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Advanced higher biology > 1.2 proteome > Flashcards

1.2 proteome Flashcards

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1
Q

Proteome definition

A

The entire set of proteins expressed by a genome

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2
Q

Proteome size comparison with gene number explain

A

The proteome is drastically larger than the number of genes in the genome, particularly in eukaryotes, because more than one protein can be produced from each gene due to alternative splicing, and post translational modifications.

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3
Q

What do non coding RNA gene produce

A

tRNA, rRNA and RNA molecules which control expression of other genes.

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4
Q

Are all genes expresses as proteins

A

No some are expressed as RNA molecules.

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5
Q

SER actual name

A

Soft endoplasmic reticulum

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6
Q

RER actual name

A

Rough endoplasmic reticulum

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7
Q

What is the purpose of the intracellular membranes

A

To increase the surface area to volume ratio, to allow for vital cellular functions to take place.

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8
Q

What is the difference between the rough and smooth endoplasmic reticulum

A

The rough endoplasmic reticulum has ribosomes, and produces protein
Whereas the soft endoplasmic reticulum does not have ribosomes and produces lipids (fats).

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9
Q

Function of the endoplasmic reticulum

A

The endoplasmic reticulum creates a network of membrane tubules continuous with the nuclear membrane to produce lipids and proteins.

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10
Q

Golgi apparatus

A

The cell organelle which receives proteins and lipids from the ER. Consisting of a series of flattened discs to process, carry out post translational modification and send these modified proteins and lipids off to their destination.

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11
Q

Lysosome’s definition

A

Membrane bound organelles containing hydrolases that digest proteins, lipids, carbohydrates and nucleic acids.

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12
Q

Hydrolase definition

A

Enzymes which use water to break down substrates such as proteins, fats, nucleic acids and carbohydrates.

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13
Q

What are genes which don’t code for protein called

A

Non - coding RNA genes

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13
Q

Factors affecting proteins expressed in a cell

A

Metabolic activity
Cellular stress
Response to signalling molecules
Disease

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13
Q

Vesicles definition

A

Cell organelles which transport materials between membrane compartments

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14
Q

What are intracellular membranes

A

They are membranes which inside a cell which increase the cell membrane surface area to volume ratio.

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15
Q

Lysosome pH

A

Acidic to allow for optimum enzyme activity

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16
Q

What is cytosol

A

Cytosol is part of the cytoplasm where the new cell organelles are suspended. (Not part of the course but important to remember).

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17
Q

Process of producing a cytosolic protein

A

mRNA will leave the nucleus and travel to a ribosome in the cytosol.
In cytosolic the ribosome will remain in the cytosol.
A polypeptide chain will be produced by the ribosome.
This will then fold into shape and become a protein.
The protein will remain in the cytosol.

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18
Q

Process of producing a transmembrane protein

A

An mRNA strand travels from the nucleus to cytosolic ribosome.
The cytosolic ribosome produces a polypeptide chain containing a signal sequence.
The cytosolic ribosome then travels to the endoplasmic reticulum and docks with it forming the RER.
translation then continues at the RER and is then packaged into a vesicles to be transported to the Golgi apparatus.
The Golgi apparatus then processes and carries out post translational modification.
Then the transmembrane protein is sent onto its destination.

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19
Q

How do proteins travel away from the rough endoplasmic reticulum.

A

They use vesicles which bud off the endoplasmic reticulum and fuse to the Golgi apparatus.

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20
Q

Signal sequence definition

A

The sequence of amino acids that informs the ribosome that it needs to dock with the endoplasmic reticulum.

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21
Q

Destination of cytosolic proteins

A

Nucleus, mitochondria, chloroplasts

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22
Q

Destination of transmembrane proteins

A

Plasma membranes
Secretory vesicles
Lysosomes

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23
Q

Secretory definition

A

Means to be sent outside the cell.

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24
Q

Post translational modification

A

Where a molecule or group is added to the protein in the Golgi apparatus after translation.

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25
Q

What is the major post translational modification

A

The addition of a carbohydrate

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26
Q

How do vesicles travel to different locations

A

By using the micro tubules of the cytoskeleton

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27
Q

Examples of secreted proteins

A

Peptide hormones
And digestive enzymes

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28
Q

What do secretory vesicles do

A

They leave the Golgi complex and fuse with the plasma membrane - releasing the protein out of the cell

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28
Q

Examples of secreted proteins

A

Peptide hormones and digestive enzymes.

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29
Q

What happens after a protein moves through the Golgi apparatus

A

It’s packaged into a secretory vesicles and transported to the plasma membrane, a lysosome or transported out of the cell.

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30
Q

Proteolytic cleavage definition

A

A form of post translational modification where a section of a polypeptide chain is removed from a protein to activate the protein.

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31
Q

Proteolytic cleavage reason

A

To activate a protein at the correct time.

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32
Q

Example of Proteolytic cleavage

A

Digestive enzymes

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33
Q

Amino acids definition

A

The small monomer molecules which make up a protein

34
Q

Proteins definition

A

Large polymer molecules consisting of many amino acids linked by peptide bonds.

35
Q

Amino group

A

NH2 in isoelectric

36
Q

Carboxyl group

A

C=OOH

37
Q

Peptide bond

A

C=ONH

38
Q

Amino acid structure

A

NH2 —CHR —C=OOH

39
Q

Amino acid different types

A

Basic
Acidic
Hydrophobic
Polar

40
Q

Basic amino acids

A

Amino acids with a positive charge on the R group

41
Q

Acidic amino acids

A

Amino acids with a negative charge on the R group

42
Q

Polar amino acids

A

Amino acids which are hydrophilic and contain functional groups such as carbonyl, hydroxyl or amine groups.

43
Q

Hydrophobic amino acids

A

Amino acids which are non polar and have an R group consisting of large numbers of Carbon and Hydrogen.

44
Q

Protein structure primary sequence definition

A

The sequence of amino acids that are synthesised into a polypeptide chain.

45
Q

How is the secondary structure formed

A

By some amino acids forming hydrogen bonds with other amino acids peptide bonds.

46
Q

Secondary structure types

A

Alpha helix
B- sheet
Turns

47
Q

Secondary structure definition

A

The polypeptide chain folded into a specific shape using hydrogen bonding.

48
Q

Types of B- sheet

A

Parallel - 2.5 beta sheets.
Antiparallel - two beta sheets

49
Q

Turns definition

A

The third type of secondary structure which changes the direction of the polypeptide chain and connect other secondary structures.

50
Q

Tertiary structure definition

A

The structure of a protein influenced by the R groups of the amino acid

51
Q

Tertiary structure types

A

Ionic
Hydrophobic
Hydrogen bonding
Disulphide bridge
London dispersion forces.

52
Q

Ionic tertiary structure

A

Creates electrostatic forces or attraction due to oppositely charged R groups

53
Q

Hydrophobic tertiary structure

A

Creates a cluster on the interior of the protein and affects protein solubility.

54
Q

Hydrogen bond tertiary structure

A

An electrostatic attraction between a hydrogen atom and N.O.F on a protein.

55
Q

Disulphide bridge tertiary structure

A

A covalent bond between two thiol (SH) groups on a protein

56
Q

London dispersion forces tertiary structure

A

A temporary attractive force which causes dipoles on a protein.

57
Q

Quaternary structure of proteins

A

The number and spatial arrangement of polypeptide subunits in a protein.

58
Q

Prosthetic groups

A

A non protein unit tightly bound to a protein, which is necessary for its function.

59
Q

pH and temp effect on a protein

A

Denaturation

60
Q

How does pH denature

A

It changes the charges of the R groups of the amino acids and means normal ionic interactions are altered.

61
Q

How does temperature denature

A

It disrupts the interactions that holds the protein in shape.

62
Q

Ligand definition

A

A substance that can bind to a protein.

63
Q

How do ligands bond to proteins

A

R groups not involved in protein folding and structure bond with the ligands.

64
Q

What is a conformational change

A

A change in the shape and function of a protein due to a ligand binding to the protein.

65
Q

Allosteric proteins definition

A

Proteins with quaternary structure which allow ligands to bond to spatially distinct sites away from the active site, allowing for conformational change to occur within the protein

66
Q

Cooperativity

A

Where in a protein with quaternary strucure on one ligand binds to the active site of one sub unit it changes the affinity of all the active sites and allows for ligand to bind to active site.

67
Q

Examples of co-operativity

A

Haemoglobin

68
Q

Rules for temperature and pH on haemoglobin saturation

A

As pH increases and temp decreases saturation increases
As pH decreases and temp increases saturation decreases

69
Q

Allosteric enzymes definition

A

An enzyme which changes conformation upon binding to a modulator at a secondary binding sites.

70
Q

Negative modulator

A

A molecule binding to the Allosteric site in a protein causing conformational change to the protein decreasing active site affinity.

71
Q

Positive modulator

A

A molecule binding to the Allosteric site in a protein causing conformational change to the protein increasing active site activity.

72
Q

Allosteric inhibitor

A

Negative modulator

73
Q

Allosteric activator

A

Positive modulator

74
Q

Phosphorylation definition

A

A form of post translational modification where a phosphate group is added or removed from a proteins R group causing conformational change.

75
Q

Why does phosphorylation occur

A

To allow for reversible conformational changes in proteins to occur and to activate the protein.

76
Q

Which phosphate is removed in ATP

A

The terminal (third) phosphate

77
Q

Protein kinase

A

An enzyme which catalyses the transfer of phosphate groups to proteins by removing a phosphate from ATP forming ADP.

78
Q

phosphatase

A

The enzyme which catalyses the removal of a phosphate from a protein and adds it to ADP producing ATP

79
Q

Phosphorylation activation rule

A

Most proteins are activated by phosphorylation but some are deactivated.

80
Q

Protein kinase process

A

Protein + ATP —> Phosphorylated protein + ADP

81
Q

Protein phosphorylase process

A

Pphosphorylated protein +ADP —-> Protein + ATP.

82
Q

Where does the phosphate bind to a protein

A

At specific complimentary R groups.

83
Q

Effect of phosphate group of tertiary structure

A

Can add negative charges to the protein, disrupting and creating New Ionic interactions.

84
Q

What varies in R groups

A

Size
Shape
Charge
Hydrogen bonding capacity
Chemical reactivity

85
Q

Why is there such a high diversity of proteins

A

Because there is a wide range of R groups.

86
Q
A

Advanced higher biology (11 decks)

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