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Advanced Higher Biology > Unit 1 - Proteins > Flashcards

Unit 1 - Proteins 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 genome?

A

The proteome is larger than the number of
genes, particularly in eukaryotes, 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 are genes that do not code for proteins called?

A

Non-coding RNA genes

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4
Q

What do the Non-coding RNA genes code for and what do they do?

A

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

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5
Q

What are the factors affecting the set of proteins expressed by a cell?

A
  • metabolic activity of the cell
  • cellular stress
  • the response to signalling molecules
  • diseased versus healthy cells
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6
Q

What do eukaryotic cells have?

A

A system of internal
membranes

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7
Q

What does the system of internal membranes do for eukaryotic cells?

A

increases the total area of membrane

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8
Q

Because of their size, what do eukaryotic cells have?

A

A small surface area to volume ratio.

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9
Q

What does the small surface area to volume ratio of the eukaryotic cells cause?

A

The plasma membrane of eukaryotic cells is
therefore too small an area to carry out all the
vital functions carried out by membranes.

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10
Q

What does the endoplasmic reticulum do?

A

forms a
network of membrane tubules continuous
with the nuclear membrane

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11
Q

What does the Golgi apparatus do?

A

is a series of flattened
membrane discs

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12
Q

What do lysosomes do?

A

are membrane-bound organelles
containing a variety of hydrolases that digest
proteins, lipids, nucleic acids and
carbohydrates

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13
Q

What do vesicles do?

A

transport materials between
membrane compartments

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14
Q

Where are proteins and lipids synthesised?

A

In the ER

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15
Q

What is the difference between the RER and SER?

A

Rough ER (RER) has ribosomes on its
cytosolic face while smooth ER (SER) lacks
ribosomes.

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16
Q

Where are lipids synthesised and what happens to them?

A

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

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17
Q

What does synthesis of all proteins take place?

A

Cytosolic ribosomes.

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18
Q

What happens during the synthesis of cytosolic proteins?

A

The synthesis of cytosolic proteins is
completed in the cytosolic ribosomes, and these proteins remain in the cytosol

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19
Q

What do transmembrane proteins do during synthesis?

A

Transmembrane proteins carry a signal
sequence, which halts translation and directs
the ribosome synthesising the protein to dock with the ER, forming RER

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20
Q

What is a signal sequence?

A

A signal sequence is a short stretch of amino
acids at one end of the polypeptide that
determines the eventual location of a protein
in a cell.

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21
Q

What does the amino acid sequence determine?

A

determines protein
structure

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22
Q

What are proteins polymers made up of?

A

amino acid monomers

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23
Q

How are amino acids linked?

A

Amino acids are linked by peptide bonds

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24
Q

What do linked amino acids form

A

to form polypeptides

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25
Q

How are amino acids similar?

A

Amino acids have the same basic structure

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26
Q

How are amino acids different?

A

differing only in the R group present

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27
Q

How are R groups different?

A

R groups of amino acids vary in size, shape,
charge, hydrogen bonding capacity and
chemical reactivity

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28
Q

How are amino acids classified?

A

Amino acids are classified according to their R groups

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29
Q

What does it mean if an amino acid is basic?

A

It is positively charged

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30
Q

What does it mean if an amino acid is acidic?

A

It is negatively charged

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31
Q

What does it mean if an amino acid is polar?

A

It has differing charges

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32
Q

What does it mean if an amino acid is hydrophobic?

A

It hates water

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33
Q

If an amino acid is basic, what molecules will it have attached to it?

A

NH2 or NH3

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34
Q

If an amino acid is acidic, what molecules will it have attached to it?

A

COO or COOH

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35
Q

If an amino acid is polar, what molecules will it have attached to it?

A

OH

36
Q

If an amino acid is hydrophobic, what molecules will it have attached to it?

A

Hydrocarbon

37
Q

Other than shape, what else determines the function of the protein?

A

The wide range of functions carried out by
proteins results from the diversity of R groups

38
Q

What is the primary structure of a protein?

A

The primary structure is the sequence in
which the amino acids are synthesised into
the polypeptide

39
Q

What is the secondary structure of a protein?

A

Hydrogen bonding along the backbone of the
protein strand results in regions of secondary
structure

40
Q

What type of bonding is involved in secondary protein structure?

A

Hydrogen bonding

41
Q

What are examples of secondary structure?

A

alpha helices, parallel or antiparallel beta-pleated sheets, or turns

42
Q

What does a polypeptide fold into?

A

Tertiary structue

43
Q

What is the bonding tertiary structures?

A

Interactions between R groups involving hydrophobic interactions, ionic bonds, London dispersion forces, hydrogen bonds; disulfide bridges

44
Q

What are disulfide bridges?

A

Disulfide bridges are covalent bonds between
R groups containing sulfur.

45
Q

What are quaternary protein structures?

A

Quaternary structure exists in proteins with
two or more connected polypeptide subunits

46
Q

What does quaternary structures describe?

A

Quaternary structure describes the spatial
arrangement of the subunits.

47
Q

What is a prosthetic group?

A

A prosthetic group is a non-protein unit tightly
bound to a protein and necessary for its
function

48
Q

What does the binding of haemoglobin to oxygen depend on

A

non-protein haem group

49
Q

What does increasing the temperature do to the protein structure?

A

Increasing temperature disrupts the
interactions that hold the protein in shape;
the protein begins to unfold, eventually
becoming denatured.

50
Q

What causes the changes to acidic and basic R groups?

A

pH

51
Q

What does increasing/decreasing pH from optimum do to the protein structure?

A

As pH increases or decreases from the
optimum, the normal ionic interactions
between charged groups are lost, which
gradually changes the conformation of the
protein until it becomes denatured.

52
Q

What is a ligand?

A

A ligand is a substance that can bind to a
protein

53
Q

Where can ligands bind to in a protein?

A

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

54
Q

How do ligands bind to proteins?

A

Binding sites will have complementary shape
and chemistry to the ligand

55
Q

What happens to a protein when a ligand binds to it?

A

As a ligand binds to a protein-binding site the
conformation of the protein changes

56
Q

What does the binding of the ligand affect as a result of the conformational change?

A

This change in conformation causes a
functional change in the protein

57
Q

What are allosteric interactions?

A

The binding of a substrate molecule to one active site of an allosteric enzyme increases the affinity of the other active sites for binding of subsequent substrate molecules.

58
Q

Why are allosteric interactions important?

A

This is of biological importance because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration.

59
Q

What is co-operativity?

A

changes in binding at one subunit alter the
affinity of the remaining subunits

60
Q

What do modulators do?

A

Modulators regulate the activity of the
enzyme when they bind to the allosteric site

61
Q

What happens when a modulator binds to an enzyme?

A

Following binding of a modulator
- the conformation of the enzyme changes and this
- alters the affinity of the active site for the substrate

62
Q

What do positive modulators do?

A

Positive modulators increase the enzyme’s
affinity for the substrate

63
Q

What do negative modulators do?

A

negative
modulators reduce the enzyme’s affinity.

64
Q

How does the binding of oxygen in haemoglobin show co-operativity?

A

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

65
Q

What conditions result in the reduced binding of oxygen in haemoglobin?

A

A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced.

66
Q

What conditions result in increased oxygen delivery?

A

Reduced pH and increased
temperature in actively respiring tissue will
reduce the binding of oxygen to haemoglobin
promoting increased oxygen delivery to tissue

67
Q

What does the addition or removal of phosphate cause?

A

The addition or removal of phosphate can cause reversible conformational change in proteins

68
Q

What is the addition or removal of phosphate known as?

A

This is a common form of post-translational
modification

69
Q

What do protein kinases catalyse?

A

Protein kinases catalyse the transfer of a
phosphate group to other proteins

70
Q

What happens to the phosphate group when it is added to the protein?

A

The terminal phosphate of ATP is transferred
to specific R groups

71
Q

What do protein phosphatase catalyse?

A

The removal of a phosphate group from a protein.

72
Q

What does phosphorylation do to the structure of the protein and what does it affect?

A

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

73
Q

What happens when a phosphate group is added to a protein?

A

Adding a phosphate group adds negative
charges. Ionic interactions in the
unphosphorylated protein can be disrupted and new ones created.

74
Q

How do molecules move through the Golgi apparatus?

A

Molecules move through the Golgi discs in
vesicles that bud off from one disc and fuse to the next one in the stack.

75
Q

What happens to the proteins that move through the Golgi apparatus?

A

undergo post-translational
modification

76
Q

What is the major modification during post translational modification?

A

The addition of carbohydrate groups is the
major modification

77
Q

How do the proteins leave the Golgi apparatus?

A

Proteins leave in vesicles that take proteins to the plasma membrane and lysosomes

78
Q

How do vesicles move around in the cell?

A

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

79
Q

What happens to the proteins once they are in the ER?

A

Once the proteins are in the ER, they are
transported by vesicles that bud off from the
ER and fuse with the Golgi apparatus

80
Q

Where are secreted proteins translated and what happens to them?

A

Secreted proteins are translated in ribosomes
on the RER and enter its lumen

81
Q

What are examples of secreted proteins?

A

Peptide hormones and digestive enzymes
are examples of secreted proteins.

82
Q

What happens to the secreted proteins at the Golgi apparatus?

A

The proteins move through the Golgi apparatus and are then packaged into secretory vesicles

83
Q

What happen to the secretory vesicles after the Golgi apparatus?

A

These vesicles move to and fuse with the
plasma membrane, releasing the proteins out
of the cell

84
Q

What might be required for secretory proteins to work?

A

Many secreted proteins are synthesised as
inactive precursors and require proteolytic
cleavage to produce active proteins

85
Q

What is proteolytic cleavage?

A

Proteolytic cleavage is another type of post-translational modification. Digestive enzymes are one example of secreted proteins that require proteolytic cleavage to become active.

86
Q

What do enzymes do in the Golgi apparatus?

A

Enzymes catalyse the addition of various sugars in
multiple steps to form the carbohydrates.

Advanced Higher Biology (31 decks)

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