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Advanced Higher Biology Unit 1 > Key Area 2 - Proteins > Flashcards

Key Area 2 - Proteins Flashcards

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1
Q

The Proteome

A
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2
Q

What is a genome?

A

All the hereditary information encoded in DNA.

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3
Q

What is a proteome?

A

The proteome is the entire set of proteins expressed by a genome.

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4
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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5
Q

Not all genes are expressed as proteins in a particular cell type - why is this?

A

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

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6
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 (introns) and 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

What are factors that affect a set of proteins being expressed?

A

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.

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8
Q

The Synthesis and Transport of Proteins

Intracellular Membranes

A
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9
Q

Explain Eukaryotic cells

A

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

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10
Q

Explain the difficulty with the size of eukaryotes

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 an area to carry out all the vital functions carried out by membranes.

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11
Q

What does the Endoplasmic Reticulum (ER) form?

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 Golgi Apparatus?

A

The Golgi apparatus is a series of flattened
membrane discs.

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13
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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14
Q

What is the role of Vesicles?

A

Vesicles transport materials between
membrane compartments.

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15
Q

What is the cytoplasm?

A

The entire contents within the cell membrane, including organelles but not the contents of the nucleus.

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16
Q

What is the cytosol?

A

The intracellular fluid which surrounds the organelles.

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17
Q

Synthesis of Membrane Components

A
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18
Q

What is synthesised in the ER?

A

Lipids and proteins are synthesised in the ER.

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19
Q

Describe the difference between the Rough ER (RER) and the Smooth ER (SER)

A

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

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20
Q

What is synthesised in the SER?

A

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

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21
Q

Where does synthesis of proteins begin?

A

The synthesis of all proteins begins in
cytosolic ribosomes.

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22
Q

What protein synthesis is completed in the cytosolic ribosomes?

A

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

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23
Q

What do transmembrane proteins carry and what does this 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.

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24
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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25
Q

What happens after docking?

A

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

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26
Q

Movement of Proteins between Membranes

A
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27
Q

What happens after 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.

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28
Q

What happens as proteins move through the Golgi Apparatus?

A

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

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29
Q

Explain Post Translational Modification

A

PTM is the alteration of the protein after translation. PTM occurs in the RER, Golgi Apparatus or at the final functional site of the protein.
PTM can involve: the addition of a chemical group; the proteolytic cleavage of the polypeptide.

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30
Q

Name types of Post Translational Modifications

A

Lipidation - attaches a lipid, fatty acid to a protein.

Ubiquitination - adds ubiquitin to a lysine residue of a target protein.

Disulfide Bond - covalently links the ‘s’ atom of two different cysteine residues.

Acetylation - adds an acetyl group to the N-terminus of a protein to increase stability.

Glycosylation - attaches a sugar, usually to an ‘N’ or ‘O’ atom in an amino acid.

Phosphorylation - adds a phosphate to serine, threonine or tyrosine.

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31
Q

What is the major modification?

A

The addition of carbohydrate groups is the
major modification.

32
Q

Describe the steps in detail as proteins 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. Enzymes
catalyse the addition of various sugars in
multiple steps to form the carbohydrates.

33
Q

What happens to vesicles that leave 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.

34
Q

The Secretory Pathway

A
35
Q

Where are secreted proteins translated?

A

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

36
Q

Give examples of secreted proteins

A

Peptide hormones and digestive enzymes
are examples of secreted proteins.

37
Q

Explain the Secretory Pathway

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.

38
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.

39
Q

Protein Structure, Ligand Binding and Conformational Change

A
40
Q

What determines protein structure?

A

Amino acid sequence determines protein
structure.

41
Q

What are proteins?

A

Proteins are polymers of amino acid monomers.

42
Q

What are amino acids linked by?

A

Amino acids are linked by peptide bonds to form polypeptides.

43
Q

How to amino acids differ?

A

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

44
Q

What are R groups?

A

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

45
Q

How are amino acids classified?

A

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

46
Q

Name and describe the different R groups:

A

Acidic - (negatively charged) amino acids are hydrophilic and the key component of their R group is a carboxylic acid group (COOH).

Basic (positively charged) amino acids are hydrophilic and the key component of their R group is an amino acid group (NH2).

Hydrophilic amino acids are polar and the key component of their R group are hydrophilic groups, carboxyl (C=O), hydroxyl (OH) or amine (NH).

Hydrophobic amino acids are non-polar and the key component of their R group is a hydrocarbon group (CH).

47
Q

What does the diversity of R groups result in?

A

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

48
Q

What is the Primary Structure?

A

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

49
Q

What is the Secondary Structure?

A

Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure — alpha helices, parallel or antiparallel beta-pleated sheets, or turns.

50
Q

What is the Tertiary Structure?

A

The polypeptide folds into a tertiary structure.

This conformation is stabilised by interactions between R groups: hydrophobic interactions;
ionic bonds; London dispersion forces;
hydrogen bonds; disulfide bridges.

51
Q

Explain Hydrophobic Interactions

A

The non-polar R groups tend to get placed in the centre of the molecule. Hydrophobic sections of proteins are classically found embedded in the phospholipid bilayer of the cell, while the hydrophilic polar parts are free to interact with the extracellular and intracellular solutions.

52
Q

Explain Ionic Bonds

A

In ionic bonds, atoms are oppositely charged and therefore, held by an electrostatic attraction.

53
Q

Explain Hydrogen Bonds

A

Hydrogen bonding is a weak polar interaction that occurs when an electropositive atom is shared between two electronegative atoms.

54
Q

Explain London Dispersion Forces (LDF)

A

Temporary attractive force that results when the electrons in two adjacent atoms occupy positions that make the atoms form temporary dipoles.

55
Q

What are Disulfide Bridges?

A

Disulfide bridges are covalent bonds between R groups containing sulfur.

56
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.

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

57
Q

Examples of Prosthetic Groups

A

Prosthetic Group - Name of Protein

Haeme - haemoglobin, myoglobin
Carbohydrate - glycoprotein
Lipid - lipoprotein
Nucleic Acid - nucleoprotein

58
Q

What is the Quaternary Structure?

A

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

Quaternary structure describes the spatial
arrangement of the subunits.

eg. Haemoglobin (tetrameric).

59
Q

What is a ligand?

A

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

60
Q

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

A

Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually
becoming denatured. 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 are lost, which gradually changes the conformation of the
protein until it becomes denatured.

61
Q

Ligand Binding Changes the Conformation of a Protein

A
62
Q

Explain ligand binding

A

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

Binding sites will have complementary shape and chemistry to the ligand.

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

This change in conformation causes a
functional change in the protein.

Allosteric interactions occur between spatially distinct sites.

63
Q

What are allosteric enzymes?

A

An allosteric enzyme is an enzyme that can have its activity altered by a ligand called a modulator.

In allosteric enzymes, modulators bind at a secondary binding site (allosteric site) away from the active site.

64
Q

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

65
Q

What do allosteric proteins consist of?

A

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

66
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.

67
Q

What regulates enzyme activity?

A

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

68
Q

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

A

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

69
Q

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

A

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

70
Q

Explain co-operativity

A

The ligand binding to one subunit of the protein increases the other subunits affinity for the ligand (positive).

Negative = the ligand binding to one subunit of the protein decreases the other subunits affinity for the ligand.

71
Q

The influence and physiological importance of temperature and pH on the binding of oxygen - explain?

A

A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced. Reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue.

72
Q

Reversible Binding of Phosphate and the
Control of Conformation

A
73
Q

What can the addition or removal of phosphate can cause?

A

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

This is a common form of post-translational
modification.

74
Q

Explain the reversible binding of phosphate and the control of conformation

A

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

The terminal phosphate of ATP is transferred to specific R groups.

Protein phosphateses catalyse the reverse
reaction.

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.

75
Q

Some proteins are activated by
phosphorylation while others are inhibited - explain?

A

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

Advanced Higher Biology Unit 1 (5 decks)

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