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BIO112 > Unit 1 Chapter 3: Proteins (Structure and Function) > Flashcards

Unit 1 Chapter 3: Proteins (Structure and Function) Flashcards

1
Q

What was the Miller-Urey experiment

A

Miller used 2 flasks (smaller one containing H2O and larger one containing CH4. NH3 and H2) and gas tubing to mimic Earth’s early atmosphere and oceans. He boiled the water in order for gases to circulate and also sent electrical discharges through (mimicking ancient lightning) to see if the early “prebiotic soup” would be recreated. After a day the solution was pink, and after a week it was red and cloudy. When he analyzed the solution he found large amount of hydrogen cyanide and formaldehyde (organic molecules)which were also present in the early prebiotic soup and are the building blocks of proteins and amino acids.

conclusion chem. evolution occurs readily if molecules with high free energy are exposed to kinetic energy

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2
Q

How many different amino acids are there

A

20

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3
Q

Structure of amino acids

A

amino group-c(bonded to h and side chain)-carboxyl

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4
Q

How do we count amino acids? Why?

A

from N to C, because N is the start of the chain when proteins are synthesized in cells

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5
Q

Non-Polar side chains

A

glycine, valine, alanine, leucine, isoleucine, tryptophan, methionine, phenylalanine, proline

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6
Q

Polar side chains

A

serine, threonine, asparagine, glutamine, cysteine, tryrosine

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7
Q

Electrically charged side chains (acidic/basic)

A
  • acidic: aspartate, glutamate

- basic: lysine, arginine, histidine

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8
Q

An amino acid is polar if

A

it has a polar side chain

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9
Q

An amino acid is non-polar if

A

it has a non-polar side chain

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10
Q

What is a protein

A

polymers of amino acids

-folding is crucial and is influenced by the sequence of amino acids

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11
Q

What is polymerization

A

the process of linking monomers (ie. amino acids) to form polymers (ie. proteins)

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12
Q

What is a macromolecule

A

a large molecule made up of smaller molecules joined together

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13
Q

Are polymers more or less stable than monomers

A

less, positive free energy

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14
Q

What is a condensation (dehydration reaction)

A
  • how monomers polymerize
  • monomer in, water out
  • HO on monomer attaches to free H on existing joined monomers and leaves
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15
Q

What is hydrolysis

A

-reverse of condensation
-breaks up polymers using H2O
-water in, polymer out
EXERGONIC

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16
Q

What type of bond links amino acids and where does it form

A

peptide bond, between the carboxyl of one amino acid and the amino group of another

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17
Q

Why are peptide bonds so stable

A

involved electrons are partially shared between peptide bond and neighbouring carbonyl functional group

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18
Q

What geometry does the peptide bond have

A

planar (double bond nature)

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19
Q

Links of amino acids are called

A

polypeptides

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20
Q

What are the 3 key points about the peptide-bonded backbone of the polypeptide

A
  1. orientation of R group (extend out making interaction with water easier)
  2. directionality- amino group (N-terminus) always on left and carboxyl (C-terminus) always on right
  3. flexibility, the whole peptide can’t rotate due to its double bond nature but the single bonds on the side can
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21
Q

What type of bonds form between polypeptide chains

A

H-bonds

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22
Q

What are the 6 main functions of proteins

A

catalysis (enzymes), defence(antibodies), movement(motor and contractile proteins ie. actin and myosin), signalling(ie. glucagon), structure,(ie.keratin), transport(ie.hemoglobin and membrane proteins)

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23
Q

Why can proteins have so many diverse functions

A

due to their diverse size and shape, and chemical properties of their amino acids

24
Q

What is the primary structure of proteins

A

the sequence of its amino acids

25
Q

What is the secondary structure of proteins

A
  • created by H-bonds between primary structures (between carbonyl of one amino acid and H on amino group of another)
  • alpha helix (coiled, R groups point outwards) or beta pleated sheet(segments bend 180 deg. and then fold in the same plane; R-groups point up and down)
  • depends on primary struc.
26
Q

H-bonding between sections of the polypeptide backbone is only possible when….

A

different parts of the SAME polypeptide bend in a way that puts the carbonyl and amino groups close together

27
Q

Why does proline NOT fit in an alpha helix or beta sheet

A

it has a strange R group position (second covalent bond with amino group) which causes a kink and disrupts H-bonding

28
Q

What is the tertiary structure of proteins

A
  • depends on side chain interactions

- multiple secondary structures bonded together

29
Q

What are the 5 types of side chain interactions

A
  1. H-bonding- between H atom and carbonyl group, and between H-atoms in side chains
  2. Hydrophobic-due to hydrophilic chains interacting with H2O and pushing hydrophobic ones together
  3. Van der Waals-hydrophobic side chains stabilized by electrical attractions “partial charges”
  4. Covalent-between S atoms to make disulphide “bridges” which occur with cysteine
  5. Ionic-between groups that have full and opposing charges ie. amino and carboxyl
30
Q

What is the quaternary structure of proteins

A

the combination of polypeptide subunits; may be held together by bonds, r-group interactions or sections of their peptide backbone

  • in simplest case= two identical subunits aka “dimer”
  • based on tertiary struc.
31
Q

A multi-enzyme complex is

A

a group of enzymes each of which catalyzes one reaction and that are physically joined to each other
-all involved in same task

32
Q

Protein structure is

A

hierarchial

33
Q

What is a coiled-coil

A

when 2 alpha helices have hydrophobic amino acids at every 4th position

34
Q

Fibrous structural proteins consist mainly of

A

alpha helices arranged in coiled coils

35
Q

Molecular chaperones are

A

specific proteins that facilitate folding, help keep proteins from inappropriately interacting with eachother

36
Q

Heat-shock proteins are

A

proteins that speed the refolding of a protein after it was denatured

37
Q

Protein turnover is

A

breakdown and resynthesis

38
Q

Prions are

A

proteinaceous infectious particles; have odd shape due to improper folding and can cause normal proteins to change shape

39
Q

Protein function depends on

A

shape/structure

40
Q

Substrates are

A

reactant molecules

41
Q

A transition state is

A

a combination of reactant/product bond

super unstable

42
Q

Activation energy is

A

the amount of energy needed to reach the transition state

43
Q

A catalyst is

A

a substance that lowers activation energy by lowering the free energy of the transition state, increases reaction rate and does not get used up in the reaction ie. enzymes

44
Q

What do enzymes do

A
  1. bring reactant molecules together in specific orientations
  2. stabilize transition states
45
Q

The active site is

A

where substrates bind and react/where catalysis occurs

46
Q

Are enzymes rigid and static or flexible and dynamic

A

flex. and dynamic

47
Q

What actually stabilizes the transition state and lowers the activation energy

A

interactions with R-groups at the active site

48
Q

What are the 3 steps of enzyme catalysis

A
  1. initiation- enzyme brings reactants together as they bind in active site
  2. transition state facilitation-interactions between substrate and R-groups lower activ. energy/shape of enzyme may change
  3. termination-reaction products to not desire to be attached to active site as much as reactants do so they are released
49
Q

Cofactors can be

A
  1. metal ions

2. small organic molecules

50
Q

What do cofactors do

A

play a key role in stabilizing transition state

51
Q

Competitive inhibition is

A

regulatory molecule binds to active site so substrate can’t bind

52
Q

Allosteric regulation (more common) is

A

regulatory molecule binds to a different spot on the enzyme and changes the enzyme’s shape

  • activation; active site becomes available
  • deactivation: active site becomes unavailable
53
Q

Rate of an enzyme catalyzed reaction depends on

A
  1. substrate concentration
  2. enzyme availability/affinity for substrate
  3. temperature(affects movement)
  4. pH(enzyme shape and reactivity)
54
Q

Is allosteric activation or deactivation more efficient

A

deactivation (inhibition)

55
Q

What is cooperative allostery

A

occurs between 2 or more subunits, as more subunits are bound the enzyme activity eventually decreases significantly( proportional to the # of subunits) as inhibitor concentration is increased

BIO112 (19 decks)

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