UNIT 1 - cells and proteins Flashcards
1
Q
what is a genome?
A
an organisms genome is its complete set of DNA
2
Q
what does a genome include?
A
the protein coding genes and the non-protein coding genes
3
Q
what are non-protein coding genes transcribed into?
A
- tRNA
- rRNA
- RNA molecules that control expressions of the other genes
4
Q
what is a proteome?
A
the proteome is the entire set of proteins that can be expressed from a genome
5
Q
what is unique about the size of the proteome?
A
it is larger than the number of genes. especially in eukaryotes. this is due to alternative RNA splicing which allows more than one protein to be expressed from a single gene.
6
Q
what is removed in RNA splicing?
A
introns are removed from RNA transcripts
7
Q
what is retained during RNA splicing?
A
exons are retained during RNA splicing
8
Q
what does the set of genes expressed by a given cell type depend on?
A
they can vary over time and under different conditions
9
Q
what are some factors that effect the proteins expressed?
A
some factors that effect the proteins expressed by a given cell type are:
- metabolic activity within the cell
- cellular stress
- the response signalling molecules
- diseased vs healthy cells
10
Q
what is unique about the size of eukaryotic cells and what does this mean?
A
because of their size, they have a relatively small surface area to volume ratio. the surface area of their plasma membrane is too small to carry out all the vital functions of membranes and their specialised proteins associated with them.
11
Q
what do eukaryotic cells have that increase the total area?
A
eukaryotic cells have a system of internal membranes that increases the area of the membrane
12
Q
what does the endoplasmic reticulum form?
A
a network of membrane tubules continuous with the nuclear membrane
13
Q
what is the endoplasmic reticulum?
A
a network of membrane tubules within the cytoplasm of a eukaryotic cell, continuous with nuclear membranes
14
Q
what is a lysosome?
A
a modified Golgi vesicle containing hydrolytic enzyme/hydrolases
15
Q
function of vesciles?
A
transport materials between membrane components
16
Q
what is synthesised in the ER?
A
the components of membranes, phospholipids and proteins
17
Q
what is a phospholipid?
A
they are a type of lipid that form the main component of the cell membrane
18
Q
what is synthesised in the smooth endoplasmic reticulum?
A
lipids
19
Q
where are lipids synthesised?
A
in the smooth endoplasmic reticulum and inserted into its membrane
20
Q
what is the difference between RER and SER?
A
RER has ribosomes on its cytosolic face whereas SER doesn’t
21
Q
where does the synthesis of proteins begin?
A
cytosolic ribosomes
22
Q
where are cytosolic proteins located?
A
the synthesis of cytosolic proteins finishes in the cytosolic ribosomes and will remain in the cytosol
23
Q
how is the RER formed?
A
transmembrane carry a signal sequence that halts translation and directs the ribosome synthesising protein to a dock with the ER forming the RER
24
Q
what is a signal sequence?
A
a signal sequence is a short stretch of amino acids at one end of a polypeptide that determines the eventual location of protein in a cell
25
what is an allosteric enzyme?
Enzymes that change conformation in response to a modulator
26
what is an alpha helix?
Polypeptide chain coiled into a helix with hydrogen bonding occurring to maintain the arrangement
27
what is alternative RNA splicing?
Removal of non-coding introns from a primary mRNA transcript to leave only the coding exons; several mature transcripts can be produced from a single primary transcript
28
what are beta-pleated sheets?
Polypeptide chain arranged in rows with the chain folding in parallel or anti-parallel arrangements
29
conformation meaning?
Structural arrangement of the polypeptide chains within a protein
30
co-operatively meaning?
Changes in binding of a target molecule to one subunit of a multiunit polypeptide. this changes the affinity of the other subunits for the target molecule
31
what is a disulphide bridge
they are strong covalent bonds between R groups that contain sulfur which stabilise the tertiary and quaternary structures of many proteins.
32
what is the endoplasmic reticulum?
A network of membrane tubules within the cytoplasm of a eukaryotic cell, continuous with the nuclear membrane
33
what is an exon?
Section of RNA that is usually retained during splicing
34
what is a glycoprotein?
A protein with a carbohydrate added by post-translational modification
35
what is the golgi apparatus?
A series of flattened discs that packages proteins into vesicles inside the cell before the vesicles are sent to their destination
36
what is hydrogen bonding?
Attractions between polar molecules in which hydrogen is bound to a larger atom, such as oxygen or nitrogen
37
what are hydorlases?
A class of enzymes that use water to break chemical bonds
38
what is an intron?
A section of RNA usually removed during splicing
39
what is an ionic bond?
A type of chemical bond that involves the electrostatic attraction between oppositely charged ions
40
what is a ligand?
A substance that can bind to a protein; the protein has a shape complementary to the ligand to allow binding.
41
what is a london dispersion force?
A temporary, weak attraction between atoms and molecules
42
what is a lysosome?
A modified Golgi vesicle containing hydrolyses
43
what are modulators?
These bind to a secondary site on an enzyme to alter its conformation; positive modulators activate enzymes and give them an increased affinity; negative modulators deactivate them and decrease their affinity
44
what is a monomer?
A molecule that can bind chemically to other monomers to form a polymer
45
what is a non-coding RNA gene?
A gene that codes for RNAs other than mRNA, so do not encode protein
46
what is a polymer?
A macromolecule composed of many repeated subunits (monomers)
47
what is post transitional modification?
Addition of different chemical groups to or modification of a protein to allow a particular function
48
what is a prosthetic group?
A non-protein unit tightly bound to a protein and necessary for its function
49
what is protein kinases?
Catalyse the transfer of a phosphate group from a donor molecule (usually ATP) to an acceptor
50
what are protein phosphates?
An enzyme that removes a phosphate group from its substrate
51
what is protein structure?
Different levels of arrangement of polypeptides within a protein
52
what is the primary structure?
Sequence in which amino acids are found within a protein. The type of bonding that occurs here is the peptide bonds between amino acids to form a polypeptide
53
what type of bonding occurs in the secondary structure?
Hydrogen bonding occurring within a polypeptide forming alpha helices or parallel/antiparallel beta-pleated sheets.
54
what happens in the tertiary structure?
The polypeptide folds into an overall more 3D shape. Bonding of many types occurring between the R groups such as hydrogen bonding, disulphide bridges, LDF and hydrophobic interactions
55
what is the quaternary structure?
It is the complex shape produced by combining two or more connected polypeptide subunits.
56
what is the proteolytic cleavage?
A major form of post-translational modification; it occurs when a protease breaks one or more bonds in a target protein to activate, inhibit, or destroy the protein’s activity
57
what is a R group?
Side groups that allow different bonding between amino acids and give them their wide range of functions
58
what is a basic R group?
- additional amino group that gives positive net charge.
- is hydrophilic (attracted to water)
- can form ionic bonds
59
what is an acidic R group?
- additional acidic groups gives us a negative net charge.
- hydrophilic and attracted to water
- can form ionic bonds
60
what is a polar R group?
- group that prefers to exist in a watery environment.
- can form hydrogen bonds
- uncharged because of a balance if tiny charges
61
what are turns?
Secondary structure that reverses the direction of a polypeptide chain
62
what is a vesicle?
Small membrane bound compartments filled with liquid. they transport materials between membrane compartments
63
are all genes expressed in a cell type?
no, not all genes are expressed in a cell type
64
what type of R group do ligands bind to?
they bind to R groups that are not involved in folding.
65
what happens as proteins move through the golgi apparatus?
they go through post translational modifaction
66
what do molecules do in 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
67
what do carbohydrates/sugars become in the golgi apparatus?
enzyme catalyse the addition of various sugars/carbohydrates in multiple steps to become glycoproteins
68
what is the major post transitional modification in the golgi apparatus?
the addition of carbohydrate groups to produce glycoproteins
69
what do vesicles that lead the golgi apparatus take?
they take transmembrane proteins to the plasma membrane and lysosomes
70
what are the 4 R group categories?
basic - postively charged
acidic - negatively charged
polar
hydrophobic
71
what are digestive enzymes and how are they activated?
an example of secreted proteins that require proteolytic cleavage of inactive precursors to become active
72
what happens when proteins move through the golgi apparatus?
when proteins move through the golgi apparatus they are then packaged into secretory vesciles
73
are proteins a monomer or polymer?
proteins are polymers of amino acid monomers
74
what are amino acids linked by?
peptide bonds from polypeptides
75
what is the structure of an amino acid decided by?
amino acids have the same basic structure differing only by the R groups present
76
what is the function of proteins decided by?
the wide range of functions from a protein are decided by the diversity of R groups
77
what are the types of interactions that happen in the tertiary structure?
```
hydrophobic interactions
ionic bonds
london dispersion forces
hydrogen bonds
disulphide bridges
```
78
what is the ability of haemoglobin to bind with oxygen dependent on?
it is dependent on the prosthetic haem group
79
what can effect the interactions of R groups?
temperature as increasing the temperature disrupts the interactions that hold the protein in shape and so the protein begins to unfold and everything becomes denatured
80
what are the charges on acidic and basic R groups affected by?
pH - as pH decreases or increases 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
what are the qualities of the binding site?
they complimentary shape and chemistry to the ligand
82
what happens when a ligand binds to a protein binding site?
the protein conformation changes, this causes a functional change in the protein.
83
describe the synthesis of secreted proteins
- DNA in the nucleus
- mRNA (RNA splicing)
- translated at the cytosolic ribosomes
- they then dock at the RER
- inserted into the lumen
- vesicles buds off and travels to the golgi apparatus
- they then move through the golgi apparatus where they are packaged inside secretory vesicles
- some secretory vesicles then move along microtubules in the cytosol to merge with the membrane for secretion from the cell while some develop into lysosomes that are retained in the cytosol
84
synthesis of transmembrane proteins?
- DNA in the nucleus
- mRNA (RNA splicing)
- synthesis begins at the cytosolic ribosomes but is halted by the signal sequence which halts translation directs the ribosome to dock in the ER where translation is completed and becomes a part of the RER
- vesicle buds off
- fuses with the Golgi apparatus
- (post-transitional modification if required)
- packaged into a vesicles
- moves to the membrane via microtubules
- merges with membrane protein becomes a part of the membrane
85
what type of bonding occurs in the quaternary structure?
further bonding between R groups on the different polypeptides that make up the subunits
86
what is a non polar-R group?
- mostly composed of carbon and hydrogen
- hydrophobic
- attracted to each other
87
how does cooperativity happen in haemoglobin with oxygen?
Haemoglobin has four subunits which all contain the oxygen binding haem prosthetic group. Oxygen binds to one subunit of haemoglobin and this makes the affinity for other subunits increase. when oxygen is released from the subunit then the affinity for other subunits is decreased and more oxygen is released
88
how can pH and temperature effect haemoglobin's affinity for oxygen?
temperature and pH affect haemoglobin as it is a protein.
- hard working tissues generate heat and carbonic acid
- temperature increases and pH decreases
- haemoglobin's affinity for oxygen decreases
- more oxygen released in hard working tissues
89
what is (de)phosphorylation ?
it is the most common form of activation. this is this reversible addition of a phosphate group to an -OH group on some amino acids. the addition or removal of a phosphate group causes a reversible conformational change in a protein
90
which enzyme is responsible for the dephosphorylation of proteins?
phosphatase
91
why is the proteome larger than the genome
an individual gene may be expressed to produce several different proteins due to alternative RNA splicing
92
what are the different types of membranes?
The endoplasmic reticulum - either the rough endoplasmic reticulum (with ribosomes on its cytosolic face) or the smooth endoplasmic reticulum (without ribosomes on its cytosolic face.
The Golgi apparatus which is related to the endoplasmic reticulum, it forms vesicles and is involved in the formation of lysosomes.
