Mid-block Test - March Flashcards
What are the three sites on a ribosome?
E - Exit
P - Peptide Bond formation
A - Arrive
What is the first amino acid used in Translation?
Met
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)
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
What is the enzyme that aids peptide bond formation in Translation?
Peptidyl Transferase
What regulates the process of translocation during Translation?
Eukaryotic Elongation Factors (EEF’s)
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
What adds a water molecule to the end of a polypeptide chain in translation?
Release Factor
What regulates the process of ribosomal subunits dissociating at the end of translation?
Releasing Factors (eRF’s)
In which way does one label condons or anticodons?
3’ to 5’
What is a polyribosome
A mRNA molecule and two or more ribosomes that make up a complex
Where does the processing of proteins take place?
ER
What causes the polyribosome to be directed towards the ER?
The “Signal Sequence” on an already-formed part of synthesising DNA
What is the name of the process whereby sugar groups are added to a newly-synthesised protein
Glycosylation
Where does folding of proteins take place?
In the ER Cisternae.
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
What part of the Golgi does a transport vesicle containing a newly-synthesised strand of protein attach to?
The cis face
What are the products that exit the Golgi after protein processing
Secretory Vesicle
Membrane Vesicle
Lysosomal Vesicle
What is the role of Tetracylins
Blocks the A site of 30S ribosomal subunit of prokaryotes
What do Aminoglycoside Antibiotics do
Modify ribosomal proteins
What two molecules inhibit the elongation step of translation in bacteria
Macrolide
Peptidal Transferase Inhibitors
What molecule disrupts the elongation step of translation in all cells
Aminoacyl tRNA analogues
What do Dipheria Toxins do
modify the EEF-2 in all mammalian cells - Inhibiting translation
Where do the sidechains of hydrophobic proteins point
Point to the outside
Where do the sidechains of hydrophilic proteins point
Point to the centre
What differentiates a peptide and a protein
A peptide is less than 30 amino acids long
A protein is longer
What constitutes the primary level of protein structure
Peptide bonds between amino acids, making a chain
What constitutes the secondary level of protein structure
Backbone interaction (H bonds) making a structured chain
What two types of secondary protein structure are there
Alpha helix
Beta sheet
What constitutes the tertiary level of protein structure
3D structure of a chain
What molecular interactions enable a tertiary protein structure to be formed
H bonds
Ionic bonds
Hydrophobic interaction
VDW forces
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
What type of amino acid can be phosphorylated?
Any amino acid containing a hydroxyl (OH)
What two processes regulate chromatin organisation
methylation and acetylation
What process regulates degradation of proteins in the proteasome?
Polyubiquination
What process regulates protein sorting (making sure proteins get transported to correct location)
Monoubiquination
What is the role of p53
Acts as a tumour suppressor
Where does glycosylation happen?
ER
Golgi
Cytoplasm
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
What is autophagy used for
Used to break down things INSIDE the cell
Describe the process of Microautophagy
When endogenous proteins (inside the cell) get endocytosed into lysosome of cell
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
Which molecules are involved with the folding of proteins
hsp60 protein-like complex
GroES Cap
What is the core component of the proteasome made of
Catalytic (proteolytic) sites
What are the funcations of the regulatory caps on each end of the proteasome
Recognises proteins
Unfolds proteins
Feeds proteins in
Which steps of the proteosome function require ATP
Unfolding protein
Feeding protein in
What is Ubiquitin activating enzyme? What does it do?
E1
Forms a bond with ubiquitin
What is Ubiquitin-conjugating enzyme? What does it do?
E2
Recieves ubiqutin from E1
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
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)
What is the role of proteases in the immune system?
Cleaves bits of proteins into correct length to be displayed on MHC molecules
What is the main cause of the malfunctioning of the proteasome pathway?
Intracellular accumulation of misfolded proteins
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)
What is PP2B also called? What does it do?
A phosphoserine and Phosphotheronine Phosphatase
It is also called Calcineurin (binds Ca to get activated)
What does malfunctioning of the proteasome pathway lead to?
Degenerative diseases such as Alzheimers and Parkinsons Disease
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
What is SDS-PAGE used for
To separate and identify proteins
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
What is PAGE
Poly-acrylamide gel electrophoresis
What determines the speed of migration of proteins in PAGE?
Molecular weight
In PAGE, what does a lower concentration of acrylamide result in?
Bigger pores
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
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
If you can’t see a protein after SDS-PAGE, what should you do
use a Silver Stain or Coomassie Stain
What is isoelectric focusing (IEF)
When you use a gel that has a pH gradient to separate proteins based on their pH
What is the pH gradient in IEF caused by?
Presences of ampholytes in IEF gel causes pH gradient
When do proteins stop moving in IEF
At their Isoelectric point. This is when the Isoelectric Charge is equal to their pH
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
What are the specific protein properties that are used for protein purification?
Size
Charge
Hydrophobicity
Biorecognition
What is used as a solvent that proteins can run through in the process of protein purification
Beads with specific properties
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)
What splits the plasmid’s DNA or the desired gene’s DNA in protein recombination?
Restriction Enzyme
What are the two words used when introducing rDNA in Bacteria and Eukaryotes respectively
Transformation - Bacteria
Transfection - Eukaryotes
What are two methods of Transformation in protein recombination
Electropolation (creates holes by current)
Chemicals (Ca salts + Heat Shock)
What are four methods of Transfection in protein recombination
Electropolation (creates holes by current)
Chemicals (Ca salts + Lipids)
Microinjection
Opticalation
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
How many Restriction Endonuclease sites does an ideal cloning vector have in gene recombination
One
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)
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
What binds to the active site of a protein kinase
Protein & ATP
Which amino acids have OH groups? What is the significance of this?
Serine, Tyrosine, Threonine
This enable the amino acid to be phosphorylated
What kind of phosphate does a protein kinase add to target proteins? Where does it get this?
Adds a gamma phosphate from ATP
What is a motif? What can it also be called?
A specific short amino acid sequence. Also called a Consensus Sequence
How does phosphorylation of a protein result in conformational changes
Phosphorylation adds two negative charges which changes the protein’s structure
What are the types of Cytoplasmic Serine & Theonine Kinases
MAPK
AKT
PKA
PKC
What are the types of Receptor Serine & Theonine Kinases
Transform growth factor beta
TGFBRI
TGFBRII
What are the types of Cytoplasmic Tyrosine Kinases
SRC
What are the types of Receptor Tyrosine Kinases
EGFR
JAK
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
How many amino acids does a kinase consist of
250 - 300 amino acids
What are the two lobes that the catalytic domain of a kinase consists of
N terminal lobe
C terminal lobe
What is the function of the N terminal lobe of a kinase
Binds ATP
What is the function of the C terminal lobe of a kinase
Binds substrate (protein)
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.
In what types of kinases is the regulatory section part of the same chain as the catalytic domain?
Ca Calmodulin Kinase
SRC Tyrosine Kinase
In what types of kinases is the regulatory section part of a different protein chain as the catalytic domain
PKA
CDK
What amino acid does Ca Calmoduin dependent kinase phosphorylate?
Serine and Threonine
How does Ca Calmodulin dependent kinase get activated
When calmodulin with attached Ca binds to regulatory domain
What amino acid does CDK phosphorylate?
Serine and Threonine
What is one disease that can result from an overactive Wnt pathway
Ankylosing Spondylitis
What amino acid does PKA phosphorylate
Serine and Threonine
What does the structure of PKA consist of
It is tetrameric:
- 2 regulatory subunits
- 2 catalytic subunits
How does PKA get activated
cAMP binds to a regulatory subunit
How does a Tyrosine Kinase Receptor get activated?
Dimerisation of catalytic sites
What are the two regulatory domains of an SRC Tyrosine Kinase called?
SH2 & SH3
How is an SRC Tyrosine Kinase activated
Dephosphorlatioon
What is PP2A
A Phosphoserine and Phosphotheronine Phosphatase.
It reverses phosphorylation in signalling pathways activated by growth factors
What is PP2B also called? What does it do?
A phosphoserine and Phosphotheronine Phosphatase
It is also called Calcineurin (binds Ca to get activated)
What does a Ligand-Receptor complex function as in Intracellular Signalling
Works as a transcription factor
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
Name the three most common Hydrophobic first messengers
Steroid hormones
Thyroid hormones
Vitamins
What is the main mechanism used in Hydrophilic signalling
Protein kinases are activated resulting in:
- Proteins with altered functions
- Transcription factors activated
What is the main example of a membrane receptor without associated kinase activity
G protein coupled receptor
What kinase is a cytokine receptor associated with
JAK (tyrosine kinase) that phosphorylates the tail-end motif sequence containing Tryosine
How many domains does an adaptor protein consist of
two or three
What are the two functions of adaptor proteins
Link proteins together
Pass signals on
What is the name of the domain in an adaptor protein that links phosphorylated tyrosine amino acids
SH2
What do scaffold proteins do
Bind other proteins to bring them into a complex
Where is a Conserved Consensus Sequence found? What does it do?
Found in the promotor
Binds general transcription factors
Binds specific transcription factors
What happpens when a scaffold protein is phosphorylated?
Many different proteins with SH2 domains are recruited
Which two proteins of the Wnt pathway are scaffold proteins
Axin and APC
What is intrinsic GTPase activity
When cells convert GTP to GDP to switch themselves off.
Used in G proteins
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
What is the immediate result of activation of heterotrimeric G proteins
Activation of effector enzymes
What is the function of effector enzymes
To produce second messengers (e.g. cAMP, IP3)
What is the function of 2nd messengers
To activate kinases
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.
What membrane receptor do 50% of modern drugs tarted
G Protein Coupled Receptor
What shape is the G Protein coupled receptor? How many times does it span the membrane
Serpentine in shape
Spans the membrane 7 times
In the G Protein, which subunit dissociates and regulates the target protein
Alpha subunit
What is the active form of the G Protein? Vice versa?
Active = GTP on alpha subunit Inactive = GDP on alpha subunit
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
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
Which are the signalling pathways that are involved with regulating growth factors
Tyrosine Kinase Receptor Pathways (MAPK, PI3-K)
What can unregulated RTK Signalling lead to?
Cancer
Inflammatory diseases
Diabetes
What are the main therapies against the RTK fmaily
Trastuzumab: Herceptin (Anti-HER2)
Gefitinib (anti-EGFR)
What is FGF and what role does it play
Growth Factor
Fibroblast Growth Factor. Crucial role in control of development
What is VEGF and what role does it play
Growth factor
Vascular Endothelial Growth Factor. It plays an important role in agiogenesis
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
What two ligands are predominantly involved in both the PI3K and MAPK pathways
EGF (Epidermal Growth Factor)
PDGF (Platelet Derived Growth Factor).
What is one defining characteristic of the EGF Ligand
It gets anchored in the plasma membrane due to it containing a hydrophobic domain
What is one defining characteristic of PDGF
It sometimes needs to be cleaved by proteases in ECM to become activated
What is the role of Heparon Sulphate Proteoglycans
Bind growth factors such as FGF and PDGF restricting their action
What are two RTK receptors used in both the MAPK and PI3K Pathways
EGFR
PDGFR
What are the defining characteristics of RTK receptors
1: Need to be dimerised
2: Made of groups of Tyrosine Amino Acids
What type of adaptor is used the in MAPK pathway
SH2 adaptor
What directly activates the MAPK Cascade
RAS (Small monomeric G Protein) activated by GEF giving it an ATP
What are the results of the MAPK Pathway
Altered proteins
Altered transcription factors
Proliferation due to G1 cyclins being produced (proto-oncogenes)
What is the adaptor used in the PI3K Pathway
SH2 adaptor
What is the direct role of PI3K
Phosphorylates PIP2 to turn it into PIP3
What is the role of PIP3
Binds AKT (using it’s PH domain) which enables other enzymes to phosphorylate AKT
What happens to AKT once it is phosphorylated
Acts as a kinase and phosphorylates proteins (NOT TRANSCRIPTION FACTORS) involved in survival and proliferation
What three things does the Wnt pathway play an important role in?
Embryogenesis
Proliferation of colorectal epithelia
Bone formation
What is one disease that can result from an inhibited Wnt pathway
Rheumatoid Arthritis
What is one disease that can result from an overactive Wnt pathway
Ankylosing Spondylitis
What is the receptor-related protein for that of Frizzled
LRP
What makes up the degradation complex in the Wnt pathway
Axin
GSK
APC
Beta-catenin
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
What is the function of GSK
Kinase that acts on beta-catenin in the degradation complex of the Wnt Pathway
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
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
How does beta-catenin act as a transcription factor
It binds to TCF
What are the four phases of the cell cycle
M
G1
S
G2
In which stage of the cell cycle is the signal recieved to replicate
G1
Which is the length-determining phase of the cell cycle
G1
Where are the checkpoints found in the cell cycle
G1 and G2
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
What causes the cell to proceed from the G1 phase into the S phase?
Phosphorylated G1 substrates
What causes phosphorylation of G1 substrates
Complexes made of:
- G1 Cyclin
- CDK 2
What causes the cell to proceed from the G2 phase into the M phase?
Phosphorylated Mitotic Substrates
What causes phosphorylation of Mitotic Substrates
Complexes made of:
- Mitotic Cyclin
- CDK 1
Fundamentally, what regulates apoptosis
Caspases
What is the DISK made up of?
Death ligand
Death receptor
Adaptor Protein
Procaspase 8
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
What is the role of initiator caspase 8
It cleaves procaspases into effector caspases
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
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
What does a BAX dimer do? Where is it located?
Secretes Cytochrome C
Located in the mitochondrial membrane
What happens to Cytochrome C once it is released into the cytoplasm
It joins with APAF and Procaspase 9 to form an Aptosome
What is the function of the aptosome
Activates Captase 9 (initiator Captase)
How do effector captases get activated
Captase 9 cleaves Procaspases into Effector Caspases
What is the role of effector captases
Cause celllular proteolysis (protein degradation) which in turn cause cellular apoptosis
What are autoimmune diseases caused by?
Not enough apoptosis of antibody producing B-cells after infection
What is Lupus Erythematosus
An autoimmune disease in which one’s own tissues are attacked
What is Rheumatoid arthritis
An autoimmune disease in which your joints become inflamed
What is the most common cancer as a result of not enough apoptosis
Lymphoma
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)
What is the role of microtubules
Determine position of organelles
Directs intracellular transport
What is the role of Actin filaments
Determine the shape of the cell’s surface
Responsible for locomotion
What is the role of intermediate filaments
Provide mechanical strength for the cell
What types of cellular junctions use Cadherins
Adherens Junction
Desmosomes
What type of intracellular filaments are adherens junctions involved with
actin filaments
What type of intracellular filaments are desmosomes involved with
Intermediate filaments
Which end of the protein does the joining of cadherins occurs
N-terminal end
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
What is pemiphigus
When there are antibodies attached to cadherins of the skin
What is pemphigoid
When there are antibodies attached to components of the hemidesmosome
How many different alpha chains and beta chins are involved in integrins
18 alpha chains
8 beta chains
What is the sequence of amino acids that integrins always bind to
RGD:
- Arganine
- Glycine
- Aspartic Acid
How are integins connected to collagen in cell-ECM adhesion
Laminin connects Integrins to Collage
What is adjacent to integrins in the cell-ECM adhesion structure
Collagen XVII
Describe Inside-out activation of integrins
1: Talin is phosphorylated and activated
2: Activated talin binds to integrin and activates it
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
What is anchorage dependent
When most cells need to be attached to ECM to proliferate and survive
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
What are selectins
Transmembrane proteins that bind carbohydrates on another cell’s surface
Used for cellular adhesion
What are ICAMs
Transient (unstable) cell-cell adhesion molecules that do not interact with the cytoskeleton of either cell
Which molecular family are ICAMs a part of
Immunoglobin superfamily
What two main regulators of cell proliferation
Proto-oncogenes
Growth inhibitors
What determines a cell’s fate
1: The receptor that a cell has
2: The growth factors that it encounters
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
What two types of stem cells are there
embryonic stem cells
adult stem cells
What are some examples of adult stem cells
Intestinal villus
Muscle satellite cell
Hair follicle
Haematopoeitic stem cells
What keeps adult stem cells from differentiating
Intrinsic cell signals
Stem cell niche - gives signals to remain as it
Which immune cells are produced in the bone marrow
myeloid cells
natural killer cells
B and T lymphocytes
Which cells are the myeloid cells
Granulocytes (Basophils and Eosinophils)
Macrophages
Dendritic cells
Mast cells
Which cells mature in the thymus
Immature precursors of T lymphocytes
What are the mechanical factors of the immune system
Mucus secretions and their ciliated cells
Tear secretion
Flushing action of urine
What are the biochemical factors associated with the immune system
Lysozymes in tears
HCL of stomach
Antimicrobial substances
What are the microbial factors associated with the immune system
Commensal bacteria
Other microorganisms
What do the receptors of the innate immune cells recognise
Common components of pathogen walls
Complement/antibodies that opsonise the pathogen
What are the innate immune cells
Macrophages Neutrophils Basophils Mast cells Eosinophils Dendritic cells Natural Killer Cells
Which is the one type of cell in the innate immune system that kills infected body cells
Natural Killer Cells
Which are the two receptors in the innate immune system that recognise specific molecules
Mannose receptor
LPS (lipopolysaccharide receptor)
What are receptors that recognize pathogen associated molecular patterns
TLRs
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)
What is the TLR found intracellularly? What does it recognise?
TLR3 - dsRNA
What are the two receptors that recognise opsonins? What part does each recognise?
FcR - constant domain of antibody
CR - 3b on surface
What are the four phagocytes
Macrophages
Neutrophils
Dendritic cells
Eosinophils
How does phgocytosis occur in the innate immune system?
1: Pathogen binds to receptor and is engulfed
2: Phagosome formed which fuses with lysosome
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)
What are oxygen independent molecules secreted by phagosomes
Lysozymes
Basic proteins
What are the complement proteins to act as chemo-attractants
3a
5a
What are the complements proteins to act as opsonins
3b
What are two proteins made by the liver in response to activated macrophages and neutrophils
CRP (C reactive protein)
MBL (Mannose binding lectin)
What do dendritic cells activate
naive CD4 and CD8 T cells
How are the peptides from cyoplasmic proteins displayed? What recognises them?
MHC I
Recognised by TCR of CD8 cytotoxic T cells
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
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
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.
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
What are the secondary lymphoid organs
lymph nodes
spleen
MALT (mucosa associated lymphoid tissue)
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
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
What are the three parts of the MALT
Tonsils
Peyers patches
Appendix
What is the role of Effector CD8 cytotoxic T cells
Kill cells infected with viruses and bacteria
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
What are two things that activate B cells
Binding of pathogen to BCR
Effector T cells
What is a secreted BCR
Antibody
What are the principal functions of macrophages
Phagocytosis
inflammation
T-cell activation
Tissue repair
What are the principal functions of neutrophils
phagocytosis
inflammation
What are the principal functions of eosinophils
defense against parasites
What are the principal functions of basophils
inflammation
Defense against parasites
Whatare the principal functions of mast cells
inflammation
What are the principal functions of natural killer cells
killing of infected or tumour cells
What are the principal functions of dendritic cells
phagocytosis
activation of naive T-cells
What is the first cell on the scene of infection
macrophages as they live in tissues under barriers
What are the receptors that macrophages have
mannose receptors
opsonised antigen - CR and Fc receptors
LPS
TLR
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)
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
What recpetors do neutrophils have
TLR
CR and Fc
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
What are the cytokines that are released by a neutrophil
TNF-alpha (enhances endothelium expression of adhesion molecules)
INF-gamma
What do eosinophils release when activated
prostaglandins and cytokines which cause inflammation
What causes the levels of eosinophil levels to increase
TH2 cells secreting IL5
What receptors do basophils have
IgE recpetors
What do basophils release when activated
histamine and IL4
Which cells are involved in allergic responses
basophils
What do mast cells release
histamine
What receptors to mast cells have
IgE receptors
What receptors do NK cells have
Stress receptors - for MICA
Receptors for MHC I
FcR receptors (for antibodies)
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
What are the cytokines secreted by NK cells
IFN-gamma (activate macrophages)
What do NK Cells secrete to kill a cell
Granzyme and perforin
What is the most important cell in activating naive T cells
Dendritic cells
What receptors do dendritic cells have
TLR and mannose receptors
What two chemokines activate dendritic cells
IFN-alpha
IFN-beta
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)
Which released mediators stimulate nerve endings in inflammation
TNF-alpha
bradykinin
histamine
What is C reactive protein?
Acute phase proteins
Opsonin on microbes
Activates classical complement pathway
What is mannose binding lectin (MBL)
Activates mannose binding complement pathway
Acute phase protein
What is Ferritin
Acute phase protein
Binds iron - inhibits microbe iron uptake
What is Fibrinogen
acute phase protein
causes coagulation
What is serum amyloid A
recruitment of immune cells to inflammatory sites
acute phase protein
What two things can activate the classical pathway? What recognizes these things?
CRP
Antibodies binding to pathogen surface
Recognised by C1 complex
What activates the alternate pathway
C3 converted to C3b in plasma/ECM
What is the function of the C1 complex in the classical pathway? What does it bind to?
Cleaves c2 and c4
Binds to IgG
What makes c5 convertase? Which complement pathway is it associated with?
c4b
c2a
c3b
Associated with the classical pathway
What makes up the the MAC (membrane attack complex) in the complement
C5b c6 c7 c8 many c9
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.
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
What do the epithelial cell receptors for C3a and C5a do?
Make the endothelial lining more premeable
What makes up C3 convertase
C2a
C4b
What is the primary role of the enhancer
To control the rate of the promotor activation
What binds to the promotor
RNA Polymerase
What are the sequences found in the promotor region
TATA
CAAT
How far upstream from the transcription start site is the promotor
27 bases upstream
What is the DNA sequence of a splice site
AG/…exon…/GT
What is the initiation codon at the transcription start site
ATG
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
How many base pairs of DNA can a histone wrap
147
What part of the histone can be enzymatically modified
N-terminal tails
Which part of the DNA strand holds nucleosomes together
Linker DNA
What are the sequences for a stop codon
TAA/TAG/TGA
What is the collective term for a base and sugar
nucleoside
Which direction does DNA replication occur
5’ —> 3’
What are released from when a phosphodiester bond forms DNA bonds
Pyrophosphate (PPi) and a Proton
Which molecule undergoes proofreading activity? What is this activity called?
DNA Polymerase
Exonuclease activity
What are the Purine Bases
G and A
What are the Pyrimidine Bases
C, T and U
Which strand of DNA is not transcribed? What is it called?
Coding Strand
Sense strand
Which part of DNA is transcribed? What is it called?
Template Strand
Antisense Strand
3’ —–> 5’
What are the three classes of RNA Polymerase
Type 1 - makes rRNA
Type 2 - makes mRNA
Type 3 - makes tRNA
What does RNA Polymerase attach to
Transcription factors at the promotor
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
What happens in the elongation stage of transcription
- RNA polymerase form elongation (replication ) bubble
- Nucleotides are added
- RNA/DNA hybrids are formed
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
What does quinobnes do? What are two examples?
antibiotic that inhibits topoisomerase
Norfloxacin (prokaryotes only)
Etoposide
What does rigampicin do
antibiotic
inhibits a subunit of bacterial RNA polymerase from creasting first phosphodiester bond
What does Actinomycin D do
antibiotic
Inserts between two GC pairs in DNA (prokaryotic and eukaryotic)
What are two things that regulate gene expression
Chromatin structure Signal transduction (environmental signals causing transcription factors to get activated)
What is another name for an enhancer region
Regulatory sequence
What is a transcription initiator complex
Activators (bind to enhancer) and General transcription factors which enable transcription to happen
What happens to the 5’ end of an mRNA
Capped with 7-methyguanosinetriphosphate
What happens to the 3’ end of mRNA
polyadenylated
What makes it possible for there to be many more mRNAs than genes?
Alternative splicing - many different ways an mRNA can be spliced
What are the four arms of a tRNA
Acceptor Arm (top D arm (right) Anticodon Arm (bottom T, psudouridine, C arm (left)
What is added to the 3’ group on the acceptor arm of tRNA
CCA
How long is one tRNA
75 nucleotides long
What is the chemical modification that rRNA undergoes to become a ribosome
Methy groups added
Pseudouridine added
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
What is the polycistronic (many) hairpin loop chain called in RNA interference
Pri-miRNA
What causes the hairpin loops from pri-miRNA to be cleaved off into separate ones? What does this form?
Drosha and DCGR8
Pre-miRNA
What cleaves the head of the hairpin off pre-miRNA? What forms as a result?
Dicer and TRBP
RISC RNA Induced silencing complex
What causes degradation of mRNA
When the miRNA matches perfectly
What causes translation suppression of mRNA
When the miRNA does not match perfectly
What happens to RISK
The passenger strand is removed from complementary guide strand
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
What do viruses do with miRNA
Inhibit cellular factors involved in immunity
Downregulate expression of viral proteins
What is a directly labelled probe in fish called
fluorophore
What is an indirectly labelled probe in FISH called
Hapten
An antibody can be raised against it which makes it flourescent
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
What do you see if fish is imaged during metaphase
Chromosomes
What do you see if fish is imaged during interphase
nuclei
How is the sample prepared during FISH
Cells are fixed (formaldehyde) and Permeabilised (detergents)
How is the probe prepared during FISH
DNase I - Introduces Nicks into probe
DNA Polymerase - Fills in nicks with modified dNTP
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
What type of polymerase is used in PCR
Taq Polymerase
What is the formula for PCR
y=a*2^x
y – copy number
a – starting number
x – cycle number
What is used to prepare for viewing the product of PCR
Agarose Gel Electrophoresis
What two types of hydrophobic (non-polar) amino acids are ther
Aliphathic (chain)
Aromatic (ring)
What are the two ends of a hydrophilic (polar) amino acid
Hydroxyl - positive
Amide - negative
Which end of the Amino Acid is added to tRNA? What regulates this?
COOH group - added to 3’ end
tRNA synthases
