Integrity upto immunity Flashcards
Where do you start to acquire your microbiome?
Start to acquire it in the uterus, can be altered by mother’s antibiotics use and what she is eating
Mode of delivery gives different microbiome- vagina vs a c-section
What is the function of the microbiome?
- energy synthesis
- protection from pathogenic bacteria
- Imuune system education
- Vitamin system education
- Drug metabolism
- Bile salt metabolism
What sugar is present in breast milk that babies cannot digest?
Milk oliogosaccharides- promotes production of anti-inflammation molecules
B infantis contains the enzymes needed to break it down.
How is the microbiome involved in energy biosynthesis?
Starch that does not get broken down in the small intestine is broken down to small chain fatty acids.
SCFA is the main sources for enterocyte cells in the small intestine
How does the microbiome stop pathogenic bacteria?
Produce bacteriocins (toxins) that directly kill salmonella, listeria and clostidium
How is the microbiome involved in bile acid metabolism?
Microbiota produce secondary biles which can activate cell surface receptors- help reduce gut inflammation, regulate synthesis of bile acids
How are the microbiome and obesity linked?
- bacteria are involved in ernegy production
- they stimulate production of mediators that alter insulin/glucagon production
- involved in satiety
- regulate intestinal inflammation
What are prebiotics and probiotics?
Probiotics are foods or supplements that contain live microorganisms intended to maintain or improve the “good” bacteria (normal microflora) in the body. Prebiotics are foods that act as food for human microflora.
What is some of the advantages to taking probiotics?
Evidence they can lower cholesterol and have a general improvement in microbial composition and functions
What are some of the targeted research therapies with obesity and the microbiome?
Bioengineering bacteria to produce glucagon-like peptide 1 which increases insulin release and reduces hyperglycaemia
Bioengineer bacteria that effect satiety.
What are the two major conditions of inflammatory bowel disease?
Ulcerative colitis; effects the colon
Crohn’s disease; can effect any part of digestive tract from mouth to anus
Both have chronic inflammation, relapsing and remitting. Common presentation is abdominal pain, diarrhoae and weight loss
What is the microbiome like in patients with inflammatory bowel disease?
There is decreased microbial diversity, decrease of bacteria such as Firmicutes and clostridium. Some are increased such as E. coli
What is the current treatment for inflammatory bowel disease?
Anti-inflammatory treatment (glucocorticoids) and anti-tumour necrosis factor (TNF= a cytokine, induces inflammation)
There is no routine place for microbiome based therapy
How does colon cancer screening work?
Starts at the age of 50, test is for blood in stool, if there is a positive test a colonoscopy is given)
What increases the risk of colon cancer?
Obesity
Insulin resistance
Increased red meat intake
Decreased fibre intake
What are the microbiome protective effects against colon cancer?
Produce short-chain fatty acids
Phytochemicals (compounds in plants) are metabolised in colon
Both have anti-inflammatory effects
What are the harmful effects of the microbiome to the gut?
Secondary bile acids produced can promote DNA damage
Ammonia is produced- damage colonic epithelia
N-nitroso formed from certain foods which can be carcinogenic
Fermentation of of diet derived proteins to phenols
What bacteria do probiotics usually contain?
Lactobacillus and bifidobacterium, derived from cultured milk sources
What occurs in a helicobacter pylori infection?
What are the symptoms of peptic ulcer disease?
Often asymptomatic but can cause bleeding, leading to anaemia
Sometimes can cause upper abdominal pain, indigestion and heartburn
How is the helicobacter pylori infection detected?
A urea breath test, also use a stool antigen test or endoscopy or biopsy
How is the helicobacter pylori infection treated?
Proton pump inhibitor- supresses acid secretion
Antibiotics 7 day course- such as amoxicillin
What can a clostridiodides difficile infection cause?
Causes antibiotics associated colitis (bowel inflammation).
How does a clostridiodes difficile infection arise?
Comes about after taking a course of antibiotics which then kills certain bacteria in the healthy microbiome. It does not kill C diff however, which fills the void left. When antibiotics are stopped, healthy humans return to normal state.
What can occur if Clostridioides difficile proliferates instead of returning to normal levels after a course of antibiotics?
Creates a dysbiotic environment- a more pro-inflammatory environment. After antibiotics are stopped, in some patients C diff progresses and an inflammatory environment in the colon is created. Presents as colitis- dihorrea, colon can become dilated.
What is the treatment for clostridioides difficile infection?
Most cases respond to antibiotic treatment
Avoiding antibiotics more likely to cause the infection
Faecal microbiota transplantation- oral capsule, tube or colonoscopy
What is an infection?
The invasion, multiplication and establishment of one or more pathgoens/ microorganisms in the body
Can be bacteria, viruses, yeast, parasites or prions (proteins able to bend their shape to initate another protein)
What does pathogenicity mean?
The ability of an organism to inflict damage on the host
What does virulence mean? And what are virulence factors?
The relative ability of a pathogenic organism to cause disease.
Virulence factors include genes, molecules or structures that contribute to virulence
What are commensals, pathogens, primary and secondary pathogens?
What type of organisms are saprophytes and zoonoses?
Saprophytes= organisms that live in the environemnt
Zoonoses= organisms associated with animals
What happens when a pathogen colonises a person?
When microorganisms, including those that may be pathogenic, are present at a body site (E.g. on the skin, mouth, intestines or airway) but are doing no harm and are not causing symptoms of infection.
The person colonised can also be called ‘a carrier’.
What are the 3 categories of the innate immune system?
Physical defences eg anatomical barriers, mechanical defences and microbial colonisation resistance.
Chemical defences
Cellular defences
What are the different types of physical barrier?
(lots of extra info)
What are the different types of chemical defenses in the innate immune system?
Chemicals and enzymes in the body- Acid in stomach, urine and vagina
Antimicrobial peptides that kill bacteria by attacking membranes
Plasma protein mediators (c-reactive protein)
Cytokines
What are examples of phagocytic cells?
- Neutrophils
- Eosinophils
- Monocytes (natural killer cells)
How do host defences fail againsy protecting from pathogens?
- Physical barriers= wounds
- Flushing mechanisms- smoking causes damaged respiratory cilia, catheter in bladder
- Chemical- decreased acidity in the stomach (H2 blockers)
- Microbial colonisation resistance- antibiotics
What are the main entry points for pathogens to enter the body?
Break in skin; wound or infection in hair follicle
Sucking blood out of a cut= mouth
Infection at mucosal surfaces
Why are mucosal surfaces more prone to pathogen invasion?
- have thinner epithelia due to functions
- more prone to trauma
How do pathogens spread around the body?
- Blood- most common
- Lymphatics
- Nerve cells
- Body spaces e.g. pleura
What are the most common routes of transmission of pathogens?
Respiratory
Salivary
Faecal-oral
Sexually
Vector
What are virulence factors?
Virulence factors are the molecules that assist the bacterium colonize the host at the cellular level.
What is straphylococcus aureus?
The hospital superbug
Bacteria- half of the population is colonised with it in their noses
Causes lots of infections such as pneumonia, endocarditis, meningitis, sepsis and UTIs
What makes a patient more susceptible to a S aureus infection?
If the patient has previously been on antibiotics recently, their microbiome will be disrupted
What is MRSA?
Methicillin resistant S. aureus infection
What are the diseases associated with Neisseria meningitidis?
- Meningitis
- Pneumonia
- Arthritis
- Urethritis
- Meningococcaemia
- Meningoencephalitis
Where is streptococcus pneumonia colonised?
Nasopharynx and throat
What can strepococcus pneumoniae cause?
Mucosal infections such as sinusitis
Lobar pneumonia
Invasive infections such as meningitis and sepsis
What is the most common cause of meningitis?
pneumococcal pneumoniae
How does Streptococcus pneumoniae get past the mucosal barrier?
It has a negatively charged capsule, protects the bacteria from being trpped in the mucus
What are PAMP’s?
Pathogen associated molecular patterns
What are the steps in microbial pathogenesis?
- Entry
- Niche establishment
- Multiply
- Spread
- Exit the host
What mechansims so pathogens use to move and stick to cell walls once in contact with an organism?
Flagella or chemotoxis to move
Uses adhesives to adhere to epithelium walls
What diseases put you more at risk of infection?
- Diabetes
- Chronic renal disease
- COPD
- Malignancy
- Immnosupression e.g. congenital, drugs or HIV
What is a common cause of UTIs?
E. coli
How do you stop the chain of infection?
Controlling or eliminating the agent at the source
Hand washing, decontamination of environment- stopping transmission
Intervening aginst portals of entry= PPE
Increase host defences= vaccines, herd immunity
What are important healthcare-associated infections?
Straphylococcus aureus
Clostridium difficile
COVID-19
What are the standard infections control precautions?
- Hand hygiene
- PPE
- linen managment
- equipment managment
- patient placement
- respiratory and cough hygeine
- fluid spillage management
- waste management
How is Neisseria meningitidis transmitted?
Person-to-person
Inhaling respiratory secretions or direct contact e.g. kissing
What diseases can neisseria meningitidis cause?
Meningitis and bacteraemia
Can be severe and sometimes fatal
Notifiable to public health
What is a genome?
A complete set of genetic info, provides all the info an organism requires to function
Stored in long molecules of DNA, within chromosomes. In eukarytoic cells contained within the nucleus
What charges are DNA and histone proteins?
DNA= negative
Histone proteins= positive
What is the name given to the base, sugar and phosphate group in DNA?
NUCLEOTIDE
How many carbon is the sugar in DNA?
5
What makes up the backbone of DNA?
Sugar and phosphate
What is the sugar present in DNA?
2-deoxyribose
What are the different types of bases in DNA?
What is the name given to a base and sugar in DNA?
Nucleoside
What is the start and the end of a DNA chain?
5’ end is the start and 3’ is the finish
What is a nucleosome?
A nucleosome is the basic repeating subunit of chromatin packaged inside the cell’s nucleus.
What is the structure of histone proteins?
The DNA strand winds around the octo-histone structure. Each histone also has a long amino acid tail which extends out from the nucleosome core particle. The tails are subject to reversible chemical reactions that help to control many aspects of chromatin structure.
How many pairs of chromosomes do humans posses?
Humans have 23 pairs of chromosomes- 22 pairs of autosomes and one set of sex chromosomes
Why is DNA replication semiconservative?
It is known as semi-conservative because in each round of replication, half of the parent strand is kept within the daughter strand.
Where does DNA replication occur?
The replication origin- either direction is known as a replication fork
In what direction is DNA synthesised?
5’ to 3’ direction
How are bases added to replicating DNA?
DNA polymerase adds nucleotides to the 3’ end of the growing chain. Added as deoxyribonucleotide triphosphates (dNTPs). Base pairing dictates which nucleotide is added. Energy required for synthesis reactions comes from hydrolysis of the dNTPs high energy phosphate bond.
What is the leading and lagging strands?
What enzyme joins up the Okazaki fragements?
DNA ligase
What is the functions of DNA and RNA polymerase?
DNA polymerase can only continue an existing strand, not initiate new ones.
And RNA polymerase known as primase makes an RNA primer first (later removed) that is around 10 bases long. DNA polymerase can then extend the RNA chain.
What enzyme helps to unwind the double helix?
DNA helicase
What process proofreads DNA replication?
DNA polymerase proofreads
Then DNA mismatch repair
What are the differences between mitochondrial DNA v nuclear DNA?
What are the steps of PCR reactions?
How do COVID tests work?
Sample taken on a swab
In lab, the RNA is isolated and everything else is removed from the sample
The RNA is mixed with enzymes, nucleotides, co-factors, primers and probes.
The primers can recognise the viral DNA
Called reverse PCR as the RNA first has to be transcribed into a DNA copy
What are the differences between DNA and RNA?
What enzyme makes an RNA copy of one DNA strand?
RNA polymerase II
How does transcription occur?
Transcription produces an RNA copy of the coding strand of DNA. (except U not T).
RNA polymerase II synthesis in 5’ to 3’ end direction, does not require a primer
What is a promoter?
Promoter= made up of the sequence elements found immediately 5’ to the gene that interact with RNA polymerase and other compnenets of the transcription machinery
What are enhancers?
Increase transcription from a nearby gene can can operate over considerable distances
What are transcription factors?
Proteins which bind d to specific DNA sequences within the promotor or enhancers so as to increase or decrease gene expression.
How do transcription factors change myosin gene transcription in muscle and skin cells?
What are the different ways that a gene can be controlled to give various different products?
- Alternative promotion
- Alternative splicing
- Alternative polyadenylation
What are exons and introns?
Exons contain coding sequences, introns are founnd between exons
What is splicing?
introns can be removed to give a functional RNA molecule. Different variations of splicing can occur. Exons can be skipped or included, but their order cannot be changed.
What are the RNA processing steps that RNA must undergo before it can be exported from the nucleus?
- slicing
- capping
- polyadenylation
What is RNA capping?
It modifies the 5’ end of a RNA transcript. The cap contains an atypical neucleotide, a guanine nucleotide that has a methyl group- protects the ways mRNA is protected from degradation
What are the different types of RNA?
What is polyadenylation?
A polyA tail is a string of adenylate residules added to the 3’ end of an mRNA
It is only found on mRNAs
Transcript is cleaved past the polyA site
What are codons?
Groups of 3 nucleotides
What is the start codon?
AUG
What are the 3 stop codons?
UAA
UGA
UAG
Where are the places on tRNA molecules that are not base paired and are unbound?
At the anticodon region
The 3’ end at the top where the amino acid will bind
What eznyme is involved in attaching tRNA to an amino acid?
aminoacyl tRNA synthetases
energy for reaction given by ATP hydrolysis
What is a tRNA after it has given up it’s amino acid?
spent tRNA
What are ribosomes made of?
Made of rRNAs and proteins
What are the 3 tRNA docking sites?
What are the 4 steps of translation at a ribosome?
How do some antibiotics work in terms of protein synthesis?
Some antibiotics work by inhibiting prokaryotic proteins synthesis
What are genes that code for proteins found in most cells called?
‘Housekeeping genes’
Include ribosomal genes which are essential for the production of proteins
What changes are there in the genes of specialised cells?
All cells in a multicellular organism have a full complement of genes. Cells are specialised because of differences in gene activity and not gene content.
What are transcriptional regulators?
Switch genes on and off
What is an operon?
An operon is a cluster of genes that are transcribed together to give a single messenger RNA (mRNA) molecule, which therefore encodes multiple proteins
What is an example of bacteria switching on and off based on resources?
E. coli has 5 genes that code for enzymes tryptophan biosynthesis pathway.
When trytophan is low the genes are switched ON, and when it is abundant they are off.
Where do transcription factors bind to?
Enhancer regions
What is the role of a transcription factor?
It influences the activity of RNA polymerase by switching genes on or off
What is MyoD?
Binds to DNA and ultimately leads to the development of muscles
What is a chromatin?
DNA is packaged into nucleosomes. DNA is associated with proteins: histones and other nonhistone chromosomal proteins, this DNA-protein complex is known as a chromatin
What can transcription factors attract in nueclosomes?
Histone modification enzymes
Chromatin remodelling complexes
Histone chaperones
How do transcription factors cause nucleosomes to unwind and become more accessible?
Change the composition of the histones
This unwinds the chromatin
These combine to histones and remove them from the nucleosome, exposing the DNA.
What are differentiated cells that never divide?
Neurons and skeletal muscle
How can histone tails be modified?
Histone tails can be reversibly chemically modified to make the chromatin more or less accessible e.g. to increase or decrease gene expression.
What reinforces a cell’s memory and passes the memory onto daughter cells?
Histone modification
DNA methylation
What is DNA methylation?
DNA methylation is a biological process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence
How are different cell types produced based on intracellular signals?
When a cell is about to divide, if there is an uneven distribution of a particular molecule e.g. a transcription factor on one side of cell, it will produce two cells that have inherited different amounts of TF.
What extracellular signals allow different cells to be produced?
If the TF tells the cell to produce a signal and if the TF blocks the production of the receptors signal, this will mean the blue cell does not have the receptor and the grey does. Cells can signal but only cells close to it can pick it up, which leads to a third cell type.
What is Waddington’s landscape?
Waddington prosed a landscape made of ridges and valleys down which a marble could roll. As it moves it could make choices until it found its resting place. Similar is a cells path towards being specialised.
What is the fist step in the differentiation of blood cells?
A multipotent hematopoitic stem cell differentiate into lymphoid or myeloid fate
What is commitment to proginotors regulated by in hematopoietic stem cells?
Specific TF e.g. GATA1
Where would erythropoieten act on the following pathway?
Create more erthyroblasts
What is the haematopoitic stem cell niche?
Stromal cell signals regulate stem cell regulate stem cell differentiation. Progenitor cells are surrounded by protective tissue cells called stromal cells- niche
What is stemness?
Stemness refers to the molecular processes underlying the fundamental stem cell (SC) properties of self-renewal and generation of differentiated daughter cells
How are stem cells able to differentiate?
They maintain their stemness by contact between receptor on stem cell and ligand in stromal cell
When a stem cell divides one daughter will lose contact with the receptor and will differentiate
When is erythrocyte production selectively increased?
Anaemia (lack of Hb)
Blood loss
Accclimatization at high altiude
What is the hormone produced in response to lack of O2/ shortage of erthrocytes?
Erythropoiten- produced by kidney
Acts on erythrocyte precursor cells to increase their proliferation/survival
A GATA1 knock out mouse would have a deficit from which step?
What is GATA1?
The GATA1 gene provides instructions for making a protein that attaches (binds) to specific regions of DNA and helps control the activity of many other genes. On the basis of this action, the GATA1 protein is known as a transcription factor.
What stimulates neutrophil and macrophage differentiation from precursor cells?
Infection
Colony stimulating factors are released by fibroblasts, endothelial cells, fibroblasts and lymphocytes in response to tissue factor
CSFs act on precursor cells
What are kinases and what do they do?
Kinases are enzymes that control whether or not a cell divides. They need to be activated in a specific order to allow to replicate
These kinases are activated by external signals known as mitogens
What are mitogens?
Extracellular signals that stimulate cell division by triggering a wave of G1/S-Cdk activity tht relieves intracellular negative controls blocking the cell cycle.
What is a signal that specifically inhibits the growth and proliferation of fibroblasts?
Myostatin
What is the experiment with mice being implanted with 5 foetal spleens and 5 foetal thymus glands?
What this suggests is that thymus gland is regulated by local mechanisms, whereas the spleen controlled by feedback mechanisms which senses the size of the spleen in comparison to the body as a whole.
What are the defining characteristics of a stem cell?
- Is not itself terminally differentiated
- It can divide without limit
- Upon division each daughter has a choice: stem cell or terminal differentiation.
Where do cells from the small intestine come from?
Cells lining the villi live for an approximate 5 days. They are replaced by cells found in the crypts.
The daughters of some cells will remain stem, but some will differentiate and move up the villi in a conveyer belt fashion.
What is the intestinal stem cell niche?
Stem cells fate is induced by signals from Paneth cells and connective tissue surrounding the crypt
What is produced by Paneth cells?
WNT
How does WNT influence intestinal cells?
Why is mitochondrial DNA more sussceptible to damage?
Not protected by histone proteins
What contributes to loss of cell function and death?
