Mid-block Test - March Flashcards Preview

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Flashcards in Mid-block Test - March Deck (353):
1

What are the three sites on a ribosome?

E - Exit
P - Peptide Bond formation
A - Arrive

2

What is the first amino acid used in Translation?

Met

3

What happens in initiation of Translation? What regulates it?

5' end of mRNA binds to small ribosomal subunit
Large ribosomal subunit attaches to this

Binding of the Large ribosomal subunit is regulated by Eukaryotic Initiation Factors (EIF's)

4

What form of energy is used in the elongation stage of Translation? What processes is it used for?

GTP is used as energy

1: When the tRNA attaches to the A site
2: When the ribosome is translocated to make space for another tRNA

5

What is the enzyme that aids peptide bond formation in Translation?

Peptidyl Transferase

6

What regulates the process of translocation during Translation?

Eukaryotic Elongation Factors (EEF's)

7

What processes occur at part of Termination of Translation?

1: Stop codon appears in A site
2: Water molecule added to end of polypeptide chain
3: Ribosome subunits dissociate

8

What adds a water molecule to the end of a polypeptide chain in translation?

Release Factor

9

What regulates the process of ribosomal subunits dissociating at the end of translation?

Releasing Factors (eRF's)

10

In which way does one label condons or anticodons?

3' to 5'

11

What is a polyribosome

A mRNA molecule and two or more ribosomes that make up a complex

12

Where does the processing of proteins take place?

ER

13

What causes the polyribosome to be directed towards the ER?

The "Signal Sequence" on an already-formed part of synthesising DNA

14

What is the name of the process whereby sugar groups are added to a newly-synthesised protein

Glycosylation

15

Where does folding of proteins take place?

In the ER Cisternae.

16

What happens after protein folding in the processing of newly-synthesised proteins?

The protein is enclosed in transport vesicles and budded off from the ER. It then travels to the Golgi for further processing

17

What part of the Golgi does a transport vesicle containing a newly-synthesised strand of protein attach to?

The cis face

18

What are the products that exit the Golgi after protein processing

Secretory Vesicle
Membrane Vesicle
Lysosomal Vesicle

19

What is the role of Tetracylins

Blocks the A site of 30S ribosomal subunit of prokaryotes

20

What do Aminoglycoside Antibiotics do

Modify ribosomal proteins

21

What two molecules inhibit the elongation step of translation in bacteria

Macrolide
Peptidal Transferase Inhibitors

22

What molecule disrupts the elongation step of translation in all cells

Aminoacyl tRNA analogues

23

What do Dipheria Toxins do

modify the EEF-2 in all mammalian cells - Inhibiting translation

24

Where do the sidechains of hydrophobic proteins point

Point to the outside

25

Where do the sidechains of hydrophilic proteins point

Point to the centre

26

What differentiates a peptide and a protein

A peptide is less than 30 amino acids long
A protein is longer

27

What constitutes the primary level of protein structure

Peptide bonds between amino acids, making a chain

28

What constitutes the secondary level of protein structure

Backbone interaction (H bonds) making a structured chain

29

What two types of secondary protein structure are there

Alpha helix
Beta sheet

30

What constitutes the tertiary level of protein structure

3D structure of a chain

31

What molecular interactions enable a tertiary protein structure to be formed

H bonds
Ionic bonds
Hydrophobic interaction
VDW forces

32

What is a proprotein? What processes does it undergo?

A proprotein is an inactive protein. It is activated by the removal of a terminal amino group

33

What type of amino acid can be phosphorylated?

Any amino acid containing a hydroxyl (OH)

34

What two processes regulate chromatin organisation

methylation and acetylation

35

What process regulates degradation of proteins in the proteasome?

Polyubiquination

36

What process regulates protein sorting (making sure proteins get transported to correct location)

Monoubiquination

37

What is the role of p53

Acts as a tumour suppressor

38

Where does glycosylation happen?

ER
Golgi
Cytoplasm

39

Describe the general pattern of digestive processes mediated by the lysosome

1: Protein taken into cell
2: Enters Early Endosome, forming a multivesicular body
3: The multivesicular body fuses membrane with a lysosome

40

What is autophagy used for

Used to break down things INSIDE the cell

41

Describe the process of Microautophagy

When endogenous proteins (inside the cell) get endocytosed into lysosome of cell

42

Describe the process of Macroautophagy

1: Phagopore surrounds large cellular components of cell
2: Phagopore closes to form Autophagosome
3: Autophagosome fuses membrane with lysosome

43

Which molecules are involved with the folding of proteins

hsp60 protein-like complex
GroES Cap

44

What is the core component of the proteasome made of

Catalytic (proteolytic) sites

45

What are the funcations of the regulatory caps on each end of the proteasome

Recognises proteins
Unfolds proteins
Feeds proteins in

46

Which steps of the proteosome function require ATP

Unfolding protein
Feeding protein in

47

What is Ubiquitin activating enzyme? What does it do?

E1
Forms a bond with ubiquitin

48

What is Ubiquitin-conjugating enzyme? What does it do?

E2
Recieves ubiqutin from E1

49

What is an E3 ligase? What does it do?

E3 ligase is another name for E3
It transfers the ubiquitin from E2 onto the protein

50

How can the E3 ligase subunit be changed to enable it to bind to a protein?

Phosphorylation
Ligand binding (causes allosteric transition)
Protein subunit addition (causes allosteric transition)

51

What is the role of proteases in the immune system?

Cleaves bits of proteins into correct length to be displayed on MHC molecules

52

What is the main cause of the malfunctioning of the proteasome pathway?

Intracellular accumulation of misfolded proteins

53

What are the variable properties that are manipulated in beads that are used in protein purification

Affinity for proteins (some won't stick to beads)
Size-exclusion (some proteins will get trapped)
Ion-exchange (proteins with opposite charge will stick)

54

What is PP2B also called? What does it do?

A phosphoserine and Phosphotheronine Phosphatase

It is also called Calcineurin (binds Ca to get activated)

55

What does malfunctioning of the proteasome pathway lead to?

Degenerative diseases such as Alzheimers and Parkinsons Disease

56

What is the anti-cancer drug that uses the proteasome pathway to operate? What does it do?

Bortezomib

Blocks the proteasome - resulting in increased apoptosis of cancer cells

57

What is SDS-PAGE used for

To separate and identify proteins

58

What does SDS do to proteins

Coats them with a uniform negative charge - masks intrinsic charge. This uniform charge is proportion to the protein's molecular mass

59

What is PAGE

Poly-acrylamide gel electrophoresis

60

What determines the speed of migration of proteins in PAGE?

Molecular weight

61

In PAGE, what does a lower concentration of acrylamide result in?

Bigger pores

62

In PAGE, how is the migration distance of the protein related to it's mass

The migration distance is negatively proportional to the log of its mass

63

In PAGE, how would one estimate the mass of a protein

For proteins of both known and unknown masses -
Plotting Rf (relative migration distance) vs. log of its mass

64

If you can't see a protein after SDS-PAGE, what should you do

use a Silver Stain or Coomassie Stain

65

What is isoelectric focusing (IEF)

When you use a gel that has a pH gradient to separate proteins based on their pH

66

What is the pH gradient in IEF caused by?

Presences of ampholytes in IEF gel causes pH gradient

67

When do proteins stop moving in IEF

At their Isoelectric point. This is when the Isoelectric Charge is equal to their pH

68

How does one perform 2D gel electrophoresis

1: do isoelectric focusing in a tube gel to separate according to charge
2: perform SDS-PAGE on this tube gel to separate according to mass

69

What are the specific protein properties that are used for protein purification?

Size
Charge
Hydrophobicity
Biorecognition

70

What is used as a solvent that proteins can run through in the process of protein purification

Beads with specific properties

71

What are the variable properties that are manipulated in beads that are used in protein purification

Affinity for proteins (some won't stick to beads)
Size-exclusion (some proteins will get trapped)
Ion-exchange (proteins with opposite charge will stick)

72

What splits the plasmid's DNA or the desired gene's DNA in protein recombination?

Restriction Enzyme

73

What are the two words used when introducing rDNA in Bacteria and Eukaryotes respectively

Transformation - Bacteria
Transfection - Eukaryotes

74

What are two methods of Transformation in protein recombination

Electropolation (creates holes by current)
Chemicals (Ca salts + Heat Shock)

75

What are four methods of Transfection in protein recombination

Electropolation (creates holes by current)
Chemicals (Ca salts + Lipids)
Microinjection
Opticalation

76

What are the four required features of a cloning vector in protein recombination

1: Appropriate origin of replication
2: Marker genes
3: Restriction endonuclease (ER) sites
4: Promotors

77

How many Restriction Endonuclease sites does an ideal cloning vector have in gene recombination

One

78

What can be used as plasmids in protein recombination

Plasmids (Extrachromosomal molecules in bacteria)
Bacteriophages (viruses that infect bacteria)
Cosmids (specialised DNA plasmids with sequences called cos sites)

79

What is the function of reverse transcriptase? What is it used for?

Reverse transcribes mRNA into DNA.

It is used to take an mRNA molecule and change it into it's corresponding DNA strand to insert it into a recombinant plasmid

80

What binds to the active site of a protein kinase

Protein & ATP

81

Which amino acids have OH groups? What is the significance of this?

Serine, Tyrosine, Threonine

This enable the amino acid to be phosphorylated

82

What kind of phosphate does a protein kinase add to target proteins? Where does it get this?

Adds a gamma phosphate from ATP

83

What is a motif? What can it also be called?

A specific short amino acid sequence. Also called a Consensus Sequence

84

How does phosphorylation of a protein result in conformational changes

Phosphorylation adds two negative charges which changes the protein's structure

85

What are the types of Cytoplasmic Serine & Theonine Kinases

MAPK
AKT
PKA
PKC

86

What are the types of Receptor Serine & Theonine Kinases

Transform growth factor beta
TGFBRI
TGFBRII

87

What are the types of Cytoplasmic Tyrosine Kinases

SRC

88

What are the types of Receptor Tyrosine Kinases

EGFR
JAK

89

Describe the structure of a kinase

A polypeptide chain that has
-Catalytic domain (with active site)
-Regulatory domain

A polypeptide chain with a regulatory subunit

90

How many amino acids does a kinase consist of

250 - 300 amino acids

91

What are the two lobes that the catalytic domain of a kinase consists of

N terminal lobe
C terminal lobe

92

What is the function of the N terminal lobe of a kinase

Binds ATP

93

What is the function of the C terminal lobe of a kinase

Binds substrate (protein)

94

Where is the site of catalysis in a kinase? How is it regulated?

The cleft between each lobe in the catalytic domain is the site of catalysis

It is regulated by an activation loop that is phosphorylated to activate kinase itself.

95

In what types of kinases is the regulatory section part of the same chain as the catalytic domain?

Ca Calmodulin Kinase
SRC Tyrosine Kinase

96

In what types of kinases is the regulatory section part of a different protein chain as the catalytic domain

PKA
CDK

97

What amino acid does Ca Calmoduin dependent kinase phosphorylate?

Serine and Threonine

98

How does Ca Calmodulin dependent kinase get activated

When calmodulin with attached Ca binds to regulatory domain

99

What amino acid does CDK phosphorylate?

Serine and Threonine

100

What is one disease that can result from an overactive Wnt pathway

Ankylosing Spondylitis

101

What amino acid does PKA phosphorylate

Serine and Threonine

102

What does the structure of PKA consist of

It is tetrameric:
-2 regulatory subunits
-2 catalytic subunits

103

How does PKA get activated

cAMP binds to a regulatory subunit

104

How does a Tyrosine Kinase Receptor get activated?

Dimerisation of catalytic sites

105

What are the two regulatory domains of an SRC Tyrosine Kinase called?

SH2 & SH3

106

How is an SRC Tyrosine Kinase activated

Dephosphorlatioon

107

What is PP2A

A Phosphoserine and Phosphotheronine Phosphatase.

It reverses phosphorylation in signalling pathways activated by growth factors

108

What is PP2B also called? What does it do?

A phosphoserine and Phosphotheronine Phosphatase

It is also called Calcineurin (binds Ca to get activated)

109

What does a Ligand-Receptor complex function as in Intracellular Signalling

Works as a transcription factor

110

What is a Hormone Response Element

Short sequence of DNA within promotor of a gene able to bind a specific hormone receptor complex and regulate transcription

111

Name the three most common Hydrophobic first messengers

Steroid hormones
Thyroid hormones
Vitamins

112

What is the main mechanism used in Hydrophilic signalling

Protein kinases are activated resulting in:
-Proteins with altered functions
-Transcription factors activated

113

What is the main example of a membrane receptor without associated kinase activity

G protein coupled receptor

114

What kinase is a cytokine receptor associated with

JAK (tyrosine kinase) that phosphorylates the tail-end motif sequence containing Tryosine

115

How many domains does an adaptor protein consist of

two or three

116

What are the two functions of adaptor proteins

Link proteins together
Pass signals on

117

What is the name of the domain in an adaptor protein that links phosphorylated tyrosine amino acids

SH2

118

What do scaffold proteins do

Bind other proteins to bring them into a complex

119

Where is a Conserved Consensus Sequence found? What does it do?

Found in the promotor

Binds general transcription factors
Binds specific transcription factors

120

What happpens when a scaffold protein is phosphorylated?

Many different proteins with SH2 domains are recruited

121

Which two proteins of the Wnt pathway are scaffold proteins

Axin and APC

122

What is intrinsic GTPase activity

When cells convert GTP to GDP to switch themselves off.
Used in G proteins

123

What makes holes in the mitochondrial membrane enabling cytochrome C to be released? Which secretions do this?

Cyototoxic CD8 T cell & NK Cell

Release:
- Granzymes
- Perforin

124

What is the immediate result of activation of heterotrimeric G proteins

Activation of effector enzymes

125

What is the function of effector enzymes

To produce second messengers (e.g. cAMP, IP3)

126

What is the function of 2nd messengers

To activate kinases

127

How do small monomeric G proteins activate kinases? Where do they get their energy to do this?

Bind GEF (Gaunine nucleotide exchange factor)
In the process, use GTP.

128

What membrane receptor do 50% of modern drugs tarted

G Protein Coupled Receptor

129

What shape is the G Protein coupled receptor? How many times does it span the membrane

Serpentine in shape
Spans the membrane 7 times

130

In the G Protein, which subunit dissociates and regulates the target protein

Alpha subunit

131

What is the active form of the G Protein? Vice versa?

Active = GTP on alpha subunit
Inactive = GDP on alpha subunit

132

What are the effector enzymes, 2nd messengers and kinase cascades associated with the Gs pathway?

Effector Enzyme - Adenylate Cyclase
2nd messenger - cAMP
Kinase Cascade - PKA

133

What are the effector enzymes, 2nd messengers and kinase cascades associated with the Gq pathway?

Effector Enzyme - Phospholipase C
2nd messenger - DAG/IP3
Kinase Cascade - Ca Calmodulin/PKC

134

Which are the signalling pathways that are involved with regulating growth factors

Tyrosine Kinase Receptor Pathways (MAPK, PI3-K)

135

What can unregulated RTK Signalling lead to?

Cancer
Inflammatory diseases
Diabetes

136

What are the main therapies against the RTK fmaily

Trastuzumab: Herceptin (Anti-HER2)
Gefitinib (anti-EGFR)

137

What is FGF and what role does it play

Growth Factor
Fibroblast Growth Factor. Crucial role in control of development

138

What is VEGF and what role does it play

Growth factor
Vascular Endothelial Growth Factor. It plays an important role in agiogenesis

139

What are Agiopoeitins and what important role do they play?

Growth factor
Plays an important role in angiogenesis and cell adhesion of haematopoetic stem cells to their stem cell niche

140

What two ligands are predominantly involved in both the PI3K and MAPK pathways

EGF (Epidermal Growth Factor)
PDGF (Platelet Derived Growth Factor).

141

What is one defining characteristic of the EGF Ligand

It gets anchored in the plasma membrane due to it containing a hydrophobic domain

142

What is one defining characteristic of PDGF

It sometimes needs to be cleaved by proteases in ECM to become activated

143

What is the role of Heparon Sulphate Proteoglycans

Bind growth factors such as FGF and PDGF restricting their action

144

What are two RTK receptors used in both the MAPK and PI3K Pathways

EGFR
PDGFR

145

What are the defining characteristics of RTK receptors

1: Need to be dimerised
2: Made of groups of Tyrosine Amino Acids

146

What type of adaptor is used the in MAPK pathway

SH2 adaptor

147

What directly activates the MAPK Cascade

RAS (Small monomeric G Protein) activated by GEF giving it an ATP

148

What are the results of the MAPK Pathway

Altered proteins
Altered transcription factors

Proliferation due to G1 cyclins being produced (proto-oncogenes)

149

What is the adaptor used in the PI3K Pathway

SH2 adaptor

150

What is the direct role of PI3K

Phosphorylates PIP2 to turn it into PIP3

151

What is the role of PIP3

Binds AKT (using it's PH domain) which enables other enzymes to phosphorylate AKT

152

What happens to AKT once it is phosphorylated

Acts as a kinase and phosphorylates proteins (NOT TRANSCRIPTION FACTORS) involved in survival and proliferation

153

What three things does the Wnt pathway play an important role in?

Embryogenesis
Proliferation of colorectal epithelia
Bone formation

154

What is one disease that can result from an inhibited Wnt pathway

Rheumatoid Arthritis

155

What is one disease that can result from an overactive Wnt pathway

Ankylosing Spondylitis

156

What is the receptor-related protein for that of Frizzled

LRP

157

What makes up the degradation complex in the Wnt pathway

Axin
GSK
APC
Beta-catenin

158

What is the function of Axin and APC

Axin and APC both act as scaffold proteins in the degradation complex formed in the Wnt Pathway

159

What is the function of GSK

Kinase that acts on beta-catenin in the degradation complex of the Wnt Pathway

160

How is Beta-catenin degraded when there is no ligand attached to the Frizzled membrane receptor protein

GSK causes beta-catenin to become phosphorylated which causes it to be ubiquinated by E3 Ligase

161

How is the degradation complex prevented from forming when the Wnt ligand is attached to the Frizzled membrane receptor

Axin (scaffold protein) binds to LRP
GSK (kinase) is inhibited by Frizzled

162

How does beta-catenin act as a transcription factor

It binds to TCF

163

What are the four phases of the cell cycle

M
G1
S
G2

164

In which stage of the cell cycle is the signal recieved to replicate

G1

165

Which is the length-determining phase of the cell cycle

G1

166

Where are the checkpoints found in the cell cycle

G1 and G2

167

What is the significance of the restriction point? Where is it found in the cell cycle?

Once past restriction point, cells are committed to divide

Restriction point happens late in the G1 phase

168

What causes the cell to proceed from the G1 phase into the S phase?

Phosphorylated G1 substrates

169

What causes phosphorylation of G1 substrates

Complexes made of:
- G1 Cyclin
- CDK 2

170

What causes the cell to proceed from the G2 phase into the M phase?

Phosphorylated Mitotic Substrates

171

What causes phosphorylation of Mitotic Substrates

Complexes made of:
- Mitotic Cyclin
- CDK 1

172

Fundamentally, what regulates apoptosis

Caspases

173

What is the DISK made up of?

Death ligand
Death receptor
Adaptor Protein
Procaspase 8

174

What happens to Procaspase 8 when the death receptors are active

The activated death receptors cause Procaspase 8 to be cleaved into Initiator Caspase 8

175

What is the role of initiator caspase 8

It cleaves procaspases into effector caspases

176

What prevents two BAX proteins binding to each other? How does it do this?

BAX binds to BCL2, preventing it from binding to another BAX

177

What enables two BAX proteins to bind to each other? How does it do this?

BAD binds to BCL2, preventing it from binding to BAX, enabling BAX to bind to another

178

What does a BAX dimer do? Where is it located?

Secretes Cytochrome C
Located in the mitochondrial membrane

179

What happens to Cytochrome C once it is released into the cytoplasm

It joins with APAF and Procaspase 9 to form an Aptosome

180

What is the function of the aptosome

Activates Captase 9 (initiator Captase)

181

How do effector captases get activated

Captase 9 cleaves Procaspases into Effector Caspases

182

What is the role of effector captases

Cause celllular proteolysis (protein degradation) which in turn cause cellular apoptosis

183

What are autoimmune diseases caused by?

Not enough apoptosis of antibody producing B-cells after infection

184

What is Lupus Erythematosus

An autoimmune disease in which one's own tissues are attacked

185

What is Rheumatoid arthritis

An autoimmune disease in which your joints become inflamed

186

What is the most common cancer as a result of not enough apoptosis

Lymphoma

187

What are the four diseases that result from too much apoptosis of body cells

Alzheimer
Parkinsons
Loss of CD4 cells in HIV/AIDS
Sepsis (apoptosis of immune regulator cells & GIT epithelial cells)

188

What is the role of microtubules

Determine position of organelles
Directs intracellular transport

189

What is the role of Actin filaments

Determine the shape of the cell's surface
Responsible for locomotion

190

What is the role of intermediate filaments

Provide mechanical strength for the cell

191

What types of cellular junctions use Cadherins

Adherens Junction
Desmosomes

192

What type of intracellular filaments are adherens junctions involved with

actin filaments

193

What type of intracellular filaments are desmosomes involved with

Intermediate filaments

194

Which end of the protein does the joining of cadherins occurs

N-terminal end

195

What are the two main anchor proteins in the inside of the cell used in the functioning of a Caderin

p-120 catenin
beta-catenin

196

What is pemiphigus

When there are antibodies attached to cadherins of the skin

197

What is pemphigoid

When there are antibodies attached to components of the hemidesmosome

198

How many different alpha chains and beta chins are involved in integrins

18 alpha chains
8 beta chains

199

What is the sequence of amino acids that integrins always bind to

RGD:
- Arganine
- Glycine
- Aspartic Acid

200

How are integins connected to collagen in cell-ECM adhesion

Laminin connects Integrins to Collage

201

What is adjacent to integrins in the cell-ECM adhesion structure

Collagen XVII

202

Describe Inside-out activation of integrins

1: Talin is phosphorylated and activated
2: Activated talin binds to integrin and activates it

203

Describe the outside-in activation of integrins

1: Ligands bind to extravellular integrin domain

This can result in:
1: The activation of pathways ---- such as MAPK
2: These ligands can phosphorylate nearby proteins in cell membrane to create docking sites for other signalling proteins

204

What is anchorage dependent

When most cells need to be attached to ECM to proliferate and survive

205

Describe the process of cell migation

Makes use of transient adhesion

1: Protrusion of cell at leading edge (direction of movement) using actin filaments
2: Adhesion at leading ends using integrins
3: Deadhesion at trailing edge using inside-out signal to let go

206

What are selectins

Transmembrane proteins that bind carbohydrates on another cell's surface

Used for cellular adhesion

207

What are ICAMs

Transient (unstable) cell-cell adhesion molecules that do not interact with the cytoskeleton of either cell

208

Which molecular family are ICAMs a part of

Immunoglobin superfamily

209

What two main regulators of cell proliferation

Proto-oncogenes
Growth inhibitors

210

What determines a cell's fate

1: The receptor that a cell has
2: The growth factors that it encounters

211

What are transient amplification cells?

Cells that give rise to other differentiating cells (like stem cells) but that differentiate themselves later on into the desired tissue

212

What two types of stem cells are there

embryonic stem cells
adult stem cells

213

What are some examples of adult stem cells

Intestinal villus
Muscle satellite cell
Hair follicle
Haematopoeitic stem cells

214

What keeps adult stem cells from differentiating

Intrinsic cell signals
Stem cell niche - gives signals to remain as it

215

Which immune cells are produced in the bone marrow

myeloid cells
natural killer cells
B and T lymphocytes

216

Which cells are the myeloid cells

Granulocytes (Basophils and Eosinophils)
Macrophages
Dendritic cells
Mast cells

217

Which cells mature in the thymus

Immature precursors of T lymphocytes

218

What are the mechanical factors of the immune system

Mucus secretions and their ciliated cells
Tear secretion
Flushing action of urine

219

What are the biochemical factors associated with the immune system

Lysozymes in tears
HCL of stomach
Antimicrobial substances

220

What are the microbial factors associated with the immune system

Commensal bacteria
Other microorganisms

221

What do the receptors of the innate immune cells recognise

Common components of pathogen walls
Complement/antibodies that opsonise the pathogen

222

What are the innate immune cells

Macrophages
Neutrophils
Basophils
Mast cells
Eosinophils
Dendritic cells
Natural Killer Cells

223

Which is the one type of cell in the innate immune system that kills infected body cells

Natural Killer Cells

224

Which are the two receptors in the innate immune system that recognise specific molecules

Mannose receptor
LPS (lipopolysaccharide receptor)

225

What are receptors that recognize pathogen associated molecular patterns

TLRs

226

What are the TLRs found on the surface of an innate immune cell? What does each one recognise?

TLR1 - Peptidoglycan
TLR4 - LPS
TLR5 - Flagellin
TLR6 - Peptidoglycan (heterodimer)

227

What is the TLR found intracellularly? What does it recognise?

TLR3 - dsRNA

228

What are the two receptors that recognise opsonins? What part does each recognise?

FcR - constant domain of antibody
CR - 3b on surface

229

What are the four phagocytes

Macrophages
Neutrophils
Dendritic cells
Eosinophils

230

How does phgocytosis occur in the innate immune system?

1: Pathogen binds to receptor and is engulfed
2: Phagosome formed which fuses with lysosome

231

How does oxygen dependent phagocytisis occur

1: NADPH oxidase causes: O2------>Superoxide O2
2: SOD converts it into hydrogen peroxide

1: Myeloperoxidase and chloride: ----->HOCL (hypochlorite)

232

What are oxygen independent molecules secreted by phagosomes

Lysozymes
Basic proteins

233

What are the complement proteins to act as chemo-attractants

3a
5a

234

What are the complements proteins to act as opsonins

3b

235

What are two proteins made by the liver in response to activated macrophages and neutrophils

CRP (C reactive protein)
MBL (Mannose binding lectin)

236

What do dendritic cells activate

naive CD4 and CD8 T cells

237

How are the peptides from cyoplasmic proteins displayed? What recognises them?

MHC I
Recognised by TCR of CD8 cytotoxic T cells

238

How are the peptides from endocytosed or phagocytosed pathogens presented? What recognises them?

On MHC II on Antigen presenting cells
Recognised by TCR of CD4 Helper T Cells

239

What do effector CD4 cells do

1: Activate dendritic cells to increase activation of naive CD8 T cells
2: Increase killing activity of macrophages which present peptides on MHC II
3: Activate B cells, that present peptides on MHC II to become plasma cells

240

Describe the basic workings of the adaptive immune response

Each lymphocytes has its own unique variant of receptors that are specific for one peptide on a MHC protein or epitop on a pathogen.

These are T lymphocytes with a TCR or B lymphocyte with a BCR

These lymphocytes need to proliferate to create the adaptive immune response.

241

What can activate the adaptive immune response

Dendritic cells with MHC II --activate TCR-CD4 T cells (helper and regulatory)

Somatic cells with MHC I -- activate TCR-CD8 T cells (cytotoxic)j

242

What are the secondary lymphoid organs

lymph nodes
spleen
MALT (mucosa associated lymphoid tissue)

243

What is the significance of the lymph nodes in the innate immune system

Dendritic cells carry pathogens to the lymph nodes where they meet circulating lymphcytes

244

What is the significance of the spleen in the innate immune system

Pathogens present in blood are trapped here by macrophages and they activate lymphocytes

245

What are the three parts of the MALT

Tonsils
Peyers patches
Appendix

246

What is the role of Effector CD8 cytotoxic T cells

Kill cells infected with viruses and bacteria

247

What is the role of Effector CD4 helper T cells

Activate dendritic cells to activate CD8 T cells more efficiently
Activate macrophages
Activate B cells

248

What are two things that activate B cells

Binding of pathogen to BCR
Effector T cells

249

What is a secreted BCR

Antibody

250

What are the principal functions of macrophages

Phagocytosis
inflammation
T-cell activation
Tissue repair

251

What are the principal functions of neutrophils

phagocytosis
inflammation

252

What are the principal functions of eosinophils

defense against parasites

253

What are the principal functions of basophils

inflammation
Defense against parasites

254

Whatare the principal functions of mast cells

inflammation

255

What are the principal functions of natural killer cells

killing of infected or tumour cells

256

What are the principal functions of dendritic cells

phagocytosis
activation of naive T-cells

257

What is the first cell on the scene of infection

macrophages as they live in tissues under barriers

258

What are the receptors that macrophages have

mannose receptors
opsonised antigen - CR and Fc receptors
LPS
TLR

259

What are the cytokines produced by macrophages? What do they do?

TNF-alpha (enhances endothelium expression of adhesion molecules)

IL6 (Causes production of acute-phase proteins)

IL1 (fever)

CXCL8 (recruits neutrophils from bloodstream)

IL12 (activates NK cells; causes production of TH1 cells)

260

What are the five steps of extravastion

1: rolling adhesion through carbohydrate ligands binding to P selectin molecules on endothelial surface

2: tight adhesion through integrins binding to ICAMs

3: transmigration through endothelial cells using PECAM proteins

4: MMPs break down basement membrane

5: Follow chemokine gradient

261

What recpetors do neutrophils have

TLR
CR and Fc

262

What are two ways that neutrophils can kill pathogens

1: forming a phagolysosome
2: Forming NETs (neutrophil extracellular traps) using chromatic and secreting toxic granules

263

What are the cytokines that are released by a neutrophil

TNF-alpha (enhances endothelium expression of adhesion molecules)

INF-gamma

264

What do eosinophils release when activated

prostaglandins and cytokines which cause inflammation

265

What causes the levels of eosinophil levels to increase

TH2 cells secreting IL5

266

What receptors do basophils have

IgE recpetors

267

What do basophils release when activated

histamine and IL4

268

Which cells are involved in allergic responses

basophils

269

What do mast cells release

histamine

270

What receptors to mast cells have

IgE receptors

271

What receptors do NK cells have

Stress receptors - for MICA
Receptors for MHC I
FcR receptors (for antibodies)

272

What causes NK cells to kill infected cells

increased stress receptors on infected cells

Lack of MGC I on infected cells

Infected cells coated in antibody

273

What are the cytokines secreted by NK cells

IFN-gamma (activate macrophages)

274

What do NK Cells secrete to kill a cell

Granzyme and perforin

275

What is the most important cell in activating naive T cells

Dendritic cells

276

What receptors do dendritic cells have

TLR and mannose receptors

277

What two chemokines activate dendritic cells

IFN-alpha
IFN-beta

278

What are the cytokines produced by dendritic cells? What are their functions?

TNF-alpha (enhances endothelium expression of adhesion molecules)

IL6 (Causes production of acute-phase proteins)

IL1 (Causes production of acute-phase proteins; fever)

IL12 (activates NK cells; causes production of TH1 cells)

IFN-alpha (antiviral)

279

Which released mediators stimulate nerve endings in inflammation

TNF-alpha
bradykinin
histamine

280

What is C reactive protein?

Acute phase proteins
Opsonin on microbes
Activates classical complement pathway

281

What is mannose binding lectin (MBL)

Activates mannose binding complement pathway
Acute phase protein

282

What is Ferritin

Acute phase protein
Binds iron - inhibits microbe iron uptake

283

What is Fibrinogen

acute phase protein
causes coagulation

284

What is serum amyloid A

recruitment of immune cells to inflammatory sites
acute phase protein

285

What two things can activate the classical pathway? What recognizes these things?

CRP
Antibodies binding to pathogen surface

Recognised by C1 complex

286

What activates the alternate pathway

C3 converted to C3b in plasma/ECM

287

What is the function of the C1 complex in the classical pathway? What does it bind to?

Cleaves c2 and c4

Binds to IgG

288

What makes c5 convertase? Which complement pathway is it associated with?

c4b
c2a
c3b

Associated with the classical pathway

289

What makes up the the MAC (membrane attack complex) in the complement

C5b
c6
c7
c8
many c9

290

Describe the lectin pathway, using the classical pathway as a reference

MBL (mannose binding lectin) and MASPs bind to mannose.

This complex and cleaves C2 and C4.
Remaing steps are identical to the classical pathway.

291

What are the steps of the alternate pathway

1: production of c3b continuously in ECF

2: C3 hydrolysed to C3-H2O in plasma. This binds factor B which is cleaved by factor D (into Ba and Bb)

3: Complex of C3-H2O and Bb makes up a c3 convertase

4: This above-mentioned complex adds a C3b to form the C5 convertase

5: MAC formed

292

What do the epithelial cell receptors for C3a and C5a do?

Make the endothelial lining more premeable

293

What makes up C3 convertase

C2a
C4b

294

What is the primary role of the enhancer

To control the rate of the promotor activation

295

What binds to the promotor

RNA Polymerase

296

What are the sequences found in the promotor region

TATA
CAAT

297

How far upstream from the transcription start site is the promotor

27 bases upstream

298

What is the DNA sequence of a splice site

AG/...exon.../GT

299

What is the initiation codon at the transcription start site

ATG

300

What causes a bacterial genome to become compacted? By how much is it compacted?

Loop domains
Supercoiling within loop domains

It is compacted 1000 fold

301

How many base pairs of DNA can a histone wrap

147

302

What part of the histone can be enzymatically modified

N-terminal tails

303

Which part of the DNA strand holds nucleosomes together

Linker DNA

304

What are the sequences for a stop codon

TAA/TAG/TGA

305

What is the collective term for a base and sugar

nucleoside

306

Which direction does DNA replication occur

5' ---> 3'

307

What are released from when a phosphodiester bond forms DNA bonds

Pyrophosphate (PPi) and a Proton

308

Which molecule undergoes proofreading activity? What is this activity called?

DNA Polymerase
Exonuclease activity

309

What are the Purine Bases

G and A

310

What are the Pyrimidine Bases

C, T and U

311

Which strand of DNA is not transcribed? What is it called?

Coding Strand
Sense strand

312

Which part of DNA is transcribed? What is it called?

Template Strand
Antisense Strand
3' -----> 5'

313

What are the three classes of RNA Polymerase

Type 1 - makes rRNA
Type 2 - makes mRNA
Type 3 - makes tRNA

314

What does RNA Polymerase attach to

Transcription factors at the promotor

315

What happens in the Initiation stage of transcription

-- Helicase, a subunit of RNA Polymerase, unwinds DNA
-- First 8/9 nucleotides are linked
-- Transcription factors and RNA polymerase are released from the promotor region and RNA polymerase moves along

316

What happens in the elongation stage of transcription

-- RNA polymerase form elongation (replication ) bubble
-- Nucleotides are added
-- RNA/DNA hybrids are formed

317

Wat happens in the termination stage of transcription

"transcription termination sequence" (polyadenylation signal) signals termination

RNA is cleaved 10-30 BPs after

RNA polymerase continues to transcribe

318

What does quinobnes do? What are two examples?

antibiotic that inhibits topoisomerase

Norfloxacin (prokaryotes only)
Etoposide

319

What does rigampicin do

antibiotic

inhibits a subunit of bacterial RNA polymerase from creasting first phosphodiester bond

320

What does Actinomycin D do

antibiotic

Inserts between two GC pairs in DNA (prokaryotic and eukaryotic)

321

What are two things that regulate gene expression

Chromatin structure
Signal transduction (environmental signals causing transcription factors to get activated)

322

What is another name for an enhancer region

Regulatory sequence

323

What is a transcription initiator complex

Activators (bind to enhancer) and General transcription factors which enable transcription to happen

324

What happens to the 5' end of an mRNA

Capped with 7-methyguanosinetriphosphate

325

What happens to the 3' end of mRNA

polyadenylated

326

What makes it possible for there to be many more mRNAs than genes?

Alternative splicing - many different ways an mRNA can be spliced

327

What are the four arms of a tRNA

Acceptor Arm (top
D arm (right)
Anticodon Arm (bottom
T, psudouridine, C arm (left)

328

What is added to the 3' group on the acceptor arm of tRNA

CCA

329

How long is one tRNA

75 nucleotides long

330

What is the chemical modification that rRNA undergoes to become a ribosome

Methy groups added
Pseudouridine added

331

What are the three groups that are cleaved off the rRNA strand, once is has been chemically modified

18s RNA (contributes to small ribosomal subunit - 40s)

Contributes to Large Ribosomal subunit (60s)
5,85s RNA
28s RNA

332

What is the polycistronic (many) hairpin loop chain called in RNA interference

Pri-miRNA

333

What causes the hairpin loops from pri-miRNA to be cleaved off into separate ones? What does this form?

Drosha and DCGR8
Pre-miRNA

334

What cleaves the head of the hairpin off pre-miRNA? What forms as a result?

Dicer and TRBP
RISC RNA Induced silencing complex

335

What causes degradation of mRNA

When the miRNA matches perfectly

336

What causes translation suppression of mRNA

When the miRNA does not match perfectly

337

What happens to RISK

The passenger strand is removed from complementary guide strand

338

What is the role of Nuclear RNAi

Guide strand (of the mRNA/miRNA complex) directs Ago-2 to promotor regions of genes and Ago-2 methylates them, turning off the gene

339

What do viruses do with miRNA

Inhibit cellular factors involved in immunity

Downregulate expression of viral proteins

340

What is a directly labelled probe in fish called

fluorophore

341

What is an indirectly labelled probe in FISH called

Hapten
An antibody can be raised against it which makes it flourescent

342

What are the steps involved in FISH

1: Probe and sample prepared
2: Probe labelled
3: denaturing
4: Probe hyybridised to sample
5: sample imaged

343

What do you see if fish is imaged during metaphase

Chromosomes

344

What do you see if fish is imaged during interphase

nuclei

345

How is the sample prepared during FISH

Cells are fixed (formaldehyde) and Permeabilised (detergents)

346

How is the probe prepared during FISH

DNase I - Introduces Nicks into probe
DNA Polymerase - Fills in nicks with modified dNTP

347

What are the three steps in PCR? What temperatures do they take place at?

Denaturisation (95 degrees) - forms single DNA strand

Annealing/Hybridisation (55 degrees) - Primer anneals

Extension/Elongation (72 degrees) - dNTPs added

348

What type of polymerase is used in PCR

Taq Polymerase

349

What is the formula for PCR

y=a*2^x

y -- copy number
a -- starting number
x -- cycle number

350

What is used to prepare for viewing the product of PCR

Agarose Gel Electrophoresis

351

What two types of hydrophobic (non-polar) amino acids are ther

Aliphathic (chain)
Aromatic (ring)

352

What are the two ends of a hydrophilic (polar) amino acid

Hydroxyl - positive
Amide - negative

353

Which end of the Amino Acid is added to tRNA? What regulates this?

COOH group - added to 3' end
tRNA synthases