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A/ AH Biology: Unit 1 > Key Area 2: Proteins > Flashcards

Key Area 2: Proteins Flashcards

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1
Q

What is the proteome?

A

Entire set of proteins expressed by the genome

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2
Q

What is the genome?

A

Entire hereditary information encoded in the dna

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3
Q

What accounts for the proteome being larger than the genome?

A

RNA splicing and post translational modifications

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4
Q

Why is the entire protein not expressed in all cells?

A

Differentiation

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5
Q

What molecule determines protein structure?

A

Amino acids

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6
Q

What are the four main amino acid groups?

A

Acidic
Basic
Polar
Non-polar

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7
Q

What are the main features of the acidic r group?

A

Hydrophilic
Negatively charged
Carboxyl groups that ionise to make them acidic

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8
Q

What are the main features of the basic r group?

A

Hydrophilic
Positively charged
Additional amino groups that ionise to NH3+

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9
Q

What are the main features of the polar r group?

A

Hydrophilic

OH, SH or O

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10
Q

What are the main features of the non-polar r group?

A

Hydrophobic

Hydrocarbons

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11
Q

What bond occurs between amino acids and how does it form?

A

A Peptide bond forms between amino group of one acid and the carboxyl group of the next and they are formed through loss of water (dehydration)

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12
Q

What is the primary structure of a protein?

A

Polypeptide

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13
Q

What results in the secondary structure of proteins?

A

Hydrogen bonding

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14
Q

What are the secondary structures of proteins?

A
  • alpha helix-helix formation
  • beta sheet-can be parallel or anti parallel
  • turns-direction of chain is reversed
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15
Q

What type of bonding holds the tertiary structure of a protein together?

A
  • ionic bonding
  • hydrogen bonding
  • Van Der Waals forces
  • disulphides bridges
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16
Q

Explain how hydrophobic interactions affect a molecule.

A

Hydrophobic interactions occur in non-polar molecules and tend to get placed in the centre of the molecule causing globular proteins

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17
Q

What is a prosthetic group?

A

A non-protein part added to a protein

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18
Q

Give three examples of prosthetic groups.

A
  • haeme-haemoglobin protein
  • lipid-lipid protein
  • nucleic acid-nucleoprotein protein
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19
Q

What is quaternary structure of a protein?

A

When two or more tertiary subunits join together

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20
Q

What are two factors that influence R group interactions?

A
  • temperature- increased temperature means increased kinetic energy so more stress on bonds
  • pH- changes in pH changes the concentration of ions in solution which changes the relative charge on the protein and places stress on the bonds
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21
Q

What does hydrophobic mean?

A

To repel water

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22
Q

What does hydrophilic mean?

A

Mixes with water

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23
Q

What is the current accepted model of the plasma membrane structure?

A

The fluid mosaic model

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24
Q

Where are hydrophilic r group predominantly found?

A

The surface of a protein in the cytoplasm

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25
Q

Where are the hydrophobic r groups predominantly found?

A

In the centre of a protein in the cytoplasm

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26
Q

How are globular proteins formed?

A

A result of the hydrophobic and hydrophilic r group interactions in the cytoplasm

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27
Q

What are the two main components of the fluid mosaic membrane model?

A

Phospholipids and proteins

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28
Q

How do hydrophobic and hydrophilic interactions hold together the membrane?

A

Hydrophobic interactions in the membrane between lipid tails holds the double membrane together and hydrophilic heads of phospholipids allow the outer layers of the membrane to be surrounded by aqueous solutions

29
Q

What is an integral membrane protein?

A

They span the membrane and have a stretch of non-polar amino acids in the hydrophobic region

30
Q

What are three examples of integral membrane proteins?

A
  • channels
  • transporters
  • many receptors
31
Q

What are peripheral proteins?

A

Not embedded in the lipid layer but have loose associations with the surface of the membrane and few hydrophobic r group interactions with the phospholipids

32
Q

What are peripheral proteins responsible for?

A

Cell-cell interactions

33
Q

What is a ligand?

A

A substance that binds to a protein

34
Q

What is the regions of proteins that are involved in ligand binding?

A

The amino acid R groups that are not involved in the confirmation of the protein

35
Q

How does the dna backbone bind to proteins?

A

The dna backbone has a negative charge and the protein has a positive charge so they are attracted to each other

36
Q

What protein does dna bind to?

A

Histones

37
Q

What forms when dna binds to histones?

A

Nucleosomes

38
Q

What linear structure forms as a result of tight packaging of dna in eukaryotes?

A

Chromosomes

39
Q

What other proteins can bind to double stranded dna?

A

Transcription factors

40
Q

What is a transcription factor?

A

Initiate or halt transcription by recruiting RNA polymerase

41
Q

What happens when a ligand binds to a protein?

A

Conformational change

42
Q

What does conformational change cause?

A

A change in affinity therefore a change in the function/behaviour of the protein

43
Q

What is the function of phosphatase?

A

Removal of phosphate by hydrolysis

44
Q

What is the function of ATPase?

A

Hydrolysis of ATP

45
Q

What is the function of kinase?

A

Transfer of phosphate group to another molecule

46
Q

What is the function of synthase?

A

Joining two molecules by dehydration

47
Q

What is the function of nuclease?

A

Breakdown of nucleic acid by hydrolysis

48
Q

What is the function of polymerase?

A

Addition of molecules in series in a chain

49
Q

What is the function of protease?

A

Breaking down proteins by hydrolysis

50
Q

What happens in induced fit?

A

The enzyme active site forms a complimentary shape to the substrate after binding to the ligand

51
Q

What does the chemical environment from the enzyme/substrate binding do?

A

Lowers the activation energy needed for the reaction

52
Q

What happens to the confirmation of the enzyme after catalysis?

A

It reverts to its original confirmation

53
Q

What is an allosteric enzyme?

A

An enzyme that can have its activity altered by a ligand called a modulator

54
Q

What is a modulator?

A

A ligand that binds to an area of the protein that is not the active site

55
Q

What is a positive modulator?

A

Changes the conformation to promote the binding of enzyme and substrate so increase enzyme activity

56
Q

What is a negative modulator?

A

Prevents the enzyme and substrate binding so decrease enzyme activity

57
Q

What level of protein structure shows cooperativity?

A

Quaternary

58
Q

What is cooperativity?

A

Changes in any protein binding site changes affinity of all other groups

59
Q

What is an example of a protein that shows cooperativity?

A

De-oxyhaemoglobin

60
Q

What are two factors that influence the binding of de-oxyhaemoglobin?

A
  • temperature

* pH

61
Q

What level of temperature reduces affinity of ligand?

A

High temperature

62
Q

What level of pH reduces affinity of ligand?

A

Low pH

63
Q

What is phosphorylation?

A

The addition or transfer of phosphate to another molecule

64
Q

What is dephosphorylation?

A

The removal of a phosphate from a molecule

65
Q

What occurs when a phosphate is added or removed from a molecule?

A

Conformational change

66
Q

What are two types of protein that can be regulated using post-translational modifications?

A
  • enzymes

* channels

67
Q

What type of protein used ATP for their phosphorylation?

A

ATPase

68
Q

What are the steps in a muscle contraction?

A
  • muscle receives an impulse from a nerve cell generated by calcium
  • impulse causes myosin binding sites on actin to be exposed
  • myosin Hess from a flexed shape and bind to the actin
  • ADP and Pi are released from the myosin, causing it to return to its relaxed shape and moving the actin filament to the centre of the sacromere
  • ATP binds to the myosin head which causes it to release the actin
  • the myosin head acts as ATPase as it breaks down the ATP to ADP and Pi causing the head of the myosin to flex again

A/ AH Biology: Unit 1 (6 decks)

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