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AH Biology > 1.2 Cells and Proteins: Proteins > Flashcards

1.2 Cells and Proteins: Proteins Flashcards

1.2 (92 cards)

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1
Q

what is the proteome?

A

the entire set of proteins expressed by a genome

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2
Q

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

A

because more than one protein can be produced from a single gene due to alternative RNA splicing

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3
Q

Why aren’t all genes expressed in every cell type?

A

Some genes are turned off in certain cells.

Some are transcribed into RNA but not translated into protein.

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4
Q

what are some of the factors that can affect the set of proteins expressed by a given cell type?

A

metabolic activity of the cell
state of cellular stress
response to signalling molecules
state of health or disease

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5
Q

what is the term used to describe genes that do not code for proteins?

A

non-coding RNA genes

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6
Q

what are examples of non-coding RNA genes?

A

RNA molecules such as; tRNA, rRNA etc

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7
Q

describe the process of alternative RNA splicing:

A

during splicing, different exons may be retained and different introns may be removed from the mature transcript

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8
Q

what affects metabolic activity of the cell?

A

age, senescence, dormancy

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9
Q

what affects cellular stress levels?

A

extremes of temperature, pH, exposure to toxins and mechanical damage

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10
Q

what is meant by the response to signalling molecules?

A

the cells response to signalling molecules such as hormones or antigens

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11
Q

what affects the cells health?

A

apoptosis

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12
Q

Why do eukaryotic cells have a system of internal membranes?

A

the surface area of their plasma membrane is too small to carry out all the vital functions that rely on membranes and the specialised proteins associated with them

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13
Q

What is the endoplasmic reticulum (ER)?

A

an internal system of specialised membranes which forms a network of membrane tubules continuous with the nuclear membrane

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14
Q

what are the two types of ER?

A

smooth and rough

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15
Q

what is the difference between the smooth and rough ER?

A

the RER has docked ribosomes on its cytosolic face while the SER lacks ribosomes

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16
Q

what is the Golgi apparatus?

A

a series of flattened membrane discs related to the ER and has associated vesicles that transport materials between membrane compartments

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17
Q

what are lysosomes and what can they digest?

A

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

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18
Q

how are lysosomes formed?

A

formed from specialised Golgi vesicles

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19
Q

what are the main components that make up the membrane?

A

phospholipids and proteins

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20
Q

where does the synthesis of all proteins begin?

A

cytosolic ribosomes

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21
Q

Where are cytosolic proteins made, and what do they do

A

they begin and complete synthesis in cytosolic ribosomes and remain in the cytosol where they carry out their specialised functions

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22
Q

describe the synthesis of lipids:

A

synthesised in the SER and inserted into its membrane

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23
Q

Describe the synthesis of transmembrane proteins:

A

The synthesis of transmembrane proteins begins in cytosolic ribosomes.
These proteins carry a signal sequence that halts translation and redirects the ribosome to dock with the endoplasmic reticulum (ER), forming the rough ER (RER).

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24
Q

what happens after the ribosomes docks with the ER to form the RER?

A

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

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25
what does a signal sequence consist of?
a short stretch of 16-30 amino acids at one end of the polypeptide chain
26
where is the signal sequence located on the protein and why?
at the N terminus of the protein so it is synthesised first
27
where specifically does the cytosolic ribosome bind on the ER?
ER docking site
28
what happens to proteins once they are in the ER membrane?
they are transported in the membranes of vesicles that bud off from the ER fuse with the Golgi apparatus
29
what do proteins undergo as they move through the Golgi apparatus?
post-translational modification
30
what is the major modification made?
the addition of carbohydrate groups
31
How are glycoproteins produced?
Enzymes catalyse the addition of various sugars in multiple steps to form the added carbohydrates, this results in the production of glycoproteins.
32
how do molecules move through the Golgi apparatus?
they move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack
33
what can happen to vesicles containing glycoprotein?
they can be recruited to other membranes including the plasma membrane
34
what are three examples of proteins for secretion?
peptide hormones digestive enzymes lysosome hydrolases
35
where do vesicles from the Golgi apparatus transport proteins?
vesicles leaving the Golgi apparatus transport proteins to the plasma membrane for secretion or to lysosomes for use within the cell
36
how do vesicles travel and deliver their contents inside the cell?
vesicles move along microtubules to other membranes and fuse with them within the cell
37
Where are secreted proteins synthesised and where do they go
proteins for secretion are translated in ribosomes on the RER and enter its lumen
38
describe the process of the secretory pathway:
proteins for secretion are translated in ribosomes docked on the RER but enter its lumen rather than becoming integrated with the lipid components. These proteins move through the Golgi apparatus and are packaged inside secretory vesicles, some vesicles that leave the Golgi apparatus take proteins to the plasma membrane for secretion from the cell while some develop into lysosomes
39
what are the two possible fates for secretory vesicles:
leaves the Golgi apparatus to take proteins to plasma membrane for secretion from the cell leaves Golgi apparatus to develop into lysosomes which are retained in the cytosol
40
how (specifically) are proteins secreted?
the secretory vesicle fuses with plasma membrane to secrete its contents
41
what are many proteins to be secreted synthesised to?
inactive persecutors
42
what do inactive persecutors require to become active proteins?
proteolytic cleavage
43
what is proteolytic cleavage?
another type of post-translational modification
44
what is an example of an inactive persecutor?
digestive enzymes
45
what would happen if digestive enzymes were synthesised in active form?
they could digest the tissues in which they are synthesised
46
describe the difference between the various proteins synthesised in cells:
cytosolic proteins are synthesised in cytosolic ribosomes and remain in the cytosol, transmembrane proteins begin synthesis in cytosolic ribosomes and finish in docked ribosomes on the RER and are then inserted into the ER membrane, secretory protein begins in cytosolic ribosomes and finished in RER docked ribosomes, they then enter the ER lumen
47
what determines the structure of a protein?
the sequence of amino acids
48
what can proteins be termed as?
polymers of amino acids
49
what type of bonding occurs between amino acids to form polypeptide chains?
peptide bonds
50
how do individual amino acids differ in terms of structure?
their R group
51
what is meant by a primary structure of amino acids?
the sequence in which the amino acids are synthesised into the polypeptide
52
what are the different types of R groups?
non-polar - hydrophobic basic - acidic - (hydrophilic) polar -
53
what type of reaction forms a peptide bond?
condensation reaction
54
what determines the primary structure of a protein?
the base sequence in the mature mRNA transcript
55
what type of bonding is present in secondary structures?
hydrogen bonds
56
how are hydrogen bonds formed?
when weak positive charges are attracted to weak negative charges on oxygen or nitrogen atoms
57
where does hydrogen bonding occur?
along the backbone of the protein strand
58
what are the three types of secondary structures produced as a result of hydrogen bonding?
alpha helix beta-pleated sheet turns
59
where do turns occur?
in between changes between beta-pleated sheets and alpha helices
60
how is a tertiary structure formed?
interactions between R groups
61
what are the types of interactions between R groups?
hydrophobic interactions (between non-polar side groups that clump together to avoid water) ionic bonds ( occur between R groups of opposite charges) disulphide bridges (covalent bonds between amino acids containing sulfur) London dispersion forces (caused by electrons) Hydrogen bonds (attractions between hydrogen and oxygen/nitrogen
62
what can influence the interactions of R groups?
temperature and pH
63
what happens to the protein when there is an increase in temperature?
disrupts the interactions that hold the protein in shape and the protein begins to unfold, eventually becoming denatured
64
how does pH affect the interactions?
affects the charge of R groups - as pH increase/decreases from optimum, normal ionic interactions between charged groups are lost, which gradually changes the conformation until it becomes denatured
65
what is a quaternary structure?
two or more connected polypeptide subunits
66
how are the subunits bonded together?
by other interactions between the R groups of the different subunits
67
what is a prosthetic group?
non-protein unit tightly bound to a protein and necessary for its specific function
68
what is an example of a prosthetic group?
haem group in haemoglobin allows binding to oxygen
69
what is a ligand?
a substance that can bind to a protein
70
What role do R groups not involved in protein folding play
can form binding sites that allow ligands to bind
71
What determines ligand binding at a protein's binding site?
The binding site has a complementary shape and chemical properties that match the ligand
72
What happens when a ligand binds to a protein-binding site?
conformational change in the protein, which causes a functional change in the protein
73
What are allosteric interactions?
when a molecule binds to a site on a protein that is spatially distinct from the active site (causing a change in protein conformation and function)
74
What structural feature is common in many allosteric proteins?
Many allosteric proteins have multiple subunits, meaning they have a quaternary structure
75
Why do allosteric proteins with multiple subunits show cooperativity in binding
because ligand binding to one subunit causes a conformational change that is transmitted to the other subunits, altering their affinity for the ligand
76
what is the name of the second site on allosteric enzyme other than the active site?
allosteric site
77
what is the term used to describe negative modulators?
inhibitors
78
what effect does inhibitors have on enzymes?
they reduce the enzymes affinity for the substrate
79
what is the term used to describe positive modulators?
activators
80
what effect do activators have on enzymes?
they increase the enzymes affinity for the substrate
81
what is the name of the enzymes which catalyses the transfer of a phosphate group to other proteins?
protein kinases
82
what does phosphorylation bring about?
conformational changes that can affect a proteins activity
83
what does protein kinases catalyse?
the transfer of a phosphate group to other proteins
84
What happens to the terminal phosphate of ATP during phosphorylation?
the terminal phosphate group of ATP is attached to specific R groups
85
what is the name of the enzyme that catalyses the reverse reaction?
protein phosphatases
86
what does the addition of a phosphate group to a protein do?
adds a negative charge which can disrupt the ionic interactions, this means that some proteins are activated by phosphorylation and some are inhibited
87
describe cooperativity in haemoglobin:
as pH decreases and temperature increases, it lowers the affinity of haemoglobin for oxygen, making it easier for oxygen to be released to muscle tissues
88
describe allosteric sites and how modulators affect enzyme action:
allosteric sites are sites on an enzyme that are spatial distant from the active site. there are activators and inhibitors; activators increase the enzymes affinity for the substrate and inhibitors reduce the enzymes affinity for the substrate
89
explain how phosphorylation can affect the functioning of proteins:
the phosphorylation of proteins is by protein kinases, the binding of a phosphate group changes the conformation of the protein (activate the protein) de-phosphorylation by protein phosphatases changes the conformation of the protein and can deactivate protein
90
what is phosphorylation another example of?
post-translational modification
91
which part of the cell does the vesicles arriving at the Golgi apparatus come from?
ER
92
what two substances can be produced by respiring muscle cells that would reduce the pH?
carbon dioxide lactic acid

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