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Advanced Higher Biology > Unit 1: Key Area 2 > Flashcards

Unit 1: Key Area 2 Flashcards

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1
Q

What is a proteome?

A

The proteome is all of the proteins made by a genome (genetic sequences of bases found on DNA)

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2
Q

Explain why the proteome is bigger 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

Protein structure

What determines the structure of a protein

A

The structure of a protein is determined by the sequence of amino acids

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4
Q

Protein structure

What are proteins and what are they made up of

A

Proteins are polymers made up of amino acid monomers

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5
Q

Protein structure

What are amino acids linked by and what do they form

A

The amino acids are linked by peptide bonds to form polypeptides

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6
Q

Protein structure

What determines an amino acids characteristics

A

All amino acids have the same basic structure apart from their R group.
The R group of used to classify each amino acid. They can be described as basic, acidic, polar or hydrophobic.

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7
Q

Protein structure

Describe the characteristics of R groups

A

The R groups vary in size, shape, change, their ability to form hydrogen bonds and chemical reactivity.

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8
Q

Classifying amino acids
Describe a basic amino acid and what group it contains.
Name 3 examples

A

Basic- hydrophilic contain anime group (N+H)

Examples: Hisitidine, Lysine & Arginine

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9
Q

Classifying amino acids
Describe an acidic amino acid and what group it contains.
Name 3 examples

A

Acidic- Hydrophilic contain COOH-

Examples: Aspartic Acid & Glutamic acid

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10
Q

Classifying amino acids
Describe a polar amino acid and what group it contains.
Name 3 examples

A

Polar- Hydrophilic contains C=O, NH or OH

Examples: Cysteine, Serine & Theronine

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11
Q

Levels of protein structure

What will determine the structure and function of an protein

A

As the R groups on the amino acids are quite different, the order which they take to form a protein will determine a structure which will dictate its function.

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12
Q

Levels of protein structure

How many different levels of protein structures are there

A

There are 4 different levels of protein structure

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13
Q

Describe the primary structure in proteins

A

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

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14
Q

Describe the secondary structure in proteins

A

The arrangement of amino acids in the primary structure results in the secondary structure where hydrogen bonding along the backbone of the protein strand results in regions of secondary structure — alpha helices, parallel or anti- parallel beta-pleated sheets, or turns

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15
Q

Describe the tertiary structure in proteins

A

Then the folded tertiary structure is made by interactions between R groups:
The conformation is stabilised by interactions between R groups: hydrophobic interactions, ionic bonds, London Dispersion Forces, hydrogen bonds and disulfide bridges

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16
Q

What are disulfide bridges

A

Disulfide bridges (covalent bonds between R groups containing sulfur)

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17
Q

In what proteins do quaternary structures exists

A

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

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18
Q

What does the quaternary structure describe

A

The quaternary structure describes the spatial arrangement of subunits

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19
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.

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20
Q

What is the ability of haemoglobin to bind with oxygen

A

The ability of haemoglobin to bind oxygen is dependent upon the non protein haem group

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21
Q

What factors affect R group interactions

A

Temperature and pH are factors which can affect the interactions between R groups

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22
Q

Describe what happens to the R group interactions when you increase the temperature

A

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

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23
Q

Describe what happens the the R group interactions in proteins and the charges on acidic and basic R groups by changing the pH

A

The charges on the acidic and basic R groups are affected by pH. As pH increases and 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.

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24
Q

What does ligand binding do to a protein

A

Ligand binding changed the conformation of a protein

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25
Q

What is a ligand

A

A ligand is a substance that bacon bind to a protein

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26
Q

What can happen to the R groups that are not involved in protein folding

A

R groups which are not involved in protein folding can allow ligand binding

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27
Q

Describe the R group binding site

A

The R group binding sites will have a complementary shape and chemistry to the ligand

28
Q

What happens to the ligand when it binds to a protein binding site

A

When the ligand binds to a protein binding site the conformation of the protein changes
This change in conformation causes a functional change in proteins

29
Q

Where do allosteric interactions occur and what does this mean

A

Allosteric interactions occur between spatially distinct sites. This means a molecule binds at one site and has an effect on another

30
Q

What do allosteric enzymes contain

A

Allosteric enzymes contain a second type of site, called an allosteric site

31
Q

Describe the binding of a substrate molecule to one active site of an allosteric enzyme

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
This is biologically important because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration

32
Q

Describe the structure of allosteric proteins

A

Many allosteric proteins consist of multiple subunits (have quaternary structure)

33
Q

What do allosteric proteins with multiple subunits show

A

Allosteric proteins with multiple subunits show co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits

34
Q

What do modulators do

A

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

35
Q

What happens after the binding of a modulator

A

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

36
Q

What do positive and negative modulators do to the enzyme’s affinity

A

Positive modulators increase the enzyme’s affinity for the substrate whereas negative modulators reduce the enzyme’s affinity for the substrate

37
Q

What does the binding and release of oxygen in haemoglobin show

A

The binding and release of oxygen in haemoglobin shows co operativity.
Changes in binding of oxygen at one subunit alters the affinity of the remaining subunits for oxygen

38
Q

Describe the influence and physiological importance of temperature on the binding of oxygen

A

An increase in temperature lowers the affinity of haemoglobin for oxygen so the binding of oxygen is reduced

An increase of temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue

39
Q

Describe the influence and physiological importance of pH on the binding of oxygen

A

A decrease in pH lowers the affinity of haemoglobin for oxygen so the binding of oxygen is reduced

A decrease of pH in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue

40
Q

How does the addition or removal of phosphate affect proteins

A

The addition or removal of phosphate can cause reversible conformational change in proteins
This is a common form of post translational modification

41
Q

What do protein kinases catalyze

A

Protein kinases catalyze the transfer of a phosphate group to other proteins
ATP —> ADP + Pi

42
Q

What happens to the terminal phosphate of ATP

A

The terminal phosphate of ATP is transferred to specific R groups

43
Q

What does protein phosphatases catalyze

A

protein phosphatases catalyses the reverse reaction
Removes phosphate from molecule
ADP + Pi —-> ATP

44
Q

What does phosphorylation bring about

A

Phosphorylation brings about conformational changes, which can affect a protein’s activity
The activity of many cellular proteins such as enzymes and receptors is regulated in this way

45
Q

What does phosphorylation do to proteins

A

Some proteins are activated by phosphorylation while others are inhibited
This is because adding a phosphate group adds negative charges. Ionic interactions in the unphosphorylated protein can be disrupted and new ones created.

46
Q

Are all genes expressed as proteins in a cell. Explain why?

A

Not all genes are expressed as proteins in a particular cell type
Genes that do not code for proteins are called non-coding RNA genes and include those that are transcribed to produce tRNA, rRNA and RNA molecules that control the expression of other genes

47
Q

What affects the set of proteins produced by a given cell

A

The set of proteins expressed by a given cell type can vary over time and under different conditions
Some factors affecting the set of proteins expressed by a given cell type are the metabolic activity of the cell, cellular stress, the response to signalling molecules, and diseased versus healthy cells.

48
Q

Describe the structure of eukaryotic cells

A

Eukaryotic cells have a system of internal membranes, which increases the total area of membrane

Because of their size, eukaryotes have a relatively small surface area to volume ratio. The plasma membrane of eukaryotic cells is therefore too small an area to carry out all the vital functions carried out by membranes.

49
Q

What does the endoplasmic reticulum (ER) form

A

The endoplasmic reticulum (ER) forms a network of membrane tubules continuous with the nuclear membrane

50
Q

What is the Golgi apparatus

A

The Golgi apparatus is a series of flattened membrane discs

51
Q

What are lysosomes

A

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

52
Q

What do vesicles do

A

Vesicles transport materials between membrane compartments

53
Q

What do Rough ER (RER) and smooth ER (SER) contain

A

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

54
Q

Where are Lipids synthesized and what happens to it afterwards

A

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

55
Q

Where does the synthesis of all proteins begin and where do cytosolic proteins finish synthesis

A

The synthesis of all proteins begins in cytosolic ribosomes

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

56
Q

What do transmembrane proteins carry and what does it do

A

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

57
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.

58
Q

When does translation continue and what happens to the protein

A

Translation continues after docking, and the protein is inserted into the membrane of the ER

59
Q

What happens once the proteins 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

60
Q

What happens as the proteins move through the Golgi apparatus

A

As proteins move through the Golgi apparatus they undergo post-translational modification

Molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack. Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates.

61
Q

What does the addition of a carbohydrate group do

A

The addition of carbohydrate groups is the major modification

62
Q

What do vesicles that leave the Golgi apparatus do

A

Vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes
Vesicles move along microtubules to other membranes and fuse with them within the cell

63
Q

Where ate secreted proteins translated

A

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

64
Q

Name examples of secreted proteins

A

Peptide hormones and digestive enzymes are examples of secreted proteins.

65
Q

What happens to the proteins once they are translated

A

The proteins move through the Golgi apparatus and are then packaged into secretory vesicles
These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell
Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins

66
Q

What is proteolytic cleavage and name an example of a certain types of secreted proteins that require proteolytic cleavage to become active.

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.

Advanced Higher Biology (12 decks)

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