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ADVH BIO > Proteins > Flashcards

Proteins Flashcards

1
Q

What is the proteome

A

The entire set of proteins expressed by a genome

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2
Q

Why is the proteome much larger

A

As more than one protein can be produced from a single gene resulting from alternative RNA splicing

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3
Q

In what case are not all genes expressed as a protein

A

In a particular cell type

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4
Q

What can happen to the set of proteins expressed by a given cell type

A

It can vary over time and under different conditions

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5
Q

What factors ca affect the set of protein expressed by a given cell type

A
  • Metabolic activity of cell
  • cellular stress
  • response to signalling molecules
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6
Q

What ratio do eukaryotic cells present in terms of size

A

A relatively small surface area to volume ratio

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7
Q

How does the small plasma membrane of the eukaryote affect its roles

A

As the plasma membrane is too small an area, it cannot carry out all of the vital functions carried out by membranes

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8
Q

What type of system do eukaryotic cells have

A

Eukaryotic cells have a system of internal membranes that increases the total area of membrane

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9
Q

What is the endoplasmic reticulum (ER)

A

The endoplasmic reticulum forms a network of membrane tubules continuous with the nuclear membrane
(Where lipids and proteins are synthesised)

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10
Q

What is the Golgi apparatus

A

The Golgi apparatus is a series of flattened membrane discs

Where proteins undergo post translational modification

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11
Q

What are lysosomes

A

Lysosomes are membrane bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates

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12
Q

What are vesicles

A

Vesicles carry out the transport of materials between membrane compartments

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13
Q

What are proteins polymers of

A

Amino acid monomers

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14
Q

What are the four distinct stages after translation that proteins are synthesised in

A
  • Primary structure
  • Secondary structure
  • Tertiary structure
  • quaternary structure
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15
Q

What is the primary structure of a protein

A

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

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16
Q

What groups are attached onto amino acids

A 
Amine group (NH3) 
Carboxylic acid (COOH) 
Hydrogen 
R variable group 
            H
            |
H3N—C—C= O
            |      \ OH
            R
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17
Q

What are the 5 ways R groups can differ

A
  • size
  • shape
  • charge
  • Hydrogen bonding capacity
  • chemical reactivity
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18
Q

What are the 4 amino acid classes

A
  • Acidic Carboxylic acid COOH
  • Basic Amine group (NH3)
  • Polar Hydroxide -OH
  • Hydrophobic Hydrocarbon -CH
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19
Q

What charge are amino acids and the key component of acid amino acid R group

A

Negatively charged with key component being Carboxylic acid

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20
Q

What charge are basic amino acids and their key r group component

A

Positively charged with key component being amine group (NH2)

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21
Q

What is the charge of polar amino acids and their r group key component

A

Very slightly charged and hydrophobic with key component of hydroxyl group -OH

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22
Q

What are hydrophobic amino acids and their key component r group

A

They are non-polar with key component of hydrocarbon group -CH3

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23
Q

What class is a benzene ring

A

Hydrophobic

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24
Q

How are peptide bonds formed

A

An enzyme causes a condensation reaction between two adjacent amino acids

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25
Q

How is the secondary structure stabilised

A

Secondary structure of protein is stabilised by hydrogen bonds along the backbone of the protein strand

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26
Q

What are the 3 main components of the secondary structure

A

1) Alpha helix
2) Beta pleated sheets
3) turns

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27
Q

What is the alpha helix

A

It is a spiral with the R groups sticking outwards

R groups such as acidic,basic,polar etc

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28
Q

What are beta pleated sheets

A

It has parts of the chain running along side each other to form a corrugated sheet. R groups sit above and below the sheet

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29
Q

What are the two types of beta pleated sheets

A

Parallel and anti-parallel

30
Q

Explain anti-parallel and parallel beta pleated sheets

A
  • B-pleated sheet are usually anti-parallel —> chains run in opposite directions from each other
  • Some can also be parallel —> chains run in same direction

Sheets are anti-parallel or parallel depending on their N - C polarity

31
Q

What are turns

A

The third type of secondary structure which serve to reverse the direction of the polypeptide chain and folds back on itself

32
Q

What is the tertiary structure

A

The final folded structure of the polypeptide

33
Q

How is the folding at the tertiary structure stabilised

A

Stabilised by interactions between the R groups of amino acids

34
Q

What is a hydrophobic interaction between the R group

A

The hydrophobic R groups are repelled by water and usually end up to the inside of the polypeptide

35
Q

What is an ionic bonds interaction between R groups

A

The COOH (Carboxylic acid) and NH2 (amino) ionise to become COO-(minus) and NH3+, As they are so strongly charged, they attract each other

36
Q

What is a hydrogen bond interaction between R groups

A

Strong attractions between molecules contacting bonds O-H or N-H or H-F

37
Q

What is the disulphide bridges interaction between R groups

A

When covalent bonds form between sulphur-containing R groups (R groups which contain sulphur)

38
Q

What is London dispersion forces interactions between R groups

A

Very weak attraction between the electron clouds of atoms

39
Q

What is the quaternary structure

A

Quaternary structure exists in proteins with two or more connected polypeptide subunits

40
Q

What is a prosthetic group

A

A non-protein group which is tightly bound to a polypeptide unit and is essential for the proteins function

41
Q

What are factors that can affect protein structure

A
  • pH

- temperature

42
Q

Is the proteome larger or smaller than the genome

43
Q

What are the two components of the cytoplasm

A

Cytosol(liquid component) and ribosome(membrane bound organelle)

44
Q

What are the names of the two parts of the Endoplasmic reticulum (ER)

A
  • The rough ER (RER)

- The smooth ER (SER)

45
Q

Why is the Rough ER rough and the smooth ER smooth

A
  • As it has ribosomes attached to the cytosolic face of its membranes
  • SER has no ribosomes attached to it
46
Q

Where are Lipids synthesised

A

Lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane

47
Q

Where does the synthesis of all proteins begins

A

At cytosolic ribosomes

48
Q

What do transmembrane proteins carry

A

They carry a signal sequence which halts translation and directs the ribosome synthesising the protein to dock with the ER —-> forming RER (rough endoplasmic reticulum)

49
Q

What occurs after docking

A

Translation occurs and the protein is inserted into the membrane of the endoplasmic reticulum (ER) ——> once translation complete, the ribosome is released back into the cytosol

50
Q

What occurs to the proteins in the endoplasmic reticulum

A

They are transported by vesicles that bud off from the endoplasmic reticulum (ER) and fuse with the Golgi apparatus

51
Q

What do proteins undergo moving through the Golgi apparatus

A

Proteins undergo post-translational modification

52
Q

What causes a major modification to the protein

A

The addition of carbohydrate groups

53
Q

What do the vesicles that leave the Golgi apparatus do

A

The vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes ——> vesicles move along microtubules to other membranes and fuse with them within the cell

54
Q

What are secreted proteins translated in

A

Secret red proteins are translated in ribosomes on the rough endoplasmic reticulum (RER) and enter its lumen

55
Q

What become packaged into secretory vesicles

A

Proteins move along the Golgi apparatus and are packaged into secretory vesicles

56
Q

What happens to secretory vesicles

A

They move along microtubules to fuse with the plasma membrane —> releasing the proteins out of the cell

57
Q

What do secreted proteins which synthesise as inactive precursors require

A

Inactive precursors require proteolytic cleavage to produce active proteins which prevents digestive enzymes becoming active and causing damage to the cell

58
Q

What is a ligand

A

A substance which can bind to a protein —> binding sites normally have complementary shape and chemistry for ligand to bind to

59
Q

How does the conformation of a protein change

A

As a ligand binds to a protein-binding site, the conformation of the protein changes and this change causes a functional change in the protein

60
Q

Where does allosteric interactions occur

A

Between spatially distinct sites

61
Q

What is cooperativity

A

When the binding of a ligand to one subunit of the protein increase the affinity of another subunit

62
Q

What is the second type of site allosteric enzymes contain

A

An allosteric site

63
Q

What is the function of modulators

A

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

64
Q

Where can co-operativity be seen

A

The binding and release of oxygen in haemoglobin

65
Q

What does the increase in temperature and decrease in pH cause

A

Causes the haemoglobin to have a lower affinity for oxygen so the binding of oxygen is reduced

66
Q

What can result from the addition or removal of phosphate

A

Can cause reversible conformational change in proteins and is a common form of post-translational modification

67
Q

What catalyses the transfer of a phosphate group to other proteins

A

Protein Kinase catalyses phosphorylation

68
Q

What is transferred to specific R groups

A

The terminal phosphate of ATP is transferred to specific R groups

69
Q

What does protein phosphatases do

A

It catalyses the reverse reaction —> dephosphorylation

70
Q

What can occur to some proteins due to phosphorylation

A

Some proteins are activated whereas some are inhibited

ADVH BIO (10 decks)

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