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1.2 Flashcards

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1
Q

What is the proteome?

A

The proteome is the entire set of proteins expressed by a genome

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2
Q

Why is the proteome larger than the number of genes?

A

Because more than one protein can be produced from a single gene as a result of alternative RNA splicing

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3
Q

What is alternative RNA splicing?

A

When different proteins can be formed from the same primary RNA transcript. (Due to alternative segments of RNA being treated as exons and introns)

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4
Q

What are non coding RNA genes?

A

Genes that dont code for proteins (not expressed)

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5
Q

What are some examples of non coding RNA genes?

A

tRNA, rRNA and RNA molecules

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6
Q

What is a responsive gene expression?

A

When a set of proteins expressed by a given cell type vary over time and under different conditions

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7
Q

What 4 factors affect the set of proteins expressed by a given cell type?

A

Metabolic activity of the cell
Cellular stress
Response to signalling molecules
Diseased versus healthy cells

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8
Q

What is differential gene expression?

A

When Identical genomes can express very different proteins
Allows cell to become more specialised and support tissue and systems which they are apart of

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9
Q

What are two post translational modifications?

A

Adding additional molecules
Proteolytic cleavage

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10
Q

Are eukaryotes or prokaryotes smaller?

A

Prokaryotic cells are smaller - limited by number of metabolic reactions it can carry out on its plasma membrane

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11
Q

What does it mean when it is said that eukaryotes have a small surface area to volume ratio?

A

Their plasma membrane is too small to carry out vital functions carried out by membranes.
Only possible because of internal membranes - increase total area of membrane

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12
Q

What is an endoplasmic reticulum?

A

Forms a network or membrane tubules continuous with the nuclear membrane.

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13
Q

What is the ER involved in?

A

The synthesis of proteins and lipids

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14
Q

What are vesicles?

A

They transport materials between membrane compartments

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15
Q

What is the golgi apparatus?

A

Series of flattened membrane discs.

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16
Q

What is the golgi apparatus involved in

A

The transport and modification of proteins

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17
Q

What are lysosomes?

A

Membrane bound organelles containing a variety of hydrolases

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18
Q

What do hydrolases digest?

A

Proteins, lipids, nucleic acids and carbohydrates

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19
Q

What is the cytoplasm of eukaryotes made up of?

A

Cytosol (liquid component)
Ribosomes (and membrane bound organelles - ER, etc)

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20
Q

What is the definition of cytosolic proteins?

A

The synthesis of cytosolic proteins is completed there (cytosolic ribosomes) and these proteins remain in the cytosol

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21
Q

What are examples of cytosolic proteins?

A

Enzymes of glycolysis
Enzymes that attach amino acids in tRNA molecules for use in protein synthesis at the ribosome.

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22
Q

Why are cytosolic ribosomes so important?

A

They are where the synthesis of all proteins begins.

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23
Q

What are the two types of endoplasmic reticulum

A

Rough endoplasmic reticulum
Smooth endoplasmic reticulum

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24
Q

What is the rough endoplasmic reticulum?

A

Has ribosomes on its cytosolic face (surface if membrane)

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25
Q

What is the smooth endoplasmic reticulum?

A

Lacks ribosomes

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26
Q

What are some examples of post translational modifications?

A

Phosphorylation
Lipidation
Hydroxylation

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27
Q

Give examples of secreted proteins

A

Include peptide hormones e.g. insulin and digestive enzymes such as pepsin

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28
Q

What is the secretary pathway of proteins?

A

Secreted proteins are translated in ribosomes on the rough endoplasmic reticulum and enter its lumen these proteins then move through the Golgi apparatus and undergo post translation notifications and are packaged into secretary vehicles that move to infuse with the plasma membrane

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29
Q

Many secreted proteins are synthesised as an active precursors. What is required to produce an active protein?

A

Proteolytic cleavage.
Digestive enzymes are an example of secreted proteins that require this to become active.

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30
Q

What type of reaction does an enzyme cause?

A

Causes a condensation reaction between two adjacent amino acids resulting in a peptide bond between them

31
Q

What is the R group?

A

A chemical group attached to the carbon of an amino acid they very incise shape charge hydrogen bonding capacity and chemical reactivity

32
Q

In what four classes are amino acids classified?

A

Basic (positively charged)
Acidic (negatively charged)
Polar
Hydrophobic

33
Q

How is it determined which class the amino acids classify into?

A

Depending on their R groups

34
Q

Given an example of an acidic functional R group

A

Carboxylic acid group (COOH)

35
Q

Given an example of a basic functional R group

A

Amine group (NH2)

36
Q

Given an example of a polar functional R group

A

Carbonyl (CO)
Hydroxyl (OH)
Amine (NH)

37
Q

Given an example of a hydrophobic functional R group

A

Hydrocarbon (CxHy)

38
Q

What are the four levels of structure in proteins?

A

Primary
Secondary
Tertiary
Quaternary

39
Q

What is the primary protein structure?

A

The sequence in which amino acids are synthesised into the poly peptide
This determines all higher levels of a polypeptide structure

40
Q

What does the primary protein structure have at each end?

A

The primary sequence has an N-terminus at one end and a C-terminus at the other

41
Q

What is the secondary protein structure?

A

Amino acids along the length of the polypeptide chain interact and hydrogen bonds (between atoms of the same chain). This stabilises the secondary structure.

42
Q

Between what do these hydrogen bonds exist?

A

Different peptide bonds, for example, the hydrogen of the amine group (N-terminus = weak positive charge) and the oxygen of the carboxyl group (C-terminus = negatively charged)

43
Q

What are the three types of secondary structure?

A

Alpha helix
Beta pleated sheets
Turn

44
Q

What is the alpha helix secondary structure?

A

A spiral formed by twisting the polypeptide chain and stabilising with hydrogen bonds
(R group sticks outwards)

45
Q

What is the beta pleated sheet secondary structure?

A

Parts of the polypeptide chain running along side each other forming a corrugated sheet with R groups sitting above and below

46
Q

What is a parallel Beta pleated sheet?

A

When all the N termini of successive strands are oriented in the same direction

47
Q

What is an anti-parallel beta pleated sheet?

A

When successive beta strands alternate directions so that the N-terminus of one strand is adjacent to the C-terminus of the next

48
Q

What can a polypeptide chain also form?

A

Turns where the chain folds back on itself

49
Q

What is the tertiary protein structure?

A

The final folded shape of the polypeptide (due to stabilised interactions between R groups

50
Q

What are the five possible interactions between R groups? (Secondary structure brings them close enough to interact)

A

Hydrophobic interactions
Ionic bonds
London dispersion forces
Hydrogen bond
Disulphide bridges

51
Q

What are hydrophobic interactions?

A

Because hydrophobic R grips are repelled by water, they end up to the inside of the polypeptide away from water = hydrophobic interactions

52
Q

What are ionic bonds?

A

Strongly charged and attracted to each other
COOH and NH2 groups ionised to COO- and NH 3+

53
Q

What are London dispersion forces?

A

We attractions between the electron cloud of atoms
May result in attraction or repulsion

54
Q

What are hydrogen bonds?

A

Weak electrostatic forces of attraction between hydrogen atom and electronegative atoms such as oxygen or nitrogen

55
Q

What are disulphide bridges?

A

Covalent bonds between sulphur containing R groups

56
Q

What is quaternary structure?

A

This term describes the spatial arrangement of two or more connected polypeptide sub units in a protein.
For example, haemoglobin is made of four sub units .

57
Q

What is a prosthetic group?

A

Non-protein units tightly bound to a protein and necessary for its function

58
Q

How does temperature affect protein?

A

Increasing temperature denatures the protein as it begins to unfold

59
Q

How does pH affect a protein?

A

As pH increases or decreases the normal ionic interactions are lost gradually changing the confirmation of the protein, denaturing it

60
Q

What is a ligand?

A

Substance that can bind to a protein

61
Q

What happens as a ligand binds to a protein binding site?

A

The confirmation of the protein changes causing a functional changes as well

62
Q

What are allosteric interactions?

A

Interactions between spatially distinct sites on the same protein

63
Q

What are allosteric enzymes?

A

Any enzymes whose activity is regulated by altering its conformation

64
Q

What is the second type of site on an allosteric enzyme called?

A

Allosteric site

65
Q

What are modulators?

A

Can regulate the activity of the enzyme when they bind to the allosteric site changing the confirmation of the enzyme therefore changing the affinity of the active site for the enzyme substrate

66
Q

What are the two types of modulators?

A

Positive and negative

67
Q

What is a positive modulator?

A

Activators that increase the enzymes affinity for the substrate

68
Q

What are negative modulators?

A

Inhibitors that reduce the enzymes affinity for the substrate

69
Q

What is cooperativity?

A

When changes in binding at one sub unit, alter the affinity of the remaining subunits

70
Q

What can cause reversible confirmational change in proteins?

A

The additional removal of a phosphate (common in post translational modification)

71
Q

What is phosphorylation and dephosphorylation?

A

Phosphorylation-addition of phosphates
Dephosphorylation -removal of phosphate

72
Q

What do protein kinases do?

A

Catalyse the transfer of the terminal phosphate of ATP to specific R groups of other proteins (KAPO)

73
Q

What do protein phosphatases do?

A

Catalyse the reverse reaction or transfer a phosphate group from proteins onto ADP to regenerate ATP (PEPA)

74
Q

What are the effects of phosphorylation?

A

Some proteins are activated whilst others are inhibited.
Ionic interactions in on phosphorated proteins can be disrupted and new ones created

Advanced Biology (2 decks)

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