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BIOL2200 > Module 1 - Organelles/Cell Machinery > Flashcards

Module 1 - Organelles/Cell Machinery Flashcards

1
Q

Proteins

A

cells functioning units, encoded by DNA translated from mRNA, structure determines function – structural, sensors, transporters, communication, signalling

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2
Q

Oligomers

A

proteins composed of more than one polypeptide chain

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3
Q

Transcription

A

in the nucleus, DNA ––> mRNA, catalysed by RNA polymerase

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4
Q

RNA splicing

A

Before RNA leaves the nucleus (during or after transcription, non coding introns are removed, exons are joined to form transcript, 5’ cap and 3’ polydenylation

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5
Q

Introns

A

Non coding sequences – removed in splicing

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6
Q

Exons

A

Coding sequence – joined in splicing to form transcript

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7
Q

Translation

A

In ribosome in cytoplasm: mRNA ––> amino acids (codons+anticodons) ––> polypeptide ––> protein,

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8
Q

N–terminus

A

beginning of a protein, the end of a polypeptide or protein that has a free amine group (–NH^2)

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9
Q

C–terminus

A

end of a protein, the end of a polypeptide or protein that has a free carboxyl group (–COOH)

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10
Q

Anterograde

A

secretory pathway, away from the cell body, exocytosis (COP II vesicle protein)

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11
Q

Retrograde

A

Uptake, endocytosis, moving backwards (COP I vesicle protein)

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12
Q

Protein turnover

A

the continual renewal or replacement of proteins, cells are not stable!!

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13
Q

Primary structure

A

sequence of amino acids, determines proteins shape and structure

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14
Q

Secondary structure

A

alpha helix or beta pleated sheet.

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15
Q

Structural motifs

A

combinations of secondary strucutres – ring finger, zinc finger

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16
Q

Tertiary structure

A

three dimensional fully folded shape of a protein, a single polypeptide chain backbone with one or more secondary structures

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17
Q

Quaternary structure

A

results of two or more proteins interacting

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18
Q

Dimerization

A

process of forming a macromolecular complex from two protein monomers

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19
Q

Oligomerization

A

process of forming a macromolecular complex from multiple protein monomer subunits

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20
Q

Dimer

A

macromolecular complex made up of two protein subunits

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21
Q

Macromolecular complexes

A

nanomachines comprising of multiple different protein subunits, built by subcomplexes around a core subunit, modular and flexible, more diverse/complex function than proteins + domains

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22
Q

Domains

A

distinct regions of tertiary protein structure – eg. globular, fibrous, transmembrane – larger than structural motifs, functional

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23
Q

Daltons (Da)

A

units to measure mass at molecular scale, proteins ––> kiloDaltons (kDa), protein complexes ––> megadaltons (MDA)

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24
Q

Svedberg (S)

A

units to measure size/shape, bigger molecule = greater svedberg unit, non standard and non linear

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25
Q

ATP

A

contains high energy phosphate bonds, energy is released when the terminal phosphate bond is broken (hydrolysis)

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26
Q

ATP hydrolysis

A

ATP ––> ADP

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27
Q

post–translational modification

A

covalent modifications that change protein structure after the protein has been synthesised, changes structure and function – regulation for trafficking or degradation etc

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28
Q

Phosphorylation

A

the addition of a phosphate group to a molecule catalysed by kinases (from ATP), example of a PTM

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29
Q

Kinase

A

an enzyme that catalyses the transfer of a phosphate group from ATP to a specified molecule

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30
Q

Ubiquitination

A

addition of one or more ubiquitin (regulatory protein – targeting for degradation) to lysine residues, example of a PTM

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31
Q

Ubiquitin

A

protein that is linked to other proteins as a way of marking the targeted protein for degradation by proteasomes.

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32
Q

Allosteric regulation

A

regulation of protein structure/function cause by non covalent binding by a ligand (eg. calcium, nucleotide, protein), interaction without chemically linking, eg. Ca 2+ and calmodulin

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33
Q

GTPase switch

A

Guanosine–triphosphate (GTP) binding changes structure to increase enzyme activity (switch on), GTPase activating protein (GAP) catalyses inactivation and turns the system off (GDP), Guanine Exchange Factor (GEF) switches on

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34
Q

GTPase activating protein (GAP)

A

increases GTPase activity, catalyses hydrolysis of GTP ––> GDP turning the system off

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35
Q

Guanine Exchange factor (GEF)

A

stimulates the release of (GDP) turning the system on

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36
Q

Polymerase

A

catalyses polymerization reactions such as the synthesis of DNA and RNA

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37
Q

Chaperonins

A

a protein complex that assists in the folding of other proteins, barrel shaped, driven by ATP hydrolysis

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38
Q

Hydrolysis

A

breaking down of polymers/complex molecules by the chemical addition of water

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39
Q

Kinesin

A

motor proteins in cellular transport (anterograde)

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40
Q

Proteasome

A

cuts peptide bonds for degradation, ubiquitin chains are used to recognise proteins

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41
Q

Nucleus

A

large membrane (inner + outer) enclosed organelle that encodes the majority of proteins in the cell, gene expression determines nature of cell and organism, highly dynamic

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42
Q

Perinuclear

A

around the nucleus

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43
Q

Nuclear lamina

A

a netlike meshwork of cytoskeletal protein filaments, adjacent to the inner membrane that maintains the shape of the nucleus by mechanically supporting the nuclear envelope

44
Q

Nucleolus

A

sub–organelle within nucleoplasm, genetically defined structure with no membrane, formed in regions of rRNA, site of ribosomal biogenesis, hotspot of transcriptional activity

45
Q

Chromatin

A

DNA + histone complex, repeating unit is nucleosomes, packages 2m on DNA, dynamic – structure determines function

46
Q

Nucleosomes

A

DNA coiled around histones, repeating unit of chromatin

47
Q

Acetylation

A

addition of acetyl group, causes chromatin to loosen/become less condensed ––> transcriptionally active/euchromatin

48
Q

Euchromatin

A

less condensed, transcriptionally active chromatin

49
Q

Unacetylated

A

highly condensed, transcriptionally inactive chromatin/heterochromatin

50
Q

Heterochromatin

A

highly condensed, transcriptionally inactive chromatin/unacetylated

51
Q

Histones

A

protein molecules around which DNA is tightly coiled in chromatin, can be targets of PTMS to determine gene expression

52
Q

Nuclear Pore Complex (NPC)

A

Large multiprotein structure forming a channel through the nuclear envelope that allows selected molecules to move between nucleus and cytoplasm

53
Q

Nucleoporins (Nups)

A

proteins that make up the nuclear pore complex – 30 different kinds, scaffold, linker, barrier + transport, cytoplasmic filaments

54
Q

Localisation signals

A

functionally distinct amino acid sequences on protein cargo to allow import or export from the NPC and overcome size barrier – Import: Nuclear Localisation Sequence (NLS), Export: Nuclear Export Sequence (NES)

55
Q

Nuclear Localisation Sequence (NLS)

A

amino acid sequence recognised by importin receptors to allow the import of protein cargo in the nucleus

56
Q

Nuclear Export Sequence (NES)

A

amino acid sequence recognised by exportin receptors to allow the import of protein cargo out of the nucleus

57
Q

Importins

A

nuclear import receptors, binding controlled by GTPase switch

58
Q

Exportins

A

nuclear export receptors ––> cytoplasm, binding controlled by GTPase switch

59
Q

Ran–GTP

A

binds importin causing it to dissociate from the cargo into the nucleus, GTP ––> GDP releases importin , binding to exportins promotes association with cargo, GTP ––> GDP releases exportin

60
Q

Ran–GDP

A

formed after Ran–GTP hydrolyses itself in the cytosol, dissociated from the receptor (exportin or importin)

61
Q

Laminopathies

A

genetic mutations impacting lamins/nuclear membranes and proteins, nuclear and genome instability ––> premature ageing (HGPS)

62
Q

Endoplasmic Reticulum (ER)

A

large continuous membrane, smooth and rough, protein modification – folding/quality control/glycosylation, secretory pathway, dynamic microtubule extension and retraction movement

63
Q

Protein secretory pathway

A

ER ––> Golgi ––> Vesicle ––> Plasma membrane

64
Q

Rough ER

A

sheet like cisternae flattened membrane, studded with ribosomes

65
Q

Smooth ER

A

branched, tubular membrane of the ER

66
Q

Reticulons

A

proteins responsible for ER membrane’s curvature, inserted in phospholipid bilayer to shape tubes

67
Q

Lumen

A

area enclosed by the endoplasmic reticulum membrane, network of membrane tubules, vesicles and cisternae

68
Q

Cotranslational translocation

A

during translation secretory protein polypeptide chains enter the ER bound to ribosomes, uses Singal Recognition Particple (SRP), SRP receptor at ER and translocon, polypeptide folds within ER lumen

69
Q

Translocon

A

protein complex that transports polypeptides with a targeting signal sequence into the lumen of the endoplasmic reticulum ER from the cytosol

70
Q

Type 1 membrane protein

A

protein translocated to ER, inserted into membrane using a stop–transfer anchor sequence, STA in embedded in lipid bilayer, cytoplasmic C–terminus and luminal N–terminus

71
Q

Type 2 membrane protein

A

protein translated in cytoplasm then translocated to ER, signal anchor sequence embedded into lipid bilayer, reverse topology to type 1, cytoplasmic N–terminus and luminal C–terminus

72
Q

Type 3 membrane protein

A

protein with same topology as type I but translocation mechanism is similar to type II, recognized by SRP, brought to translocon and anchored into membrane but in reverse orientation to Type II – same as type 1

73
Q

Type 4 membrane protein

A

multiple stop–transfer anchor and signal–anchor sequences and combination of Type I, II and III mechanisms, tail anchored proteins, C–terminal anchor sequence is inserted into the membrane after translation

74
Q

Glycosylation

A

post translational sugar modification of proteins, addition of sugar chains (glycans) to form glycoproteins, aids in folding and determines function

75
Q

Glycoproteins

A

proteins that have carbohydrates/glycans covalently bonded to them

76
Q

Golgi apparatus

A

ribbon like organelle, modifies/processes and packages proteins for export, glycosylation

77
Q

Cisternae

A

Flattened, membrane disks that make up the golgi apparatus, cis, medial, trans, each contain different enzymes, cisternal maturation

78
Q

Cis golgi network

A

section of the golgi apparatus that receives materials from the endoplasmic reticulum

79
Q

trans golgi network

A

section of the golgi apparatus where proteins are segregated into different types of membrane enclosed vesicles for delivery to the plasma membrane or organelles

80
Q

medial cisternae

A

section of the golgi apparatus between the cis and trans cisternae

81
Q

GRASPs

A

golgi reassembly and stacking proteins, membrane associated proteins, dimerise and oligomerise, holds parallel cisternae

82
Q

Golgins

A

coiled rod like proteins tethering of stacks of ribbons in golgi apparatus

83
Q

COP II

A

vesicular trafficking protein – ER ––> cis Golgi (anterograde)

84
Q

COP I

A

reverse vesicular trafficking protein, return– golgi ––> ER (retrograde)

85
Q

Cisternal maturation

A

cisterane matures to trans face (cis ––> medial ––> trans), secretory cargo remains stationary, retrograde (COP II) transport maintains cisternal residency for membrane specific enzymes

86
Q

Mitcochondria

A

multi membrane organelle, aerobic oxidation – glucose ––> ATP

87
Q

Endosymbiosis

A

theory that mitochondria evolved from bacteria, mitochondria undergo fission like bacteria

88
Q

mtDNA

A

mitochondrial DNA

89
Q

Mitochondrial proteins

A

coded in mtDNA and nucleus, imported unfolded and folds in mitochondria lumen, with an N terminus targeting sequence recognised by an outer membrane receptor, passes through outer and inner membrane translocons simultaneously

90
Q

Mitochondrial matrix

A

the compartment of the mitochondrion enclosed by the inner membrane and containing enzymes and substrates for the citric acid cycle, as well as ribosomes and DNA

91
Q

Oxidative phosphorylation

A

The production of ATP using energy redox reactions of an electron transport chain, converts energy stored in hydrocarbon bonds of sugars (glucose) and lipids into ATP

92
Q

Oxidation

A

loss of electrons

93
Q

Reduction

A

gain of electrons

94
Q

NADH

A

the reduced form of NAD+; an electron–carrying molecule that functions in cellular respiration

95
Q

FADH

A

reduced form of FAD, electron carrying molecule that functions in cellular respiration

96
Q

Glycolysis

A

glucose is converted to pyruvate (+NADH), occurs in the cytoplasm before the krebs cycle in the mitochondira

97
Q

Cellular respiration

A

glycolysis, krebs cycle/citric acid cycle, oxidative phosphorylation (electron transport chain + chemiosmosis), glucose + oxygen ––> carbon dioxide + water + ATP

98
Q

Pyruvate

A

end product of glycolysis, oxidised to Acetyl CoA and CO2

99
Q

Acetyl CoA

A

Acetyl coenzyme A; the entry compound for the citric acid cycle in cellular respiration, formed from oxidising pyruvate

100
Q

Citric Acid Cycle (Krebs Cycle)

A

second stage of cellular respiration, in which pyruvate/pyruvic acid is broken down into carbon dioxide in a series of energy–extracting reactions

101
Q

Electron transport chain

A

A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.

102
Q

Chemiosmosis

A

gradient created by H+ ions diffusing across semi–permeable membranes in the mitochondria, creates kinetic energy to drive ATP synthase to catalyse the phosphorylation to ADP to ATP

103
Q

Mitochondrial fission

A

Mitochondrial fission factors (MFF) recruit G proteins that hydrolyse GTP to pinch membranes, used to segregated and remove damaged components to target for degradation

104
Q

Mitochondrial fusion

A

Mitofusins (MFNS) G proteins hydrolyse– outer membrane followed by inner, used for growth and replication – segregation during cell division

105
Q

Parkinson’s

A

mutations on genes encoding PINK kinase and a parkin – a ubiquitin ligase, required to prevent fusion of damaged mitochondria, therefore damaged organelles are not removed

106
Q

G proteins

A

guanine nucleotide–binding proteins, family of proteins that act as molecular switches, involved in transmitting signals for movement in and out of cells

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