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Advanced Higher Biology > 1.2 Proteins > Flashcards

1.2 Proteins Flashcards

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1
Q

what is the genome

A

all of the genetic material in a cell including DNA and RNA

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2
Q

what is the proteome

A

the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time

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3
Q

why is the proteome larger than the genome

A

more than one protein can be produced from a single gene as a result of alternative splicing

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4
Q

what are genes which do not code for proteins called

A

non-coding RNA genes and include those that are transcribed to produce tRNA rRNA and RNA molecules that control the expression of other genes

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5
Q

the sets of proteins expressed over a given cell type…

A

can vary over time and under different conditions

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6
Q

which factors affect the set of proteins expressed by a given cell type

A 
metabolic activity 
rate of the cell
cellular stress
the response to signalling molecules
diseased versus healthy cells
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7
Q

what does eukaryotic cells having a system of internal membranes result in

A

increase in total area of membrane

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8
Q

because of their size, eukaryotes have a…

A

small surface area to volume ratio

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9
Q

what does eukaryotes having a small surface area to volume ratio mean

A

the plasma membrane of eukaryotic cells is too small an area to carry out all the vital functions carried out by membranes

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10
Q

what does the endoplasmic reticulum form

A

network of membrane tubules continuous with the nuclear membrane

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11
Q

what is the endoplasmic reticulum

A

a network of membranes found throughout the cell and connected to the nucleus
the membranes are slightly different from cell to cell and a cell’s function determines the size and structure of the ER

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12
Q

what are the different types of ER

A

rough ER

smooth ER

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13
Q

what is the difference between the rough ER and the smooth ER

A

they have the same types of membranes but different shapes
rough ER looks like sheets or disks of bumpy membranes while smooth ER looks more like tubes
rough ER is called rough because it has ribosomes attached to its cytosilic face

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14
Q

what is the function of the ER

A

it is mainly responsible for the transportation of proteins and other organelles, which includes lysosomes, Golgi apparatus, plasma membrane etc
they provide the increased surface area for cellular reactions
they help in the formation of the skeletal framework
they play a vital role in the synthesis of proteins, lipids, glycogen and other steroids like cholesterol, progesterone, testosterone, etc

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15
Q

what is the Golgi apparatus

A

a series of flattened membrane discs found in most cells

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16
Q

what is the function of the Golgi apparatus

A

to process and bundle macromolecules like proteins and lipids as they are synthesised within the cell
it is sometimes compared to a post office inside the cell since one major function is to modify, sort, and package proteins to be secreted

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17
Q

which cells contain more sets of Golgi apparatus than other cells

A

specialised secretory cells

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18
Q

what is the Golgi apparatus made up of

A

sacs called cisternae

usually 5 to 8 cisternae are present in one Golgi apparatus, but 60 has been observed by scientists

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19
Q

what do the bundles of sacs in Golgi apparatus have

A

five distinct and functional regions, and each region has different enzymes to help it modify the contents, depending on where they are to end up

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20
Q

why is the Golgi apparatus important

A

transports lipids throughout the cell and the creation of lysosomes

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21
Q

what are lysosomes

A

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

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22
Q

what is the importance of lysosomes

A 
lysosomes are important in different aspects of organisms which include:
intra-cellular digestion
cell renovation
apoptosis
prevent the entry of harmful agents into the cell
fertilisation
kill infection
health disorders
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23
Q

what are vesicles

A

transport material between membrane compartments

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24
Q

what are membranes composed of

A

a phospholipid bilayer with proteins and is represented by the fluid mosaic model

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25
where are lipids synthesised
in the SER and inserted into its membrane
26
where does the synthesis of all protein begin
in cytosolic ribosomes
27
where is the synthesis of cytosolic proteins completed
in cytosolic ribosomes and the proteins remain in the cytosol
28
how does the synthesis of all proteins begin
by transcription of the gene encoding that protein and translation of the mRNA (after splicing if necessary) on free ribosomes within the cytoplasm
29
where are proteins located
some are intracellular (remain inside the cell) other are located in/on the membrane others still are secreted extracellularly
30
what is a signal sequence
a short stretch of amino acids at one end of the polypeptide that determines the eventual location of that protein in a cell
31
what is the signal peptide that sends a protein into the endoplasmic reticulum during translation
a series of hydrophobic amino acids, usually found near the beginning of the proteins
32
what does a signal sequence do
halts translation and directs the ribosome synthesising the protein to dock with the ER forming RER translation continues after docking, and the protein is inserted into the membrane of the ER
33
what is stage 1 of synthesis membrane components by RER
proteins are synthesised by ribosomes in the cytoplasm
34
what is stage 2 of synthesis membrane components by RER
a signal protein (signal recognition particle) from the membrane binds to the ribosome and stops translation
35
what is stage 3 of synthesis membrane components by RER
the SRP (signal recognition particle) binds to a receptor which then directs the ribosome to attach to the endoplasmic reticulum forming the RER
36
what is stage 4 a) of synthesis membrane components by RER
translation restarts and the protein is now inserted into membrane of the ER
37
what is stage 4 b) of synthesis membrane components by RER
once translation finished, the ribosome detaches
38
what happens once the proteins are in the RER
they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus as proteins move through the Golgi apparatus they undergo post-translational modification molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one on the stack enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates the addition of carbohydrate groups is the major modification
39
vesicles move...
along microtubules to other membranes and fuse them within the cell
40
where are secreted proteins translated
in ribosomes on the RER and enter its lumen
41
examples of secreted proteins
peptide hormones | digestive enzymes
42
what happens when the proteins are in the Golgi apparatus
they 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
43
what are many secreted proteins synthesised as
inactive precursors and require proteolytic cleavage to produce active proteins
44
what is proteolytic cleavage
another type of post-translational modification
45
example of secreted proteins
digestive enzymes that requires proteolytic cleavage to become active another is insulin
46
proteins are polymers of...
amino acid monomers
47
what are enzymes linked by
peptide bonds to form polypeptides
48
amino acids have the same basic structure, differing only in the...
R group present
49
what can R groups vary in
``` size shape charge hydrogen bonding capacity chemical reactivity ```
50
amino acids are classified according to their R groups | what are they
basic (positively charges) acidic (negatively charged polar (hydrophilic) hydrophobic (non-polar)
51
what does the diversity of amino acid R groups result in
wide range of functions carried out by proteins
52
what is the primary structure
the sequence in which the amino acids are synthesised into the polypeptide
53
what is the secondary structure
hydrogen bonding along the backbone of the protein strand results in regions of secondary structure these structures are: alpha helices parallel or antiparallel beta pleated sheets turns
54
what is the tertiary structure
the polypeptide folds into a tertiary structure this conformation is stabilised by interactions between R groups such as: hydrophobic interactions ionic bonds london dispersion forces hydrogen bonds disulfide bridges - covalent bonds between R groups containing sulfur
55
what are disulfide bridges
covalent bonds between R groups containing sulfur
56
what is the quaternary structure
quaternary structure exists in proteins with two or more connected polypeptide subunits it describes the spatial arrangement of the subunits
57
what are prosthetic groups
a non-protein unit tightly bound to a protein and necessary for its function e.g. heamoglobin
58
what is heamoglobin
iron-containing oxygen transporting protein present in the red blood cells of almost all vertebrates
59
what is the ability of heamoglobin to bind to oxygen depend on
the non-protein heam group
60
what can the interactions of the R group be influenced by
temperature and pH
61
what does increasing temperature do
disrupts the interactions that hold the protein in shape | the protein begins to unfold, eventually becoming denatured
62
how are the charges on acidic and basic R groups affected by pH
as the 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
63
what is a ligand
a subunit substance that can bind to a protein
64
R groups not involved in protein folding....
can allow binding to ligands | binding sites will have complimentary shape and chemistry to the ligand
65
what happens when a ligand binds to a protein-binding site
changes the conformation of the protein
66
what does allosteric mean
interactions which occur between spatially distinct sites
67
what is the process of co-operation
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
68
what do allosteric enzymes consist of
multiple subunits which means they have a quaternary structure
69
what do allosteric proteins with multiple subunits show
co-operativity in binding
70
what does co-operativity in binding mean
changes in binding at one subunit alter the affinity of the remaining subunits
71
what is the second type of site in allosteric enzymes called
allosteric site
72
what does a modulator do
regulate the activity of the enzyme when they bind to the allosteric site
73
what happens when a modulator binds
the conformation of the enzyme changes and this alters the affinity of the active site for the substrate
74
what is a positive modulator
increases the enzyme's affinity for the substrate
75
what is a negative modulator
reduces the enzyme's affinity for the substrate
76
what does the binding and release of oxygen in haemoglobin show
co-operativity
77
what alters the affinity of the remaining subunits for oxygen
changes in binding of oxygen at one subunit
78
what is the binding of oxygen to haemoglobin affected by
pH and temperature
79
what is the effect of decreasing pH on the affinity of haemoglobin for oxygen
decreases affinity for oxygen
80
what is the effect of increasing the pH on the affinity of haemoglobin for oxygen
increasing pH increases affinity for oxygen
81
what is the effect of decreasing temperature on the affinity of haemoglobin for oxygen
increases affinity for oxygen
82
what is the effect of increasing the temperature on the affinity of haemoglobin for oxygen
decreases affinity for oxygen
83
what does a decrease in pH or an increase in temperature mean
it lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced
84
what does reduced pH and increased temperature in actively respiring tissue mean
it will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue
85
what can the addition or removal of phosphate cause
reversible conformational changes in proteins | this is a common form of post-translational modification
86
what does protein kinases catalyse
the transfer of a phosphate group to other proteins
87
which phosphate is being transferred to specific R groups in the protein
the terminal phosphate of ATP
88
what does protein phosphatases catalyse
the reverse reaction of protein kinases
89
what does phosphorylation bring 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
90
what happens to proteins by phosphorylation
some are activated while others are inhibited
91
what does adding a phosphate group result in
adding charges | ionic interactions in the unphosphorylated protein can be disrupted and new ones created

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