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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
How is the secondary structure stabilised
Secondary structure of protein is stabilised by hydrogen bonds along the backbone of the protein strand
26
What are the 3 main components of the secondary structure
1) Alpha helix 2) Beta pleated sheets 3) turns
27
What is the alpha helix
It is a spiral with the R groups sticking outwards | R groups such as acidic,basic,polar etc
28
What are beta pleated sheets
It has parts of the chain running along side each other to form a corrugated sheet. R groups sit above and below the sheet
29
What are the two types of beta pleated sheets
Parallel and anti-parallel
30
Explain anti-parallel and parallel beta pleated sheets
- 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
What are turns
The third type of secondary structure which serve to reverse the direction of the polypeptide chain and folds back on itself
32
What is the tertiary structure
The final folded structure of the polypeptide
33
How is the folding at the tertiary structure stabilised
Stabilised by interactions between the R groups of amino acids
34
What is a hydrophobic interaction between the R group
The hydrophobic R groups are repelled by water and usually end up to the inside of the polypeptide
35
What is an ionic bonds interaction between R groups
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
What is a hydrogen bond interaction between R groups
Strong attractions between molecules contacting bonds O-H or N-H or H-F
37
What is the disulphide bridges interaction between R groups
When covalent bonds form between sulphur-containing R groups (R groups which contain sulphur)
38
What is London dispersion forces interactions between R groups
Very weak attraction between the electron clouds of atoms
39
What is the quaternary structure
Quaternary structure exists in proteins with two or more connected polypeptide subunits
40
What is a prosthetic group
A non-protein group which is tightly bound to a polypeptide unit and is essential for the proteins function
41
What are factors that can affect protein structure
- pH | - temperature
42
Is the proteome larger or smaller than the genome
Larger
43
What are the two components of the cytoplasm
Cytosol(liquid component) and ribosome(membrane bound organelle)
44
What are the names of the two parts of the Endoplasmic reticulum (ER)
- The rough ER (RER) | - The smooth ER (SER)
45
Why is the Rough ER rough and the smooth ER smooth
- As it has ribosomes attached to the cytosolic face of its membranes - SER has no ribosomes attached to it
46
Where are Lipids synthesised
Lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane
47
Where does the synthesis of all proteins begins
At cytosolic ribosomes
48
What do transmembrane proteins carry
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
What occurs after docking
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
What occurs to the proteins in the endoplasmic reticulum
They are transported by vesicles that bud off from the endoplasmic reticulum (ER) and fuse with the Golgi apparatus
51
What do proteins undergo moving through the Golgi apparatus
Proteins undergo post-translational modification
52
What causes a major modification to the protein
The addition of carbohydrate groups
53
What do the vesicles that leave the Golgi apparatus do
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
What are secreted proteins translated in
Secret red proteins are translated in ribosomes on the rough endoplasmic reticulum (RER) and enter its lumen
55
What become packaged into secretory vesicles
Proteins move along the Golgi apparatus and are packaged into secretory vesicles
56
What happens to secretory vesicles
They move along microtubules to fuse with the plasma membrane —> releasing the proteins out of the cell
57
What do secreted proteins which synthesise as inactive precursors require
Inactive precursors require proteolytic cleavage to produce active proteins which prevents digestive enzymes becoming active and causing damage to the cell
58
What is a ligand
A substance which can bind to a protein —> binding sites normally have complementary shape and chemistry for ligand to bind to
59
How does the conformation of a protein change
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
Where does allosteric interactions occur
Between spatially distinct sites
61
What is cooperativity
When the binding of a ligand to one subunit of the protein increase the affinity of another subunit
62
What is the second type of site allosteric enzymes contain
An allosteric site
63
What is the function of modulators
Modulators regulate the activity of the enzyme when they bind to the allosteric site
64
Where can co-operativity be seen
The binding and release of oxygen in haemoglobin
65
What does the increase in temperature and decrease in pH cause
Causes the haemoglobin to have a lower affinity for oxygen so the binding of oxygen is reduced
66
What can result from the addition or removal of phosphate
Can cause reversible conformational change in proteins and is a common form of post-translational modification
67
What catalyses the transfer of a phosphate group to other proteins
Protein Kinase catalyses phosphorylation
68
What is transferred to specific R groups
The terminal phosphate of ATP is transferred to specific R groups
69
What does protein phosphatases do
It catalyses the reverse reaction —> dephosphorylation
70
What can occur to some proteins due to phosphorylation
Some proteins are activated whereas some are inhibited

ADVH BIO (10 decks)

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