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Advanced Higher Biology > Unit 1 Cells and Proteins: Key Area 2 - Protiens (Structure) > Flashcards

Unit 1 Cells and Proteins: Key Area 2 - Protiens (Structure) Flashcards

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1
Q

What is a distinguishing feature of proteins?

A

There folded nature and ability to bind specifically to other molecules.

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2
Q

What are proteins polymers of?

A

Amino acids.

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3
Q

What are the 2 functional groups of amino acids?

A

The amine and acid group.

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4
Q

What does the wide range of functions carried out by proteins result from?

A

The wide range of functions carried out by proteins results from the diversity of R groups.

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5
Q

What determine the structure of the protein?

A

The sequence of amino acids.

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6
Q

What makes each amino acid different?

A

The R-group.

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7
Q

What are the 5 components of an amino acid?

A

The amine group, acid group, R-group, hydrogen atom and central carbon.

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8
Q

What are amino acids linked together by and what does this produce?

A

Peptide bonds which produces a polypeptide.

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9
Q

What are the 4 main R-groups of amino acids?

A

Polar, Hydrophobic, Acidic (Negatively charged), Basic (Positively charged).

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10
Q

What can the R-group of amino acids vary in?

A

Size, shape, charge, hydrogen bonding capacity and chemical reactivity. They can be as simple as hydrogen or as complex as a chain with rings.

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11
Q

What are the key features of an aAcidic R-group?

A
  • Ends with a negatively charged group.
  • Hydrophilic.
  • Key component is a carboxylic acid group - COOH.
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12
Q

What are the key features of a Basic R-group?

A
  • Ends with a positively charged group.
  • Hydrophilic.
  • Key component of their R-group is an amine group.
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13
Q

What are the key features of a Polar R-group?

A
  • Slightly charged.
  • Hydrophilic.
  • Key component: carbonyl (CO), (OH) or amine (NH).
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14
Q

What are the key features of a Hydrophobic R-group?

A
  • Hydrophobic.
  • Do not have charged.
  • Non-Polar.
  • Key component is a hydrocarbon - CH3, long chain of CH and rings
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15
Q

What are the other levels of protein structure other than the sequence and binding of amino acids?

A
  • Primary Structure
  • Secondary Structure
  • Tertiary Structure
  • Quaternary Structure
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16
Q

What is the primary structure?

A

The primary structure is the sequence in which the amino acids are synthesised into the polypeptide.

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17
Q

What happens in the primary structure?

A

Amino acids link by peptide bonds to from a polypeptide.

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18
Q

Due to the make up of amino acids, what does the primary structure have?

A

A n-terminal and c-terminal.

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19
Q

What results in regions of a secondary structure?

A

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

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20
Q

What are the 3 types of secondary structure?

A
  • Alpha Helix
  • Beta Sheets
  • Turns
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21
Q

How are Alpha Helix formed?

A

By twisting the polypeptide chain into a spiral/helix then stabilising with hydrogen bonds. Where the R-group sticks out.

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22
Q

What are the 2 types of beta sheet?

A
  • Parallel: the chains run in the same direction.

- Anti-parallel: the chains run in opposite directions.

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23
Q

What is the structure of beta sheets like?

A

The beta sheet has parts of the chain running alongside each other, forming a sheet. The R-groups sit above and below the sheet.

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24
Q

What stabilises the alpha helix?

A

Hydrogen bonding.

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25
Q

What is the structure of turns like?

A

They reverse the direction of the polypeptide chain and the chain folds back on itself.

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26
Q

What is the tertiary structure?

A

The final folded shape of the polypeptide.

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27
Q

How Is the tertiary structure established?

A

By many different interactions between the R-groups of the amino acids.

28
Q

What are the 5 R-group interactions of the tertiary structure?

A
  • Hydrophobic Interactions.
  • Ionic Bonds.
  • London Dispersion Forces (LDFs).
  • Hydrogen Bonds.
  • Disulphides Bridges.
29
Q

How does Hydrophobic Interactions in the tertiary structure work?

A

Amino acids tend to cluster together on the interior of a protein, away from the surface (and away from water).

30
Q

How does Ionic Bonds in the tertiary structure work?

A

Occurs when atoms that are oppositely charged are held by an electrostatic attraction.

31
Q

What happens to COOH and NH2 in Ionic Bonds in tertiary structure?

A

They become COO- and they are strongly charged and attracted to each other.

32
Q

How does LDFs in the tertiary structure work?

A

Weak interactions between the electron clouds of atoms. These interactions may result in attraction or repulsion between states.

33
Q

How does Hydrogen Bonds in the tertiary structure work?

A

One of the weaker interactions between amino acids. An electrostatic attraction which occurs between a hydrogen atom and an electronegative atom, such as oxygen or nitrogen.

34
Q

How does Disulphide Bridges in the tertiary structure work?

A

A covalent bond between R-groups containing Sulphur (between two thiol- SH - group).

35
Q

What is a prosthetic group?

A

A prosthetic group is a non-protein unit tightly bound to a protein and necessary for its function.

36
Q

What is an example of a prosthetic group?

A

The haem in haemoglobin. The ability of haemoglobin to bind oxygen is dependent on the non-protein haem group.

37
Q

What can affect the interactions between R-groups?

A

Temperature and pH. Which is why pH and temperature can affect the structure and function of a protein.

38
Q

What are the effects of temperature on the interactions between R-groups?

A

Increasing the temperature disrupts the interactions that hold the protein in shape. The protein begins to unfold, eventually being denatured.

39
Q

What are the effects of pH on the interactions between 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.

40
Q

What is a Ligand?

A

A ligand is a substance that can bind to a protein.

41
Q

What R-groups can allow binding to ligand?

A

Those that are not involved in protein folding.

42
Q

What will the binding sites have to the ligand?

A

Binding sites will have complementary shape and chemistry to the ligand.

43
Q

What happens to a protein as a ligand binds to it?

A

As a ligand binds to a protein-binding site the conformation of the protein changes. This change in conformation causes a functional change in the protein.

44
Q

What is an example of a drug that acts as a ligand and how does it work?

A

Nicotine by binding to a protein receptor called acetylcholine. Where nicotine is a very small molecule in comparison to the acetylcholine.

45
Q

What is an allosteric enzyme?

A

An enzyme is an enzyme who’s activity is regulated by altering its conformation.

46
Q

Where do allosteric interactions occur?

A

Between spatially distinct sites. Active site = substrate, Allosteric site = substance other than the substrate.

47
Q

What do allosteric enzyme contain?

A

A second type of site called an allosteric site.

48
Q

What do many allosteric proteins consist of?

A

Many allosteric proteins consist of multiple subunits (have quaternary structure).

49
Q

What do modulators do?

A

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

50
Q

Following binding of a modulator what happens to the active site?

A

Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate.

51
Q

What is the function of negative modulators?

A

To reduce the enzymes affinity for the substrate = decrease activity.

52
Q

What is the function of positive modulators?

A

To increase the enzymes affinity for the substrate - increase activity.

53
Q

What shows co-operativity?

A

Allosteric points with multiple subunits show co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits.

54
Q

What does the binding of a substrate molecule to one active site of a allosteric enzyme do in terms of co-operativity?

A

Increases the affinity of the other active sites binding of subsequent substrate molecules.

55
Q

Why is co-opoerativity of biological importance?

A

The activity of allosteric enzyme can vary greatly with small changes in substrate concentration.

56
Q

What is an example of a molecule that shows co-operativity, why does it show this and how does it work?

A

Haemoglobin as it is made up of 4 polypeptide subunits, where each subunit contains a haem group. Where one of the subunits binds a molecule of oxygen, subsequently binding by other oxygen molecules is more likely. Where oxy - haemoglobin releases oxygen, the same process happens.

57
Q

What is the influence of increasing temperature and reducing pH on affinity of haemoglobin?

A

Reduced pH and increased temperature in actively respiring tissues will reduce the binding of oxygen to haemoglobin, promoting increased oxygen delivery to tissue.

58
Q

What is the influence of reducing temperature and increasing pH on affinity of haemoglobin?

A

A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced.

59
Q

What is phosphorylation?

A

The addition or removal of phosphate can cause reversible conformational change in proteins.

60
Q

What is phosphorylation a common form of?

A

This is a common form of post-translational modification.

61
Q

What is the function of protein kinases?

A

Protein kinases catalyse the transfer of a phosphate group to other proteins. Where the terminal phosphate of ATP is transferred to specific R groups.

62
Q

What is the function of protein phosphates?

A

Protein phosphatase catalyses the transfer of a phosphate group from protein onto ADP to regenerate ATP.

63
Q

What does phosphorylation bring about?

A

Phosphorylation brings about conformational changes, which can affect a protein’s activity.

64
Q

What does phosphorylation regulate?

A

The activity of many cellular proteins, such as enzymes and receptors, is regulated by phosphorylation.

65
Q

What does phosphorylation of some proteins do?

A

Some proteins are activated by phosphorylation while others are inhibited.

66
Q

What can the addition of a phosphate group change in terms of charge and how does this affect the ionic interactions?

A

Adding a phosphatase group adds negative charges. Ionic interactions in the unphosphorylated protein can be disrupted and new ones created.

Advanced Higher Biology (7 decks)

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