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AH Biology > 1.2.3 protein structure, ligand binding, conformational change > Flashcards

1.2.3 protein structure, ligand binding, conformational change Flashcards

1
Q

what determines protein structure

A

amino acid sequence

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2
Q

what are proteins

A

polymers of amino acid monomers

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3
Q

what are amino acids linked with to form polypeptides

A

peptide bonds

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4
Q

do amino acids have the same basic structure

A

yes

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5
Q

how do amino acid structures differ

A

the R group present

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6
Q

how do R groups of amino acids vary

A
  • size
  • shape
  • charge
  • hydrogen bonding capacity
  • chemical reactivity
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7
Q

how are amino acids classified

A

according to their R groups

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8
Q

what are the different amino acid classifications

A
  • basic (positively charged)
  • acidic (negatively charged)
  • polar
  • hydrophobic
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9
Q

what does the diversity of the R groups of amino acids result in

A

the amino acids having a wide range of functions carried out by their proteins

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10
Q

what is the primary structure

A

the sequence in which the amino acids are synthesised into the polypeptide

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11
Q

what results in the secondary structure

A

hydrogen bonding along the backbone of the protein strand results in regions of secondary structure

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12
Q

what are examples of the secondary structures

A
  • alpha helices
  • parallel beta-pleated sheets
  • anti-parallel beta-pleated sheets
  • turns
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13
Q

what does the polypeptide structure fold into

A

tertiary structure

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14
Q

what stabilizes the tertiary structure (give examples)

A

interactions between R groups

  • hydrophobic interactions
  • ionic bonds
  • london dispersion forces
  • hydrogen bonds
  • disulfide bridges
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15
Q

what are disulfide bridges

A

covalent bonds between R groups containing sulfur

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16
Q

when does a quaternary structure exist

A

in proteins with two or more connected polypeptide subunits

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17
Q

what is a quaternary structure

A

the spatial arrangement of the subunits

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18
Q

what is a prosthetic group

A

a non protein unit tightly bound to a protein and necessary for its function

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19
Q

what is the ability of haemoglobin to bind oxygen dependent on

A

the non protein haem group

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20
Q

what can influence the interactions of the R groups

A
  • temperature
  • pH
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21
Q

what happens to proteins when you increase the temperature

A
  • the increased temperature disrupts the interactions that hold the protein in shape
  • the protein begins to unfold, eventually becoming denatured
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22
Q

what can pH affect in relation to proteins

A

the charges on acidic and basic R groups

23
Q

why does pH affect the charges on acidic and basic R groups

A
  • as pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured
24
Q

what does ligand binding change

A

the conformation of a protein

25
Q

what is a ligand

A

a substance that can bind to a protein

26
Q

which R groups can allow binding to ligands

A

those that are not involved in protein folding

27
Q

why can ligands attach to binding sites

A

they have complementary shape and chemistry to the ligand

28
Q

what happens as a ligand binds to a protein-binding site

A

the conformation of the protein changes

29
Q

what does protein conformation cause

A

a functional change in the protein

30
Q

where do allosteric interactions occur

A

between spatially distinct sites

31
Q

what does the binding of a substrate molecule to one active site of an allosteric enzyme cause

A

an increase in the affinity of the other active sites for binding of subsequent substrate molecules

32
Q

why is the binding of substrate molecules to one active site of an allosteric enzyme of biological importance

A

the activity of the allosteric enzymes can vary greatly with small changes in substrate concentration

33
Q

what do many allosteric proteins consist of? and what does this mean for their structure?

A

multiple subunits, so they have a quaternary structure

34
Q

what does cooperativity in binding mean (when looking at allosteric proteins with quaternary structures)

A

changes in binding at one subunit alter the affinity of the remaining subunits

35
Q

what is the name of the other site on allosteric enzymes

A

allosteric site

36
Q

what do modulators do

A

they regulate the activity of the enzyme when they bind to the allosteric site

37
Q

what happens following the binding of a modulator

A

the conformation of the enzyme changes and this alters the affinity of the active site for the substrate

38
Q

what do positive modulators do

A

they increase the enzymes affinity for the substrate

39
Q

what do negative modulators do

A

they reduce the enzymes affinity for the substrate

40
Q

what does the binding and release of oxygen in haemoglobin show

A

cooperativity

41
Q

what does the change in binding of oxygen at one subunit alter

A

the affinity of the remaining subunits for oxygen

42
Q

does temperature and pH have an influence on the binding of oxygen

A

yes

43
Q

what lowers the affinity of haemoglobin for oxygen, therefore causing a reduction in the binding of oxygen

A
  • decrease in pH

- increase in temperature

44
Q

what reduces the binding of oxygen to haemoglobin, promoting increased oxygen delivery to tissue?

A
  • reduced pH

- increased temperature

45
Q

what can the addition or removal of a phosphate cause

A

reversible conformational change in proteins

46
Q

is phosphorylation a form of post translational modification

A

yes

47
Q

what do protein kinases do

A

they catalyse the transfer of a phosphate group to other proteins

48
Q

where is the terminal phosphate of ATP transferred to

A

specific R groups

49
Q

what do protein phosphotases do

A

catalyses the reverse reaction of phosphorylation (removes, rather than adds)

50
Q

what does phosphorylation bring about

A

conformational changes, which can affect a proteins activity

51
Q

how is the activity of many cellular proteins, such as enzymes and receptors, regulated?

A

through phosphorylation

52
Q

is it true that all proteins are activated by phosphorylation

A

no. some are inhibited

53
Q

does adding a phosphate group add negative or positive charges

A

negative

54
Q

can ionic interactions in the unphosphorylated protein remain undisrupted

A

no, they can get disrupted and new ones will then get created

AH Biology (60 decks)

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