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ah bio > 1.2 > Flashcards

1.2 Flashcards

1
Q

Proteome

A

The proteome is entire set of proteins expressed by a genome

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2
Q

Why is a proteome larger than the number of genes?

A

The proteome is larger than a number of genes, particularly in eukaryotes, because more than one protein to be produced. This is partly partly due to alternative RNA splicing and also due to post translational modifications of proteins

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3
Q

Are all genes expressed as proteins in a particular cell type?

A

Not all genes are expressed as protein is in a particular cell type.

E.g. DNA is transcribed but not translated

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4
Q

Genes that don’t code for proteins

A

Genes that don’t 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

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5
Q

What conditions effects expressed proteins

A

The set of proteins expressed by a given cell type can vary over time and under different conditions
- metabolic activity of the cell
- cellular stress
- response to signalling molecules
- diseased vs healthy cells

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6
Q

Genome

A

The genome of an organism is its entire hereditary information encoded in DNA.

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7
Q

Parts of cytoplasm

A

Cytosol (the liquid)

Organelles which have their own membranes around them - ER, Golgi apparatus, mitochondria and chloroplasts and membrane bound organelles

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8
Q

What do eukaryotic cells have?

A

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

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9
Q

Eukaryotic cells and their size

A

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

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10
Q

Name the internal membranes

A

Endoplasmic reticulum

Golgi apparatus

Lysosomes

Vesicles

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11
Q

Endoplasmic reticulum

A

The endoplasmic reticulum forms a network of membranes tubules continuous with the nuclear membrane

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12
Q

Golgi apparatus

A

Golgi apparatus is a series of flattened membrane disks

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13
Q

Lysosomes and what they digest

A

Lysosomes are membrane bound organelles, containing a variety of hydrolases (digestive enzymes) that digest proteins, lipids, nucleic, acids, and carbohydrates

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14
Q

Vesicles

A

Vesicles transport materials between membrane compartments

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15
Q

Where are lipids and proteins synthesised?

A

Lipids, – SER

Proteins, – SER, RER

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16
Q

Describe smooth endoplasmic reticulum (SER)

A

SER has no ribosomes on surface

The enzymes embedded in this membrane synthesise lipids and steroid hormones

SER metabolises carbohydrates and aids in the detoxification of drugs and other toxins

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17
Q

Describe rough endoplasmic reticulum (RER)

A

RER has ribosomes on its cytosolic surface to assemble proteins

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18
Q

What happens once lipids are synthesised?

A

Lipids are synthesised in the SER and inserted into its membrane

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19
Q

Where does the synthesis of all proteins begin?

A

The synthesis of all proteins begins in cytosolic ribosomes but some will be embedded within the membrane (transmembrane proteins) or secreted to be used outside the cell

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20
Q

What does secrete proteins have?

A

Proteins that follow the secretary pathway have a signal sequence

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21
Q

What is a signal sequence?

A

The 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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22
Q

What do Embedded/transmembrane proteins have?

A

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

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23
Q

What happens after the ribosomes have docked with the RER?

A

After docking, the cytosolic particle and signal sequence are removed and translation of the protein continues.

The ribosome is released back into the cytosol

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24
Q

What happens to transmembrane proteins as they are translated

A

As the polypeptide chain is translated, it is inserted directly into the membrane of the ER, it does not into the lumen.

(It is now transmembrane protein in the ER membrane)

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25
Q

Polypeptides that are to become part of the lysosome enzyme or be secreted proteins

A

Polypeptides that are to become part of a lysosome enzyme or are to become a secreted protein are

  • made in the cytosolic ribosome
  • and have a signal sequence that takes the ribosome to the RER.
  • they are released directly into the lumen of the RER.
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26
Q

Golgi apparatus functions

A

The Golgi apparatus is a series of flattened membrane discs. They are especially well developed in secretory cells.

  • Production of glycoproteins
  • secretion of carbohydrate involved in the production of new cell walls
  • Production of secretory enzymes
  • Transport and storage of lipids
  • Formation of lysosomes
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27
Q

What happens to proteins once they are in the ER?

A

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

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28
Q

What happens to proteins as they move through the Golgi apparatus

A

Add proteins move through the Golgi apparatus they undergo post translational modification

This modification can take the form of the addition of carbohydrates to form a glycoprotein. Most secreted proteins are glycoproteins.

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29
Q

What is the proteins major modification?

A

Addition of carbohydrate groups to form glycoproteins

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30
Q

What do vesicles do when they leave the Golgi apparatus

A

Vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes

31
Q

Examples of secreted proteins

A

Peptide hormones and digestive enzymes

32
Q

The secretory pathway

A

Secreted proteins are initially created by cytosolic ribosomes and are translated in ribosomes on the RER and enter its lumen, then into the Golgi apparatus where they undergo post translational modifications.

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.

33
Q

What do inactive precursors require

A

Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins. This type of post-translational modification involves removing a short section of amino acids.

34
Q

What are Lysosomes functions

A

Destruction of worn out cell organelles

The digestion of material engulfed by a cell

Release of enzymes outside the cell (exocytosis) to digest external material

The complete digestion of a cell after its death (autolysis)

35
Q

Proteins - polymers

A

Proteins are polymers of amino acids, monomers

36
Q

What joins amino acids?

A

Amino acids are linked by peptide bonds to form polypeptides which then form proteins

37
Q

What determines the characteristics of an amino acid?

A

The R-groups determines the characteristics of an amino acid.

38
Q

Types of amino acid

A

Basic (positively charged)

Acidic (negatively charged)

Polar

Hydrophobic

39
Q

Describe Acidic (negatively charged) amino acids

A

Acidic amino acids are polar and have a second carboxyl group or carboxylic acid.

They tend to donate their hydrogen atom. They are hydrophilic meaning they can form bonds with water.

40
Q

Describe basic (positively charged) amino acids

A

Basic amino acids are polar and hydrophilic. They can form bonds with water. The key components of their R-group is the extra amine group (NH2).

41
Q

Describe polar amino acids

A

Polar amino acids are hydrophilic, so can form bonds with water.

They are not charged.

The key component of their R-group are the hydrophilic groups, such as carbonyl (C=O), hydroxyl (OH), or amine (NH) groups

42
Q

Describe hydrophobic (non-polar) amino acids

A

The key component of there R-group is a hydrocarbon group. Say chains which have pure hydrocarbon alkyl groups (alkane branches) or aromatic (benzene rings) are nonpolar

43
Q

What is made when amino acids join together?

A

When amino acids join together, a peptide bond is formed between the carboxylic acid terminal of one amino acid and the amine terminal of another amino acid

This is a condensation reaction as water is produced

44
Q

What is the primary structure of a protein?

A

The primary structure of a protein is the order in which the amino acids are synthesised by translation in the polypeptide

45
Q

What makes the secondary structure of a protein?

A

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

This results in alpha helicis, parallel or antiparallel beta sheets, or turns. These cause the proteins to have a 3-D shape as the linear polypeptide backbone begins to fold.

46
Q

What does the polypeptide fold into?

A

The polypeptide folds into a tertiary structure

47
Q

How is the tertiary structure stabilised?

A

The confirmation/tertiary structure is stabilised by interactions between the R-groups.
These are:

Hydrogen bonds

Hydrophobic and hydrophilic interactions

Ionic bonds

Disulphide bridges

London dispersion forces

48
Q

What are disulphide bridges?

A

Disulphide bridges are covalent bonds between R-groups containing sulphur

49
Q

What is the quaternary structure of a protein?

A

Quaternary structure is the overall protein that results from the aggregation of two or more polypeptide chains to make one functional macromolecule.

50
Q

What are prosthetic groups?

A

Prosthetic groups are additional non-protein structures that are tightly bound to a protein and give it its final function

51
Q

How does temperature affect protein structure?

A

Increasing temperature disrupts the interactions that hold a protein in shape. The protein begins to unfold (loss of tertiary structure), eventually becoming denatured.

52
Q

How does pH affect protein structure?

A

Changes in pH affect the concentration of H+ and OH- ions in solution.

The charges on acidic and basic R groups are affected by pH. As pH increases or decreases from the optimum, the normal ionic interactions between charged groups or lost, which gradually changes the conformation of the protein until it becomes denatured

53
Q

What is a ligand?

A

A ligand is a substance that can bind to a protein

54
Q

R group is not involved in protein folding

A

R groups not involved in the territory structure of a protein allow the protein to bind to other molecules. These sites on the surface of globular proteins are called ligand binding sites.

55
Q

Describe ligand, binding sites

A

Ligand binding sites have complimentary shape and chemistry to the ligand

56
Q

What happens when a ligand and protein bind?

A

As a ligand binds to a protein binding site, the conformation of the protein changes. This causes a change in function of the protein.

57
Q

Where do allosteric interactions occur?

A

Allosteric interactions occur between spatially distinct sites

58
Q

What happens when a substrate binds to 1 active site of an allosteric enzyme?

A

The binding of a substrate molecule to 1 active site of an allosteric enzyme increases the affinity of the other active sites for binding of subsequent substrate molecules.

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

59
Q

What do many allosteric proteins consist of?

A

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

60
Q

What do allosteric proteins with multiple subunits show?

A

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

61
Q

What are the sites of allosteric enzymes?

A

Active site.

Allosteric site

62
Q

What do modulators do?

A

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

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

63
Q

Describe positive modulators

A

Positive modulators increase the enzymes affinity for the substrate

(Enhanced affinity = allosteric activation)

64
Q

Describe negative modulators

A

Negative modulators decrease the enzymes affinity for the substrate

(Reduced affinity = allosteric inhibition)

65
Q

Describe the oxygen – haemoglobin dissociation curve

A

The oxygen dissociation curve has a sigmoid sheet, showing that the haemoglobin hold less oxygen in low, oxygen surroundings and hold more oxygen in higher oxygen surroundings. This is due to co-operative binding.

66
Q

What does cooperative binding mean?

A

Cooperative binding means that haemoglobin has a greater ability to bind to oxygen after a subunit has already bound to oxygen

67
Q

Describe temperatures affect on the binding of oxygen

A

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

68
Q

Describe the effect of pH on the binding of oxygen

A

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

69
Q

Describe what happens from the addition of removal of phosphate from particular R groups

A

The addition of removal of phosphate from particular R groups can cause reversible conformational change in proteins.

This is a common form of post translational modification

70
Q

What does the protein kinase do?

A

The protein kinase is an enzyme that catalyses the phosphorylation of proteins.

Kinase adds phosphate groups from high energy donor molecules to specific target molecules.

71
Q

What does the protein phosphatases do?

A

The protein phosphatase is an enzyme that catalyses the dephosphorylation of proteins.

(Removes phosphate groups)

72
Q

What does phosphorylation cause

A

Phosphorylation brings about conformational change which can affect a proteins activity

73
Q

What happens to proteins due to phosphorylation?

A

Some proteins are activated by phosphorylation, while others are inhibited.

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

ah bio (6 decks)

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