids
65
describe bonds of living organisms
covalent bonds - condensation structure, function and energy
66
what are the most abundant macromolecules
proteins
67
what does heat do - summary
increases the disorder (S) of the environment

ANAT 212 (34 decks)

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