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bio 2 > week 1&2 - lectures 1,2 and part of 3 > Flashcards

week 1&2 - lectures 1,2 and part of 3 Flashcards

(60 cards)

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1
Q

name the 4 features of functional groups

A
  • # and type of carbon bonds: single bonds, double bonds, triple bonds
  • branching, rings
  • isomers: are compounds that have same molecular formula but different structural formulas
  • functional groups attached to the carbon backbone
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2
Q

what are functional groups

A
  • impart diverse properties to organic compounds that are the characteristics of life
  • determine the kind of reactions in which the compounds participate
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3
Q

what is metabolism

A
  • total sum of chemical reactions that occur in the cell
  • describes the transformation of substances into energy or materials that the cell can use or store
  • sum of chemical cellular reactions
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4
Q

describe dehydration synthesis and give an ex

A
  • link monomers to form polymers
  • aka condensation
  • anabolism
  • water is released
  • ex: protein synthesis
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5
Q

describe hydrolysis and give an ex

A
  • molecules are broken down to monomers
  • catabolism
  • protein digestion
  • water is used to break bond (needed)
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6
Q

describe proteins

A
  • built of 20 amino acids
  • CHNOS
  • different side chain R
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7
Q

name the 3 classifications of amino acids

A

non polar
polar
charged

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8
Q

describe non polar

A

hydrophobic
ex: glycine, alanine, valine, leucine etc
CH rich

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9
Q

describe polar

A

hydrophilic
ex: serine, threonine, cysteine
functional groups OH, amide CO - NH2, SH

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10
Q

describe charged

A

hydrophilic
ex: aspartic acid, glutamic acid - acidic, lysine, arginine, histidine - basic

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11
Q

what does cysteine mean

A

disulfide bonds
need 2 S

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12
Q

describe linkage between amino acids

A

dehydration synthesis - covalent linkage between amino acids - peptide bonds

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13
Q

where is the side chain attached to

A

the central carbon

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14
Q

what is physiological pH

A

7.3-7.4

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15
Q

which side of amino acid is positive and which is negative

A

NH3 +
COO -

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16
Q

describe zwitterion

A

a molecule or ion having separately positively and negatively charged groups
at low pH - coo accepts h bc extreme pH level
at high pH NHH acts as an acid

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17
Q

describe protein functions

A
  • buffers - albumin in blood
  • enzymes catalyzing chemical reactions; increase the rate of reaction
  • cell transport, channels and pumps
  • regulation of processes and signalling
  • maintaining homeostasis, hormones and receptors
  • defenses against diseases (immunoglobulins-antibodies)
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18
Q

describe main steps of protein structure formation

A

right after protein synthesis - primary structure
FOLD
secondary structure
FOLD - lots of bonds forming
tertiary structure - 3d shape
FORMS complex - sometimes
quaternary structure

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19
Q

describe primary structure

A

peptide bonds form backbone
carboxyl ends
aa sequence
ONLY affected by mutations or when aa chain is disrupted
boiling wont affect primary structure but will denature protein

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20
Q

describe secondary structure

A

beta sheets/strands - stretched
alpha helix - more twisted
H bonds of backbone
antiparallel

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21
Q

describe tertiary structure

A

r side chain interactions
functional (native) protein
1 polypeptide, 1 chain
disulfide bonds

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22
Q

describe quaternary structure

A

protein complex
2 or more polypeptides/chains

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23
Q

what are anfisens conclusions

A

folding of proteins depends on the primary structure
folding into native structure is spontaneous deltaG < 0

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24
Q

name the factors that affect protein structure

A

causes denaturation and loss of function
- mutations
- temp
- pH
- reducing/oxidizing agents

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25
describe how temp affects protein structure
affects secondary and above structures
26
describe how mutations affects protein structure
affects primary and above structures, beyond denaturation
27
describe how pH affects protein structure
affects ionic bonds mainly tertiary and quaternary structures
28
describe how reducing/oxidizing agents affects protein structure
affect disulfide bonds tertiary and above structures
29
name and describe side chain interactions for tertiary and quaternary structures
covalent - disulfide - 2 cysteines ionic - 2 charged - salt bridges H bonds - 2 polar aa or charge & polar aa hydrophobic - 2 nonpolar aa
30
T or F energy flows and cycles
F the first and second law explain why energy flows but does not cycle
31
describe entropy
G=0, equilibrium ∆G>0, unfavourable, endergonic ∆G<0, favourable, exergonic
32
describe exergonic reactions/processes
exergonic reaction reactants free energy > products free energy; free energy is released
33
describe endergonic reactions/processes
endergonic reaction reactants free energy < products free energy; free energy is required
34
describe catabolic reactions
breakdown of molecules and macromolecules - exergonic no energy input required releases free energy for work
35
name and describe processes that need work
chemical anabolic reactions - DNA replication, gene expression transport - exocytosis, endocytosis, active transport mechanical - muscle contraction, movement of cells (beating of cilia)
36
describe anabolic reactions and name an ex
synthesis of molecules and macromolecules - endergonic input of energy needed ATP hydrolysis provides free energy
37
describe atp hydrolysis
ATP + H2O --> ADP + Pi + energy
38
describe phosphorylation
- covalent linkage of phosphate on to a molecule/chemical reactant/enzyme/protein - energizes molecule, more reactive - release of phosphate group - overall = change in the conformation of the molecule useful for doing work
39
describe atp cycle
ATP + H20 - exergonic catabolic, hydrolysis, free energy released to power work ---> ADP + Pi - dehydration, anabolic, endergonic, ATP synthesis, input of free energy BACK to top
40
what are enzymes
proteins, highly specific for the reactions they catalyze biological catalysts that accelerate the rate of a chemical reaction by lowering the activation energy and facilitate transition state formation
41
what cant enzymes do
- change ∆G - change equilibrium concentrations of reactants (substrates) and products - catalyse overall endergonic reactions
42
describe graph of free energy for enzymes
E+S = not yet reacted old bonds broken in substrate and new bonds formed - E-S then E+P
43
what is the active site
pocket with key amino acid side chains (functional groups) located within the enzyme to which the substrate binds
44
what is induced fit
conformational/shape change of E when bound with substrate that favours the transition state formation
45
what is the transition state
high energy state where reactants break and reform covalent bonds in order to become products
46
T or F enzymes can only be used once
F they are also reused many times in the same reaction until denatured or inactivated
47
what is velocity for enzymes
rate of product formation rate of substrate disappearing
48
what is Vmax for enzymes
reached when the concentration of substrate is in excess and all enzyme molecules are bound with substrate at vmax, enzyme is saturated
49
what is Km for enzymes
Km is the concentration of substrate at which the rate is Vmax/2 and can be considered a measure of enzyme affinity for the substrate
50
describe rate of product formation graph
Vmax is limited by the active sites - parking lot once they are all filled up/saturated = caps off into a horizontal line 0 enzymes = horizontal line at 0
51
what are cofactors
help the enzyme function are not amino acids are not regulatory molecules are additional molecules
52
name the two cofactors
organic cofactors and inorganic cofactors
53
describe organic cofactors
also called coenzymes in humans - some of them can only be made by vitamins in diet
54
describe inorganic cofactors
metal ions
55
describe enzymes at below optimal temperature
substrate molecules do not have enough kinetic energy and the number of collisions is low
56
describe enzymes at above optimal temperature
denaturation - secondary tertiary and quaternary structures are disrupted
57
describe enzymes at too high or low pH
changes in charges of r groups affect their ionic interactions and therefore the 3D structures of enzymes
58
T or F denaturing agents and boiling affects the primary structure of enzymes
F, NOOO, not primary, but enzymes/proteins lose activity (active site doesnt work as efficiently or at all) and sometimes aggregate (form clumps)
59
describe metabolic pathways and enzymes
can be linear, branched, circular, anabolic or catabolic -are found in the same cellular component - function together to form a common product - like workers in a factory assembly line: product of one is substrate for next - wont ever reach equilibrium - not all are on at same time - tightly regulated
60
describe regulation of enzymatic activity
- reversible inhibition and activation - small modifying molecules = modification by activators (Pi or ADP) increase the activity of enzymes, inhibitors (ATP or end products of metabolic pathways) decrease activity of enzymes - reversible inhibition and activation (enzyme resumes its shape and function once inhibitor or activator is removed

bio 2 (6 decks)

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