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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

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Biology 101 flashcards
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
Q

describe how temp affects protein structure

A

affects secondary and above structures

26
Q

describe how mutations affects protein structure

A

affects primary and above structures, beyond denaturation

27
Q

describe how pH affects protein structure

A

affects ionic bonds
mainly tertiary and quaternary structures

28
Q

describe how reducing/oxidizing agents affects protein structure

A

affect disulfide bonds
tertiary and above structures

29
Q

name and describe side chain interactions for tertiary and quaternary structures

A

covalent - disulfide - 2 cysteines
ionic - 2 charged - salt bridges
H bonds - 2 polar aa or charge & polar aa
hydrophobic - 2 nonpolar aa

30
Q

T or F energy flows and cycles

A

F the first and second law explain why energy flows but does not cycle

31
Q

describe entropy

A

G=0, equilibrium
∆G>0, unfavourable, endergonic
∆G<0, favourable, exergonic

32
Q

describe exergonic reactions/processes

A

exergonic reaction reactants free energy > products free energy; free energy is released

33
Q

describe endergonic reactions/processes

A

endergonic reaction reactants free energy < products free energy; free energy is required

34
Q

describe catabolic reactions

A

breakdown of molecules and macromolecules - exergonic
no energy input required
releases free energy for work

35
Q

name and describe processes that need work

A

chemical anabolic reactions - DNA replication, gene expression
transport - exocytosis, endocytosis, active transport
mechanical - muscle contraction, movement of cells (beating of cilia)

36
Q

describe anabolic reactions and name an ex

A

synthesis of molecules and macromolecules - endergonic
input of energy needed
ATP hydrolysis provides free energy

37
Q

describe atp hydrolysis

A

ATP + H2O –> ADP + Pi + energy

38
Q

describe phosphorylation

A
  • 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
Q

describe atp cycle

A

ATP + H20 - exergonic catabolic, hydrolysis, free energy released to power work —> ADP + Pi - dehydration, anabolic, endergonic, ATP synthesis, input of free energy
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40
Q

what are enzymes

A

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
Q

what cant enzymes do

A
  • change ∆G
  • change equilibrium concentrations of reactants (substrates) and products
  • catalyse overall endergonic reactions
42
Q

describe graph of free energy for enzymes

A

E+S = not yet reacted
old bonds broken in substrate and new bonds formed - E-S
then E+P

43
Q

what is the active site

A

pocket with key amino acid side chains (functional groups) located within the enzyme to which the substrate binds

44
Q

what is induced fit

A

conformational/shape change of E when bound with substrate that favours the transition state formation

45
Q

what is the transition state

A

high energy state where reactants break and reform covalent bonds in order to become products

46
Q

T or F enzymes can only be used once

A

F they are also reused many times in the same reaction until denatured or inactivated

47
Q

what is velocity for enzymes

A

rate of product formation
rate of substrate disappearing

48
Q

what is Vmax for enzymes

A

reached when the concentration of substrate is in excess and all enzyme molecules are bound with substrate at vmax, enzyme is saturated

49
Q

what is Km for enzymes

A

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
Q

describe rate of product formation graph

A

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
Q

what are cofactors

A

help the enzyme function
are not amino acids
are not regulatory molecules
are additional molecules

52
Q

name the two cofactors

A

organic cofactors and inorganic cofactors

53
Q

describe organic cofactors

A

also called coenzymes
in humans - some of them can only be made by vitamins in diet

54
Q

describe inorganic cofactors

A

metal ions

55
Q

describe enzymes at below optimal temperature

A

substrate molecules do not have enough kinetic energy and the number of collisions is low

56
Q

describe enzymes at above optimal temperature

A

denaturation - secondary tertiary and quaternary structures are disrupted

57
Q

describe enzymes at too high or low pH

A

changes in charges of r groups affect their ionic interactions and therefore the 3D structures of enzymes

58
Q

T or F denaturing agents and boiling affects the primary structure of enzymes

A

F, NOOO, not primary, but enzymes/proteins lose activity (active site doesnt work as efficiently or at all) and sometimes aggregate (form clumps)

59
Q

describe metabolic pathways and enzymes

A

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
Q

describe regulation of enzymatic activity

A
  • 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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