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Flashcards in 1.2 Proteins Deck (91)
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1
Q

what is the genome

A

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

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

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

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

5
Q

the sets of proteins expressed over a given cell type…

A

can vary over time and under different conditions

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
7
Q

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

A

increase in total area of membrane

8
Q

because of their size, eukaryotes have a…

A

small surface area to volume ratio

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

10
Q

what does the endoplasmic reticulum form

A

network of membrane tubules continuous with the nuclear membrane

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

12
Q

what are the different types of ER

A

rough ER

smooth ER

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

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

15
Q

what is the Golgi apparatus

A

a series of flattened membrane discs found in most cells

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

17
Q

which cells contain more sets of Golgi apparatus than other cells

A

specialised secretory cells

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

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

20
Q

why is the Golgi apparatus important

A

transports lipids throughout the cell and the creation of lysosomes

21
Q

what are lysosomes

A

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

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
23
Q

what are vesicles

A

transport material between membrane compartments

24
Q

what are membranes composed of

A

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

25
Q

where are lipids synthesised

A

in the SER and inserted into its membrane

26
Q

where does the synthesis of all protein begin

A

in cytosolic ribosomes

27
Q

where is the synthesis of cytosolic proteins completed

A

in cytosolic ribosomes and the proteins remain in the cytosol

28
Q

how does the synthesis of all proteins begin

A

by transcription of the gene encoding that protein and translation of the mRNA (after splicing if necessary) on free ribosomes within the cytoplasm

29
Q

where are proteins located

A

some are intracellular (remain inside the cell)
other are located in/on the membrane
others still are secreted extracellularly

30
Q

what is a signal sequence

A

a short stretch of amino acids at one end of the polypeptide that determines the eventual location of that protein in a cell

31
Q

what is the signal peptide that sends a protein into the endoplasmic reticulum during translation

A

a series of hydrophobic amino acids, usually found near the beginning of the proteins

32
Q

what does a signal sequence do

A

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
Q

what is stage 1 of synthesis membrane components by RER

A

proteins are synthesised by ribosomes in the cytoplasm

34
Q

what is stage 2 of synthesis membrane components by RER

A

a signal protein (signal recognition particle) from the membrane binds to the ribosome and stops translation

35
Q

what is stage 3 of synthesis membrane components by RER

A

the SRP (signal recognition particle) binds to a receptor which then directs the ribosome to attach to the endoplasmic reticulum forming the RER

36
Q

what is stage 4 a) of synthesis membrane components by RER

A

translation restarts and the protein is now inserted into membrane of the ER

37
Q

what is stage 4 b) of synthesis membrane components by RER

A

once translation finished, the ribosome detaches

38
Q

what happens once the proteins are in the RER

A

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
Q

vesicles move…

A

along microtubules to other membranes and fuse them within the cell

40
Q

where are secreted proteins translated

A

in ribosomes on the RER and enter its lumen

41
Q

examples of secreted proteins

A

peptide hormones

digestive enzymes

42
Q

what happens when the proteins are in the Golgi apparatus

A

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
Q

what are many secreted proteins synthesised as

A

inactive precursors and require proteolytic cleavage to produce active proteins

44
Q

what is proteolytic cleavage

A

another type of post-translational modification

45
Q

example of secreted proteins

A

digestive enzymes that requires proteolytic cleavage to become active
another is insulin

46
Q

proteins are polymers of…

A

amino acid monomers

47
Q

what are enzymes linked by

A

peptide bonds to form polypeptides

48
Q

amino acids have the same basic structure, differing only in the…

A

R group present

49
Q

what can R groups vary in

A
size 
shape 
charge 
hydrogen bonding capacity
chemical reactivity
50
Q

amino acids are classified according to their R groups

what are they

A

basic (positively charges)
acidic (negatively charged
polar (hydrophilic)
hydrophobic (non-polar)

51
Q

what does the diversity of amino acid R groups result in

A

wide range of functions carried out by proteins

52
Q

what is the primary structure

A

the sequence in which the amino acids are synthesised into the polypeptide

53
Q

what is the secondary structure

A

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
Q

what is the tertiary structure

A

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
Q

what are disulfide bridges

A

covalent bonds between R groups containing sulfur

56
Q

what is the quaternary structure

A

quaternary structure exists in proteins with two or more connected polypeptide subunits
it describes the spatial arrangement of the subunits

57
Q

what are prosthetic groups

A

a non-protein unit tightly bound to a protein and necessary for its function e.g. heamoglobin

58
Q

what is heamoglobin

A

iron-containing oxygen transporting protein present in the red blood cells of almost all vertebrates

59
Q

what is the ability of heamoglobin to bind to oxygen depend on

A

the non-protein heam group

60
Q

what can the interactions of the R group be influenced by

A

temperature and pH

61
Q

what does increasing temperature do

A

disrupts the interactions that hold the protein in shape

the protein begins to unfold, eventually becoming denatured

62
Q

how are the charges on acidic and basic R groups affected by pH

A

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
Q

what is a ligand

A

a subunit substance that can bind to a protein

64
Q

R groups not involved in protein folding….

A

can allow binding to ligands

binding sites will have complimentary shape and chemistry to the ligand

65
Q

what happens when a ligand binds to a protein-binding site

A

changes the conformation of the protein

66
Q

what does allosteric mean

A

interactions which occur between spatially distinct sites

67
Q

what is the process of co-operation

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

68
Q

what do allosteric enzymes consist of

A

multiple subunits which means they have a quaternary structure

69
Q

what do allosteric proteins with multiple subunits show

A

co-operativity in binding

70
Q

what does co-operativity in binding mean

A

changes in binding at one subunit alter the affinity of the remaining subunits

71
Q

what is the second type of site in allosteric enzymes called

A

allosteric site

72
Q

what does a modulator do

A

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

73
Q

what happens when a modulator binds

A

the conformation of the enzyme changes and this alters the affinity of the active site for the substrate

74
Q

what is a positive modulator

A

increases the enzyme’s affinity for the substrate

75
Q

what is a negative modulator

A

reduces the enzyme’s affinity for the substrate

76
Q

what does the binding and release of oxygen in haemoglobin show

A

co-operativity

77
Q

what alters the affinity of the remaining subunits for oxygen

A

changes in binding of oxygen at one subunit

78
Q

what is the binding of oxygen to haemoglobin affected by

A

pH and temperature

79
Q

what is the effect of decreasing pH on the affinity of haemoglobin for oxygen

A

decreases affinity for oxygen

80
Q

what is the effect of increasing the pH on the affinity of haemoglobin for oxygen

A

increasing pH increases affinity for oxygen

81
Q

what is the effect of decreasing temperature on the affinity of haemoglobin for oxygen

A

increases affinity for oxygen

82
Q

what is the effect of increasing the temperature on the affinity of haemoglobin for oxygen

A

decreases affinity for oxygen

83
Q

what does a decrease in pH or an increase in temperature mean

A

it lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced

84
Q

what does reduced pH and increased temperature in actively respiring tissue mean

A

it will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue

85
Q

what can the addition or removal of phosphate cause

A

reversible conformational changes in proteins

this is a common form of post-translational modification

86
Q

what does protein kinases catalyse

A

the transfer of a phosphate group to other proteins

87
Q

which phosphate is being transferred to specific R groups in the protein

A

the terminal phosphate of ATP

88
Q

what does protein phosphatases catalyse

A

the reverse reaction of protein kinases

89
Q

what does phosphorylation bring about

A

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
Q

what happens to proteins by phosphorylation

A

some are activated while others are inhibited

91
Q

what does adding a phosphate group result in

A

adding charges

ionic interactions in the unphosphorylated protein can be disrupted and new ones created