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AH Biology > Proteins > Flashcards

Proteins Flashcards

1
Q

What is the genome?

A

Total genetic material in a cell (complete set of DNA)

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2
Q

What is the proteome?

A

Entire set of proteins that can be expressed from a genome

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3
Q

What are non-coding RNA genes?

A

Genes that aren’t expressed as proteins in a particular cell type

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4
Q

Non-coding RNA genes are transcribed to produce…

A

tRNA
rRNA
RNA molecules that control the expression of other genes

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5
Q

The proteome is larger than… because…

A

The number of genes (particularly in eukaryotes) because more than one protein can be expressed from a single gene due to alternative RNA splicing

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6
Q

Factors that affect the set of proteins produced in a cell type…

A

Metabolic activity of cell
Cellular stress
Response to signalling molecules
Diseased vs healthy cells

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7
Q

Boundary around outside of eukaryotic cells?

A

Plasma membrane

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8
Q

Eukaryotic cells also have a… which..

A

System of internal membranes that increases the total area of the membrane available for vital metabolic processes

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9
Q

Endoplasmic Reticulum (ER)?

A

Forms network of membrane tubules continuous with the nuclear membrane

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10
Q

What are the 2 types of ER?

A

Rough (RER) - has ribosomes
Smooth (SER)- no ribosomes

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11
Q

What is the Golgi apparatus?

A

Series of flattened membrane discs

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12
Q

What are lysosomes?

A

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

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13
Q

What are hydrolases?

A

Enzymes that catalyse the cleavage of a covalent bond using water

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14
Q

Function of vesicles

A

Transport materials between membrane components

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15
Q

Membranes are made of…

A

Lipids and proteins synthesised in the ER

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16
Q

Where are lipids synthesised?

A

SER and inserted into its membrane by enzymes

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17
Q

Where are cytosolic proteins synthesised?

A

Cytosolic ribosomes and remain in the cytosol (liquid component of cytoplasm)

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18
Q

Examples of cytosolic proteins…

A

Enzymes for glycolysis
Enzymes that attach amino acids to tRNA at ribosomes during protein synthesis

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19
Q

Where are transmembrane proteins synthesised?

A

Begins at cytosolic proteins and completed inside ER

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20
Q

Transmembrane proteins carry a…

A

Signal sequence

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21
Q

What does a signal sequence do?

A

Halts translation and directs ribosome synthesising the protein to dock with the ER, forming RER

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22
Q

What is a signal sequence?

A

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

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23
Q

Why does protein pore remove cytosol particle and signal sequence after docking?

A

To allow translation to continue

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24
Q

As translation continues after docking…

A

The protein is inserted into the membrane of the ER

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25
Q

What is post-translational modification?

A

When polypeptide chains have carbohydrates or phosphates added to them or are cleaved to form an active protein

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26
Q

What is the major modification?

A

Addition of carbohydrates

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27
Q

To form carbohydrates…

A

Enzymes catalyse the addition of various sugars in multiple steps

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28
Q

What are microtubules?

A

Structures that make the cell’s cytoskeleton and offer support and a means of transport

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29
Q

Where do vesicles that leave the Golgi apparatus take proteins?

A

Plasma membrane and lysosomes

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30
Q

Vesicles move along microtubules to…

A

Other membranes within cell and fuse with them

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31
Q

What are proteins transported by once they are in the ER?

A

Vesicles that bud off from the ER and fuse with the Golgi apparatus

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32
Q

How do molecules move through the Golgi discs?

A

In vesicles that bud off from one disc and fuse with the next in the stack

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33
Q

Due to their size, eukaryotes have a relatively small surface area to volume ratio so…

A

Plasma membrane is too small an area to carry out all the vital functions of the membrane

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34
Q

Examples of secreted proteins

A

Peptide hormones such as insulin and digestive enzymes such as trypsin

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35
Q

Many secreted proteins are synthesised as…

A

Inactivate precursors so require proteolytic cleavage to produce active proteins

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36
Q

What is proteolytic cleavage?

A

Type of post-translational modification where polypeptide is cut

37
Q

What are amino acids?

A

Building blocks of proteins

38
Q

Amino acid sequence determines…

A

Protein structure

39
Q

What are proteins?

A

Polymers of amino acid monomers

40
Q

Amino acids have the same… differing only in…

A

Basic structure, R group present

41
Q

Amino acids are linked by… (occurs during translation at ribosomes)

A

Peptide bonds to form polypeptides

42
Q

How is a peptide bond formed?

A

Enzyme causes condensation reaction between 2 adjacent amino acids (water is removed)

43
Q

What kind of bond is a peptide bond?

A

Strong covalent bond

44
Q

All amino acids contain an…

A

Amine (NH2) and acid group (COOH)

45
Q

Name R groups

A

Acidic- hydrophilic, - , COOH
Basic- hydrophilic, + , NH2
Polar- hydrophilic, slightly charged, CO, OH, NH2
Hydrophobic- hydrophobic, no charge, CH3

46
Q

R groups vary in…

A

Shape, size, charge, hydrogen bonding capacity and chemical reactivity

47
Q

Diversity of R groups accounts for…

A

The wide range of functions carried out by proteins

48
Q

What is primary structure?

A

Sequence in which amino acids are synthesised into polypeptide

49
Q

What is secondary structure?

A

Result of hydrogen bonding along backbone of protein strand

50
Q

What is tertiary structure?

A

Final folded shape of the polypeptide and stabilised by interactions between R groups of amino acids

51
Q

What are the interactions between R groups?

A

Hydrophobic interactions
Ionic bonds
London dispersion forces
Hydrogen bonds
Disulphide bridges

52
Q

What is quaternary structure?

A

Spatial arrangement of subunits, only exists in proteins with 2 or more polypeptide subunits

53
Q

Subunits are linked by…

A

Bonds between r groups of polypeptide chains

54
Q

What are London dispersion forces?

A

Very weak attractions between electron clouds of atoms

55
Q

What are hydrogen bonds?

A

Strong attractions between hydrogen atom and an electronegative atom (O2 or N2)

56
Q

What are disulphide bridges?

A

Covalent bonds between R groups containing sulphur

57
Q

What are ionic bonds?

A

COOH and NH2 groups ionise to become COO- and NH3+ which are strongly charged and attracted to each other

58
Q

What are hydrophobic interactions?

A

As a polypeptide folds into its functional shape, the hydrophobic R groups are repelled by water so usually end up on the inside of the protein away from the surface

59
Q

What is a prosthetic group?

A

Non-protein subunit bound tightly to protein and necessary for its function

60
Q

Ability of haemoglobin to bind oxygen is dependent upon…

A

non-protein haem group (prosthetic group)

61
Q

Effect of increasing temperature on interactions between R groups

A

Disrupts interactions that hold the protein in shape so protein begins to unfold and eventually denatures

62
Q

Effect of changing pH on interactions between R groups

A

As pH increases/decreases away from optimum, the normal ionic interactions between charged groups are lost which gradually changes the conformation of the protein until it denatures

63
Q

What is a ligand

A

A substance that can bind to a protein

64
Q

Binding sites on surface of protein will have…

A

Complementary shape and chemistry to ligand

65
Q

Mechanism used to regulate protein activity

A

Conformational change

66
Q

What is an allosteric enzyme?

A

Enzyme whose activity is regulated by altering its conformation, contain a second type of binding site (allosteric site)

67
Q

Where does a substrate bind?

A

Active site

68
Q

Where does a substance other than the substrate bind?

A

Allosteric site

69
Q

What does a modulator do?

A

Regulate the activity of an enzyme by binding to the allosteric site, change conformation of enzyme which alter affinity of active site for substrate

70
Q

A positive modulator…

A

Increases the enzyme’s affinity for the substrate, increasing activity

71
Q

A negative modulator…

A

Decreases the enzymes affinity for the substrate, decreasing activity

72
Q

Many allosteric proteins consist of…

A

Multiple subunits so have quaternary structure

73
Q

What does allosteric mean?

A

‘other shape’ Refers to proteins that have interactions between spatially distinct sites (on same protein)

74
Q

What happens when a ligand binds to a protein binding site?

A

Protein changes conformation so function changes

75
Q

What is phosphorylation?

A

When a phosphate group is added or removed from the protein, common form of post-translational modification

76
Q

A large subset of proteins is… when first synthesised so require…

A

Inactive, post-translational modification to become activated

77
Q

What do protein kinases catalyse?

A

The transfer of a phosphate group from ATP to other proteins, the terminal phosphate of ATP is transferred to specific R groups

78
Q

What do protein phosphatases catalyse?

A

The transfer of a phosphate group from protein to ADP to generate ATP (reverse reaction)

79
Q

What allows binding of ligands?

A

R groups not involved in protein folding

80
Q

What does phosphorylation do to a protein?

A

Conformational changes which can affect protein’s activity

81
Q

Haemoglobin is made of…

A

4 polypeptide subunits (haem groups)

82
Q

What is co-operativity?

A

When changes in binding at one subunit alter the affinity of the remaining subunits (shown by allosteric proteins)

83
Q

What causes the activity of allosteric enzymes to vary greatly?

A

Small changes in substrate concentration

84
Q

Binding of a substrate molecule to one active site of an allosteric enzyme…

A

Increases the affinity of the other active sites for binding of substrate molecules

85
Q

Haemoglobin shows co-operativity in…

A

binding and release of oxygen

86
Q

What happens when an oxygen molecule binds to one subunit of haemoglobin?

A

Conformation of the subunit changes

87
Q

what happens when an oxygen molecule is release from haemoglobin?

A

Decrease in affinity of other subunits to maximise the release of oxygen where it is needed e.g. working tissues

88
Q

When temperature is increased and pH reduced in actively respiring tissues

A

AH Biology (13 decks)

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