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Advanced Higher Biology 2025 > KA1.2 - Proteins > Flashcards

KA1.2 - Proteins Flashcards

Unit 1 (80 cards)

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1
Q

Define the ‘proteome’

A

The entire set of proteins expressed by the genome.

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2
Q

Why is the proteome larger than the number of genes, particularly in eukaryotes?

A

More than one protein can be produced from a single gene due to alternative RNA splicing.

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3
Q

What can non-coding RNA genes produce?

A
  • tRNA
  • rRNA
  • RNA molecules that control the expression of other genes
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4
Q

List factors that cause the set of proteins expressed by a given cell type to vary.

A
  • Metabolic activity of the cell
  • Cellular stress
  • Response to signalling molecules
  • Diseased versus healthy cell states
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5
Q

Why do eukaryotic cells have a system of internal membranes?

A
  • Relatively small surface area:volume ratio
  • Plasma membrane is too small to carry out all vital functions
  • Internal membranes increase the total membrane area
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6
Q

Name the four main intracellular membrane structures.

A
  1. Endoplasmic Reticulum (ER)
  2. Golgi apparatus
  3. Lysosomes
  4. Vesicles
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7
Q

Describe the general structure of the Endoplasmic Reticulum (ER).

A

A network of membrane tubules continuous with the nuclear membrane.

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8
Q

State the two types of endoplasmic reticulum

A
  1. Smooth endoplasmic reticulum (SER)
  2. Rough endoplasmic reticulum (RER)
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9
Q

What are the characteristics and primary function of the Smooth Endoplasmic Reticulum (SER)?

A
  • Lacks ribosomes.
  • Site of lipid synthesis (lipids are inserted into its membrane)
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10
Q

What are the characteristics and primary function of the Rough Endoplasmic Reticulum (RER)?

A
  • Contains ribosomes on its cytosolic face.
  • Site where synthesis of transmembrane proteins is completed
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11
Q

Describe the structure and main function of the Golgi apparatus.

A

A series of flattened membrane discs where post-translational modification of proteins occurs

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12
Q

Describe Lysosomes and their key function.

A

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

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13
Q

Describe vesicles and their role in the cell.

A

Spherical membrane containers that transport materials between membrane compartments

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14
Q

What are the two components of the cell membrane?

A
  1. Proteins
  2. Phospholipids
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15
Q

Where are the lipids that make up the phospholipids synthesised ?

A

Smooth endoplasmic reticulum

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16
Q

Where does the synthesis of all proteins begin?

A

Cytosolic ribosomes.

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17
Q

Where is the synthesis of cytosolic proteins completed, and where do these proteins remain?

A

Completed in cytosolic ribosomes; these proteins remain in the cytosol.

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18
Q

What feature directs the ribosome synthesizing a transmembrane protein to the ER?

A

A signal sequence which halts translation and directs the ribosome to dock with the ER (forming RER).

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19
Q

What is the signal sequence found on transmembrane proteins?

A

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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20
Q

What happens to a transmembrane protein after its ribosome docks with the ER?

A

Translation continues, and the protein is inserted into the membrane of the endoplasmic reticulum.

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21
Q

How are proteins transported from the endoplasmic reticulum to the Golgi apparatus?

A

By vesicles that bud off from the ER and fuse with the Golgi apparatus.

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22
Q

How do proteins move through the Golgi apparatus’s discs?

A

They 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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23
Q

What is post-translational modification?

A

Modifications that proteins undergo after their synthesis (translation) is complete.

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24
Q

Name three types of post-translational modification.

A
  1. Addition of carbohydrate groups = glycosylation
  2. Addition of phosphate groups = phosphorylation
  3. Proteolytic cleavage = removal of parts of the polypeptide chain
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25
What catalyses the addition of sugars during post-translational modification?
Enzymes catalyse the addition of various sugars in multiple steps to form carbohydrates.
26
Where do vesicles leaving the Golgi apparatus transport proteins?
To the plasma membrane and lysosomes.
27
How do vesicles move within the cell to fuse with other membranes?
Vesicles move along microtubules (a type of cytoskeleton filament) and fuse with them.
28
Where do secreted proteins (e.g., peptide hormones) begin translation?
In cytosolic ribosomes.
29
Where do secreted proteins continue translation after beginning in the cytosol, and where do they enter?
They continue translation in ribosomes on the RER and enter its **lumen**. | Lumen = inside space within tubular structure
30
How does the RER entry of secreted proteins differ from that of transmembrane proteins?
Secreted proteins enter the RER lumen, while transmembrane proteins span the RER membrane.
31
Give two examples of secreted proteins.
Peptide hormones and digestive enzymes.
32
Describe **Step 1** of the secretory pathway
Secreted proteins start translation in cytosolic ribosomes then continue translation in ribosomes on the RER and enter its lumen
33
Describe **Step 2** of the secretory pathway
Proteins are transported by vesicles that bud off from the endoplasmic reticulum and fuse with the Golgi apparatus.
34
Describe **Step 3** of the secretory pathway
The proteins move through the Golgi apparatus and are then packaged into secretory vesicles.
35
Describe **Step 4** of the secretory pathway
These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell.
36
Why do many secreted proteins require proteolytic cleavage?
They are synthesised as **inactive** precursors and require proteolytic cleavage (a type of post-translational modification) to become active.
37
Give an example of a secreted protein that requires proteolytic cleavage to become active.
Digestive enzymes
38
What are proteins polymers of, and what links these monomers?
Proteins are polymers of amino acid monomers, linked by peptide bonds to form polypeptides.
39
Amino acids have the same basic structure what differentiates them?
The **R group** present
40
Define 'R group' in the context of proteins
An R group is any group that contains a Carbon and Hydrogen atom that is attached to a molecule.
41
List characteristics that vary among amino acid R groups.
* Size * Shape * Charge * Hydrogen bonding capacity * Chemical reactivity
42
How are amino acids classified based on their R groups?
* Basic (positively charged) * Acidic (negatively charged) * Polar * Hydrophobic (Non-polar)
43
What accounts for the wide range of functions carried out by proteins?
The diversity of R groups.
44
Name the four distinct levels of protein structure.
1. Primary Structure 1. Secondary Structure 1. Tertiary Structure 1. Quaternary Structure
45
Define the primary structure of a protein
The sequence in which the amino acids are synthesised into the polypeptide.
46
How is secondary structure formed?
Formed by hydrogen bonding along the backbone of the protein strand
47
What are the **four** common secondary structures seen in proteins?
1. Alpha helices 2. Parallel beta-pleated sheets 3. Antiparallel beta-pleated sheets 4. Turns
48
How is tertiary structure of proteins formed, and what types of interactions stabilise it?
The polypeptide folds into a 3D conformation stabilised by interactions between R groups.
49
Define 'conformation' in the context of proteins?
The shape of the protein
50
List types of interactions that stabilise tertiary structure of proteins
* Hydrophobic interactions * Ionic bonds * London dispersion forces * Hydrogen bonds * Disulfide bonds
51
What are disulfide bonds?
Strong covalent bonds between R groups that contain sulfur.
52
Define 'quaternary structure'
Exists in proteins with two or more connected polypeptide subunits; describes their spatial arrangement.
53
Define 'prosthetic group'
Non-protein units tightly bound to the protein
54
Explain why prosthetic groups are important to proteins?
Often necessary for the protein to function
55
What is the prosthetic group in haemoglobin, and what is its function?
**Haem**, responsible for haemoglobin's ability to bind oxygen.
56
Why are protein structures significantly influenced by changes in temperature or pH?
Because the interactions of the R groups in the tertiary structure are sensitive to temperature and pH.
57
How does increasing temperature affect protein structure?
It disrupts the interactions holding the protein in shape, causing it to unfold and eventually denature.
58
How does changing pH affect protein structure?
It affects the charges on acidic and basic R groups. This loses normal ionic interactions, changing the conformation until the protein denatures.
59
Define a 'ligand'
A substance that can bind to a protein | e.g. an enzyme's substrate
60
What are the characteristics of protein binding sites in relation to ligands?
They have a complementary shape and chemistry to the ligand.
61
What happens to a protein's conformation and function when a ligand binds to its binding site?
The conformation of the protein changes, which causes a functional change in the protein.
62
What is an allosteric site in an allosteric enzyme?
A second type of site (separate from the active site) where modulators bind to regulate enzyme activity.
63
How do modulators regulate the activity of allosteric enzymes?
They bind to the allosteric site, changing the enzyme's conformation and altering the active site's affinity for the substrate.
64
Differentiate between positive and negative modulators.
* **Positive** modulators: Increase the enzyme’s affinity for the substrate. * **Negative** modulators: Reduce the enzyme’s affinity for the substrate.
65
What effect does the binding of a substrate to one active site have on other active sites in an allosteric enzyme?
It increases the affinity of the other active sites for binding of subsequent substrate molecules. | This is called cooperativity
66
What is the biological importance of cooperativity in allosteric enzymes?
Their activity can vary greatly with small changes in substrate concentration
67
What structural characteristic do many allosteric proteins often have?
They consist of multiple subunits (i.e., they have quaternary structure).
68
Where can allosteric interactions occur in multi-subunit allosteric proteins?
Between spatially distinct sites, where changes in binding at one subunit alter the affinity of the remaining subunits. | Cooperativity
69
Give an example of an allosteric protein with quaternary structure.
Haemoglobin
70
How does cooperativity manifest in haemoglobin's oxygen binding?
Conformational changes caused by oxygen binding to one subunit of haemoglobin will increase the affinity of the remaining subunits for oxygen. | Oxygen can bind easier as more oxygen's bind.
71
How does increasing temperature affect haemoglobin's affinity for oxygen?
As temperature increases, the affinity of haemoglobin for oxygen decreases, reducing oxygen binding.
72
How does decreasing pH (or increasing CO2) affect haemoglobin's affinity for oxygen?
As pH decreases, the affinity of haemoglobin for oxygen decreases, reducing oxygen binding.
73
What is the benefit of reduced pH and increased temperature in actively respiring tissue regarding oxygen delivery?
It reduces the binding of oxygen to haemoglobin, promoting increased oxygen delivery to the tissue where it's needed. | Important when you are exercising and need as much O2 as possible
74
What common post-translational modification can cause reversible conformational change in proteins?
The addition or removal of phosphate.
75
What enzymes catalyse the transfer of a phosphate group to other proteins?
Protein kinases
76
What is the typical source of the phosphate group transferred by protein kinases?
The terminal phosphate of ATP
77
What enzymes catalyse the reverse reaction of protein kinases (removing phosphate)?
Protein phosphatases
78
How does phosphorylation affect a protein’s activity?
Causes a conformational changes, which can either activate or inhibit the protein’s activity.
79
Give two examples of cellular proteins regulated by phosphorylation.
Enzymes and receptors.
80
What effect does adding a phosphate group have on the protein's charge and subsequent interactions?
It adds negative charges, which can disrupt existing ionic interactions and create new ones.

Advanced Higher Biology 2025 (19 decks)

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