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Advanced Higher Biology Unit 1 > Proteins > Flashcards

Proteins Flashcards

Stromg

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1
Q

What is meant by the proteome?

A

The entire set of proteins expressed/coded for by the genome.

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2
Q

Why is the proteome larger than the genome. (2 reasons)

A

Alternative RNA splicing and post translational modification.

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3
Q

Describe how different proteins are coded for through alternative RNA splicing.

A

Exons are spliced together whereas introns are discarded, different proteins are coded for based on what may be considered and intron or an exon.

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4
Q

What is post translational modification (give examples) and where might it occur?

A

Modification to complete the protein after translation. Can occur in the golgi apparatus with addition of various chemical groups such as carbohydrate or can happen outside the cell e.g. proteolytic cleavage.

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5
Q

Are all genes expressed as proteins in a given cell type? If not what do they do?

A

No. They may transcribed into functioning RNA mollecules.

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6
Q

Name 3 things that affect the set of proteins expressed by a given cell type under different conditions.

A

Diseased vs healthy cells, cellular stress, hormones.

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7
Q

Which cell type - eukaryotes or prokaryotes have membrane bound organelles giving a larger surface area to volume ratio and why?

A

Eukaryotes have membrane bound organelles because they are bigger and so need more surface area to keep their surface area to volume ratio high enough for the cell to be able to function.

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8
Q

What and where is the endoplasmic reticulum?

A

A network of membrane tubules continuous with the nuclear membrane, it can be rough or smooth.

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9
Q

What is the golgi apparatus?

A

A series of flattened membrane disks.

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10
Q

What is a lysosome and what does it do?

A

A membrane-bound organelle containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates, like recycling materials.

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11
Q

What is a vesicle, what does it do?

A

Very small membrane bound organelle - transports proteins and other mollecules inbetween membrane compartments within the cell.

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12
Q

Where are lipids synthesised?

A

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

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13
Q

Where does synthesis/translation of all proteins begin?

A

In cytosolic ribosomes.

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14
Q

What kind of protein is fully synthesised in the cytosol and where do they go?

A

Cytosolic proteins are completed here and remain in the cytosol.

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15
Q

Describe the translation of transmembrane proteins.

A

Translation begins on the ribosome in the cytosol, a signal sequence in the RNA halts translation and directs the ribosome synthesising the protein to dock with the ER, forming RER. Translation continues after docking, and the protein is inserted into the membrane of the ER.

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16
Q

How and where are transmembrane proteins transported to?

A

Transported in vesicles that bud off from the RER and then fuse with the Golgi apparatus.

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17
Q

What happens to proteins as they move through the Golgi apparatus?

A

They undergo post translational modification.

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18
Q

Name 2 modifications that take place in the Golgi apparatus.

A

Addition of carbohydrate groups and phosphorylation can occur here.

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19
Q

What 3 different pathways can a protein take from the Golgi apparatus?

A

Transported in vesicles to lysosomes, the plasma membrane or vesicles can fuse with the cell membrane and release the protein out the cell.

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20
Q

How do vesicles travel?

A

Vesicles move along microtubules to other membranes and fuse with them within the cell.

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21
Q

What is the name of a protein that leaves the cell?

A

Extracellular protein.

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22
Q

What do many secreted transmembrane proteins require to become active?

A

Proteolytic cleavage.

23
Q

What is the basic subunit of a protein and what bonds link them together?

A

Proteins are polymers of amino acid monomers. Peptide bonds link amino acids together.

24
Q

Describe the basic structure of an amino acid.

A

All amino acids have an Amine group (NH2), carboxyl group (COOH), and a specific r-group, unique to each kind of amino acid.

25
Q

What are the 4 classifications of amino acids based on r-group?

A

Polar (hydrophilic), non-polar (hydrophobic), acidic and basic.

26
Q

What structural feature makes an amino acid polar or non polar? What does this mean for proteins?

A

Polar r groups contain hydroxyl groups (OH), non polar r groups contain hydrocarbon chains e.g CH3. different r groups constitute a wide range of functions.

27
Q

Define primary protein structure.

A

The primary structure is the sequence in which the amino acids are synthesised into the polypeptide or the order of amino acids in the polypeptide chain.

28
Q

What kind of bonds stabilise secondary structure?

A

Hydrogen bonds. (Electrostatic force of attraction between polar molecules).

29
Q

Describe the different shapes that can be made in secondary structure.

A

Alpha helixes are a spiral like shape, like a spiral staircase, with r groups facing outwards. Beta pleated sheets are corrugated sheets which can be parallel or anti parallel with r groups sticking out above and below the sheet. Turns can also be made (a reversal in the direction of the polypeptide).

30
Q

The polypeptide chain makes a tertiary structure, name 5 different kinds of interactions that stabilise this structure.

A

Hydrophobic r group interactions, ionic bonds, hydrogen bonds, covalent disulfide bridges, London dispersion forces.

31
Q

What is quaternary structure and do all proteins have it?

A

The final protein consists of multiple polypeptide subunits. Not all proteins have quaternary structure, some are complete after tertiary.

32
Q

What is a prosthetic group? Give an example.

A

A non protein unit tightly bound to amino acid r groups not involved in protein folding, required for the protein to function. The haem group in haemoglobin carries oxygen.

33
Q

What 2 factors influence r group interaction? What can this cause in proteins if these factors are out with sensible limits?

A

Temperature and pH. Can cause denaturation of the protein due to a breakdown of tertiary and secondary structure due to extreme pH and or temperature.

34
Q

What is a ligand.

A

A ligand is a substance that can bind to a protein.

35
Q

What allows the binding of a ligand to take place?

A

R groups not involved in protein folding can allow binding to ligands.

36
Q

Binding sites will have complementary _____ and _________ to the ligand.

A

Shape and chemistry.

37
Q

What happens when a ligand binds to the protein’s binding site?

A

The conformation of the protein changes causing a functional change.

38
Q

What is an allosteric site on a protein?

A

A secondary, spatially distinct binding site.

39
Q

Define the term “cooperativity in binding”.

A

Changes in binding at one subunit alter the affinity of the remaining subunits for the ligand.

40
Q

What kind of protein strucutre is required for cooperativity?

A

Quaternary structure (multiple polypeptide subunits).

41
Q

Allosteric enzymes have a secondary site called an __________ ____.

A

Allosteric site.

42
Q

What is a modulator used for and how does it work?

A

Modulators regulate the activity of the enzyme by binding to the allosteric site, causing the conformation of the enzyme to change and so altering
the affinity of the active site for the substrate.

43
Q

What would be the effect on the rate of an enzyme controlled reaction if positive modulators specific the the enzyme were added and why?

A

Increacsed rate of reaction due to increased affinity of the enzyme’s active for the substrate. Negative modulators would have the opposite effect.

44
Q

How does the binding of a modulator effect enzyme conformation/shape and why is this important?

A

The binding of a modulator causes the conformation of the enzyme to change, altering the affinity of the active site for the substrate. This is important biologically as enzyme controlled rections can be regulated this way.

45
Q

Give one example of cooperativity in ligand binding.

A

The binding and release of oxygen in haemoglobin shows co-operativity. Any other relevant example, check youself.

46
Q

What change in pH and temperature would increase the affinity of haemoglobin for oxygen? How does your body use this to its advantage to maximise oxygen delivery?

A

Increase in pH decrease in temperature. Lungs are fairly neutral in pH and temperature compared with the rest of the body but during strenuos excercise, muscles get hot and acidic due to lactic acid buildup and chemical reactions taking place within them. Haemoglobin has low affinity for oxygen in your muscles so it is dropped there, this helps to increase oxygen delivery, this has great biological importance.

47
Q

Describe phosphorylation and what it does to protein structure/conformation.

A

Addition of a phosphate group which changes protein structure/conformation.

48
Q

Phosphorylation is a form of ____ _____________ modification.

A

Post translational.

49
Q

Name the enzymes that catalyse phosphorylation and dephosphorylation.

A

Protein kinases catalyse phosphorylation, protein phosphatases catalyse dephosphorylation.

50
Q

Where does a phosphate group come from and bind to?

A

The terminal phosphate of ATP binds to specific amino acid R-groups.

51
Q

How does phosphorylation/dephosphorylation change a protein’s activity?

A

Phosphorylation brings about conformational changes, which can affect a protein’s activity.

52
Q

The activity of many cellular proteins, such as enzymes and receptors, is regulated by _______________.

A

Phosphorlation or modulators.*

53
Q

What effect(s) does phosphorylation have on protein activity?

A

Some proteins are activated by phosphorylation while others are inhibited so it can increase or decrease activity.

Advanced Higher Biology Unit 1 (4 decks)

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