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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
What is the smooth endoplasmic reticulum?
Lacks ribosomes
26
What are some examples of post translational modifications?
Phosphorylation Lipidation Hydroxylation
27
Give examples of secreted proteins
Include peptide hormones e.g. insulin and digestive enzymes such as pepsin
28
What is the secretary pathway of proteins?
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
29
Many secreted proteins are synthesised as an active precursors. What is required to produce an active protein?
Proteolytic cleavage. Digestive enzymes are an example of secreted proteins that require this to become active.
30
What type of reaction does an enzyme cause?
Causes a condensation reaction between two adjacent amino acids resulting in a peptide bond between them
31
What is the R group?
A chemical group attached to the carbon of an amino acid they very incise shape charge hydrogen bonding capacity and chemical reactivity
32
In what four classes are amino acids classified?
Basic (positively charged) Acidic (negatively charged) Polar Hydrophobic
33
How is it determined which class the amino acids classify into?
Depending on their R groups
34
Given an example of an acidic functional R group
Carboxylic acid group (COOH)
35
Given an example of a basic functional R group
Amine group (NH2)
36
Given an example of a polar functional R group
Carbonyl (CO) Hydroxyl (OH) Amine (NH)
37
Given an example of a hydrophobic functional R group
Hydrocarbon (CxHy)
38
What are the four levels of structure in proteins?
Primary Secondary Tertiary Quaternary
39
What is the primary protein structure?
The sequence in which amino acids are synthesised into the poly peptide This determines all higher levels of a polypeptide structure
40
What does the primary protein structure have at each end?
The primary sequence has an N-terminus at one end and a C-terminus at the other
41
What is the secondary protein structure?
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
Between what do these hydrogen bonds exist?
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
What are the three types of secondary structure?
Alpha helix Beta pleated sheets Turn
44
What is the alpha helix secondary structure?
A spiral formed by twisting the polypeptide chain and stabilising with hydrogen bonds (R group sticks outwards)
45
What is the beta pleated sheet secondary structure?
Parts of the polypeptide chain running along side each other forming a corrugated sheet with R groups sitting above and below
46
What is a parallel Beta pleated sheet?
When all the N termini of successive strands are oriented in the same direction
47
What is an anti-parallel beta pleated sheet?
When successive beta strands alternate directions so that the N-terminus of one strand is adjacent to the C-terminus of the next
48
What can a polypeptide chain also form?
Turns where the chain folds back on itself
49
What is the tertiary protein structure?
The final folded shape of the polypeptide (due to stabilised interactions between R groups
50
What are the five possible interactions between R groups? (Secondary structure brings them close enough to interact)
Hydrophobic interactions Ionic bonds London dispersion forces Hydrogen bond Disulphide bridges
51
What are hydrophobic interactions?
Because hydrophobic R grips are repelled by water, they end up to the inside of the polypeptide away from water = hydrophobic interactions
52
What are ionic bonds?
Strongly charged and attracted to each other COOH and NH2 groups ionised to COO- and NH 3+
53
What are London dispersion forces?
We attractions between the electron cloud of atoms May result in attraction or repulsion
54
What are hydrogen bonds?
Weak electrostatic forces of attraction between hydrogen atom and electronegative atoms such as oxygen or nitrogen
55
What are disulphide bridges?
Covalent bonds between sulphur containing R groups
56
What is quaternary structure?
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
What is a prosthetic group?
Non-protein units tightly bound to a protein and necessary for its function
58
How does temperature affect protein?
Increasing temperature denatures the protein as it begins to unfold
59
How does pH affect a protein?
As pH increases or decreases the normal ionic interactions are lost gradually changing the confirmation of the protein, denaturing it
60
What is a ligand?
Substance that can bind to a protein
61
What happens as a ligand binds to a protein binding site?
The confirmation of the protein changes causing a functional changes as well
62
What are allosteric interactions?
Interactions between spatially distinct sites on the same protein
63
What are allosteric enzymes?
Any enzymes whose activity is regulated by altering its conformation
64
What is the second type of site on an allosteric enzyme called?
Allosteric site
65
What are modulators?
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
What are the two types of modulators?
Positive and negative
67
What is a positive modulator?
Activators that increase the enzymes affinity for the substrate
68
What are negative modulators?
Inhibitors that reduce the enzymes affinity for the substrate
69
What is cooperativity?
When changes in binding at one sub unit, alter the affinity of the remaining subunits
70
What can cause reversible confirmational change in proteins?
The additional removal of a phosphate (common in post translational modification)
71
What is phosphorylation and dephosphorylation?
Phosphorylation-addition of phosphates Dephosphorylation -removal of phosphate
72
What do protein kinases do?
Catalyse the transfer of the terminal phosphate of ATP to specific R groups of other proteins (KAPO)
73
What do protein phosphatases do?
Catalyse the reverse reaction or transfer a phosphate group from proteins onto ADP to regenerate ATP (PEPA)
74
What are the effects of phosphorylation?
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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