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ADVANCED HIGHER BIOLOGY > UNIT 1 - KA2 > Flashcards

UNIT 1 - KA2 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

What is an organisms genome

A
  • the genome is the total genetic material in a cell
    This includes chromosomal DNA and the extra chromosomal and also the RNA in all forms in the cell
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3
Q

Why is the proteome larger than an organisms 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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4
Q

What is selective gene expression

A

Not all genes are expressed as proteins in a particular cell

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5
Q

What are genes that do not code for proteins called

A

Genes that do not code for proteins are called non-coding RNA genes

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6
Q

What do non coding RNA genes include (3)

A

include those that are transcribed to produce tRNA, rRNA, and RNA molecules that control the expression of other genes.

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7
Q

How can the set of proteins expressed by a given cell type

A

The set of proteins expressed by a given cell type can vary over time and under different conditions

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8
Q

What are some factors affecting the set of proteins expressed by a given cell type (4)

A

the metabolic activity of the cell,
cellular stress,
the response to signalling molecules,
and diseased versus healthy cells.

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9
Q

What system do eukaryotic cells

A

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

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10
Q

What type of surface area and volume ratio do eukaryotes have

A

Because of their size, eukaryotes have a relatively small surface area to volume ratio.

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11
Q

What does the endoplasmic reticulum form a network of

A

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

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12
Q

What is the plasma membrane to small to carry out

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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13
Q

What is the Golgi apparatus a series of

A

The Golgi apparatus is a series of flattened membrane discs

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14
Q

What are lysosomes

A

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

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15
Q

What do vesicles transport

A

Vesicles transport materials between membrane compartments

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16
Q

What are the two types of endoplasmic reticulum

A
  • rough endoplasmic reticulum
  • smooth endoplasmic reticulum
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17
Q

What is the main difference between rough and smooth endoplasmic reticulum

A
  • rough ER has ribosomes on its systolic face
  • smooth ER lack ribosomes
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18
Q

What are hydrolases

A

Hydrolases are enzymes that catalyse the cleavage of a covalent bond using water

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19
Q

Describe the function of smooth endoplasmic reticulum

A

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

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20
Q

Where does the synthesis of all proteins begin

A

The synthesis of all proteins begins in cytosolic ribosomes

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21
Q

Cytosolic

A

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

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22
Q

Transmembrane proteins

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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23
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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24
Q

What is translation

A

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

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25
Q

What happens to the proteins when they are in the ER (after endoplasmic reticulum)

A

Once the proteins are made at a ribosome on the RER and put into the lumen of the RER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus

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26
Q

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

A

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

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27
Q

How do molecules move through Golgi discs

A

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

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28
Q

What do enzymes catalyse the addition of

A

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

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29
Q

Which is the major type of post - translational modification

A

The addition of carbohydrate groups is the major modification

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30
Q

Describe the function of vesicles after the Golgi apparatus

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

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31
Q

What are microtubules

A

Microtubules are structures that make up the cells cystoskeleton and offer support and a means of transport

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32
Q

Where are secreted proteins translated (SP 1)

A

Secreted proteins are translated in ribosomes on the RER and enter its lumen. They bud off the RER in a vesicle and go to the Golgi apparatus

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33
Q

What are two examples of substances which are secreted from a cell

A
  • peptide hormones
  • digestive enzymes
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34
Q

Where are the proteins packaged (SP2)

A

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

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35
Q

What happens to the secretory vesicles (SP 3)

A

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

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36
Q

How are many secreted proteins synthesised as (SP4)

A

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

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37
Q

What is proteolytic cleavage

A

Proteolytic cleavage is another type of post- translational modification.

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38
Q

What is an example of a protein which undergoes proteolytic cleavage

A

Digestive enzymes are one example of secreted proteins that require proteolytic cleavage to become active.

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39
Q

What determines the structure of a protein

A

Amino acid sequence determines protein structure

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40
Q

What are proteins polymers of

A

Proteins are polymers of amino acid monomers

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41
Q

What are amino acids linked by

A

Amino acids are linked by peptide bonds to form polypeptides

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42
Q

What do amino acids have the same of

A

Amino acids have the same basic structure, differing only in the R group present

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43
Q

How are amino acids classified

A

Amino acids are classified according to their R groups: basic (positively charged); acidic (negatively charged); polar; hydrophobic

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44
Q

What do R groups of amino acids vary in

A

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

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45
Q

What are the wide range of functions carried out by proteins the result of

A

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

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46
Q

What is the primary structure

A

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

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47
Q

Secondary structure

A

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

48
Q

What is a peptide bond

A

A peptide bond is a strong covalent bond between a carbon atom of one amino acid and the nitrogen atom of another amino acid.

49
Q

What is removed from between two amino acids

A

Water is removed from between the two amino acids to allow the bond to form

50
Q

What two groups do amino acids contain

A
  • an amine group
  • an acid group
51
Q

What are the 5 features of amino acids

A
  • central carbon
  • an amine
  • carboxylic acid
  • a hydrogen
  • variable R group
52
Q

Acidic R groups

A

Negatively charged amino acids are hydrophilic and the key component of their R group is a carboxylic acid group (negatively charged at pH 7)

53
Q

Basic R groups

A

Positively charged amino acids are hydrophilic and the key component of their R group is an anime group (positively charged at pH 7)

54
Q

Polar R groups

A

Polar amino acids are hydrophilic and the key component of their R group are hydrophilic groups, like carbonyl (c=o) hydroxyl (OH) or amine (NH)

55
Q

What are the four levels of Protein structure

A
  • primary structure
  • secondary structure
  • tertiary structure
  • quaternary structure
56
Q

What are the three types of secondary structure

A

alpha helixes , parallel or anti- parallel beta-pleated sheets, or turns

57
Q

Alpha helix

A

The alpha helix is formed by twisting the polypeptide chain into a helix and then stabilising with hydrogen bonding

58
Q

Where will a hydrogen bond from in an alpha helix

A

A hydrogen bond will form between every 4th amino acid in an alpha helix

59
Q

Beta sheet

A

The second main structure is called beta pleated sheet. The polypeptide chain is arranged In rows are linked with hydrogen bonding

60
Q

What can beta sheets be

A

Beta sheets can be either parallel or anti parallel

61
Q

What is a turn in the secondary structure of a protein

A

Turns are a third type of secondary structures it is a short section with no a/B structure. They reverse the direction of the polypeptide chain and are stabilised by hydrogen bonds

62
Q

What does the polypeptide fold into

A

The polypeptide folds into a tertiary structure

63
Q

What are disulphide bridges

A

Disulfide bridges are covalent bonds between R groups containing sulfur.

64
Q

What are tertiary structures

A

Tertiary structure refers to the overall folding of the polypeptide and its final shape.

65
Q

What is folding at the tertiary structure level stabilised by

A

By many different interactions between R groups of the amino acids

66
Q

What is tertiary structure brought about by

A

Tertiary structure is brought about by charge effects such as interactions of the R groups in hydrophobic regions

67
Q

What are the several possible R group interactions (5)

A
  • hydrophobic interactions
  • ionic bonds
  • London dispersion forces
  • hydrogen bonds
  • disulphide bridges
68
Q

Hydrophobic interactions

A
  • hydrophobic amino acids tend to cluster together on the interior of a protein, away from the surface
  • hydrophobic amino acids will predominate at the surface of a soluble protein. This hydrophobic effect is one of the main driving forces of protein folding
69
Q

Ionic bonding

A

The COOH and NH2 groups ionise to become COO- and NH3+. These groups are strongly charged and can attract each other

70
Q

London dispersion forces

A

Very weak attractions between the electron clouds of atoms

71
Q

Hydrogen bonding

A

The weak negative charge of the oxygen of c=o is attracted to the weak positive charge on a hydrogen of an OH or NH2 group

72
Q

Which proteins does quaternary structure exist in

A

Quaternary structure exits in proteins with two or more connected polypeptide subunits which are linked by binds between the R groups of the polypeptide chains

73
Q

What does quaternary structure describe

A

Quaternary structure describes the spatial arrangement of the subunits.

74
Q

What is an example of a protein which shows quaternary structure

A

Haemoglobin consists of 4 domains (polypeptide chains) connected to a haem group

75
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

76
Q

What is the ability of haemoglobin to bind to oxygen dependant upon

A

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

77
Q

What can influence the interactions of the R groups

A

Interactions of the R groups can be influenced by temperature and pH

78
Q

What is the affect of increasing temperature

A

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

79
Q

What are the charges on acidic and basic R groups affected by

A

The charges on acidic and basic R groups are affected by pH

80
Q

What is the effect of pH on the normal ionic interactions

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.

81
Q

What will any factor that changes the interactions of the R groups change

A

Any factor that changes the interactions of the R groups will change the shape of the protein.

82
Q

What is a ligand

A

A ligand is a substance that can bind to a protein

83
Q

What type of groups can allow binding to proteins

A

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

84
Q

What features of binding sites are complementary to the ligand

A

Binding sites will have complementary shape and chemistry to the ligand

85
Q

What happens as a ligand binds to a protein binding site

A

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

86
Q

What happens as a result of the confirmation of a protein changing

A

This change in conformation causes a functional change in the protein

87
Q

What is an allosteric enzyme

A

An allosteric enzyme is an enzyme whose activity is regulated by altering its conformation

88
Q

What do allosteric interactions occur between

A

Allosteric interactions occur between spatially distinct sites

89
Q

What do allosteric enzymes contain along side an active site

A

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

90
Q

Draw a simple diagram to explain what the allosteric site of an enzyme is

A

Check jotter

91
Q

Active site =
Allosteric site =

A

Active site = substrate joins
Allosteric site = substance other than substrate joins

92
Q

What does the binding of a substrate molecule to one active site of an allosteric enzyme increase

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

93
Q

What can happen to the activity of allosteric enzymes

A

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

94
Q

What do many allosteric proteins consist of

A

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

95
Q

How can the rate of product formation be regulated

A

The rate of product formation (rate of reaction) by a metabolic pathway can be regulated by raising or lowering the activity of just one enzyme in the pathway

96
Q

Where do modulators bind in allosteric enzymes

A

In allosteric enzymes modulators bind at secondary binding sites (allosteric sites)

97
Q

How do modulators regulate the activity of the enzyme

A

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

98
Q

What happens following binding of a modulator

A

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

99
Q

Positive modulators

A

Positive modulators increase the enzyme’s affinity for the substrate and increase enzyme activity

100
Q

Negative modulators

A

Negative modulators decrease the affinity of the enzyme for the substrate and so decrease the enzyme activity

101
Q

What does the binding and release of oxygen in haemoglobin show

A

The binding and release of oxygen in haemoglobin shows co-operativity

102
Q

What do some proteins with quaternary structure show

A

Some proteins with quaternary structure show cooperatively between their polypeptide subunits

103
Q

What do changes in binding of oxygen at one subunit alter the affinity of

A

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

104
Q

What is the effect of a high temperature on haemoglobins affinity for binding oxygen

A

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

105
Q

What is the effect of low pH on haemoglobins affinity for binding oxygen

A

As pH decreases haemoglobin affinity for oxygen decreases

106
Q

What can the addition or removal of phosphate cause in proteins

A

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

107
Q

What is a common form of post translational modification

A

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

108
Q

What is the effect of protein kinase on protein

A

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

109
Q

What is the effect of protein kinase on ADP/ATP

A

The terminal phosphate of ATP is transferred to specific R groups

110
Q

What is the effect of protein phosphate on proteins

A

Protein phosphatases catalyse the reverse reaction

111
Q

What is the effect of protein phosphatase on ADP/ATP

A

They catalyse the transfer of a phosphate group from proteins onto ADP to regenerate ATP

112
Q

What type of changes does phosphorylation bring about

A

Phosphorylation brings about conformational changes which affect a proteins activity

113
Q

How is the activity of many cellular proteins, such as enzymes and receptors regulated

A

Through phosphorylation which brings about conformational changes and affects a proteins activity

114
Q

What are the two ways proteins are activated

A

Some proteins are activated by phosphorylation while others are inhibited

115
Q

What type of charge do phosphate groups add

A

Adding a phosphate group adds negative charges

116
Q

What can happen to ionic interactions in unphosphorylated proteins

A

Ionic interactions in the unphosphorylated protein can be disrupted and new ones created

ADVANCED HIGHER BIOLOGY (13 decks)

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