brief overview of thinsg Flashcards
explain DNA replication
- initiation - DNA helicase unwinds the 2 strands. DNA primase synthesises a small RNA primer which acts as a kick starter for DNA polymerase. DNA polymerase attaches to the original unzipped strands
- elongation - DNA polymerase syntheses new DNA to match the templates. Leading strand 5’ to 3’ and lagging strand 3’ to 5’
- termination - the process of expanding the new DNA continues until there is either no more DNA template left to replicate or 3 replication forks meet and terminate. RNAase H removes the RNA primer that was at teh begining of each okazaki fragment and DNA ligase joins fragments together to complete one full strand
what is rRNA
combines with proteins to form ribisomes where protein synthesis takes place
what is tRNA
carries amino acids to be incorporated into protein
Anticodons consist of 3 nucleotides
what is mRNA
carries genetic information for protein synthesis
what is Pol I, II, III
Three multisubunit RNA polymerase (Pol) enzymes, Pol I, II, and III, transcribe the eukaryotic genome
what is TFIID
general transcription factor required for all Pol II transcribed genes
when are the introns spliced out
after transcription and before translation
explain transcription
- RNA polymerase binding
which requires transcription factors - DNA chain separation - unwinding of DNA
- Transcription initiates
- Elongation due to addition of further nucleotides to RNA chain in 5’ to 3’ direction
- Termination - release of finished RNA
explain translation
(anticodons of tRNA form base pairs with codons of mRNA)
- Initiation - GTP provides energy. Ribosomal subunit binds to 5’ end of mRNA and moves along until the start codon is found. Initiator tRNA pairs to start codon. Large subunit joins assembly and initiator tRNA is located in P site
- Elongation - elongation factor brings aminoacyl-tRNA to A site
- Peptidyl transferase catalyses peptide bond formation between amino acids in P and A sites
- Termination - Occurs when A site of ribosome encounters a stop codon (UAA, UAG, UGA). Finished proteins cleaves off tRNA
what are the 3 binding sites in ribosome
Exit, Peptidyl, Aminoacyl
what is post translational and co-translational in regards to protein formation
- Free ribosomes in cytosol proteins for - cytosol, nucleus, mitochondria – Post translational
- Bound ribosomes on rough ER - plasma membrane, ER, Golgi, secretion – Co-translational
what are enzymes without a cofactor and with a cofactor called
Without = apoenzyme
With = holoenzyme
what is induced fit
binding of the substrate induces a conformational change in the shape of the enzyme resulting in a complentery fit
what carries out phosphorylation reactions
protein kinases
what is Vmax
maximal rate of reaction at unlimited substrate concentration
what is Km (Michaelis constant)
50% of Vmax
what graphs are drawn for enzyme kinetics and what are the axis
Lineweaver Burk plots
y axis = 1/V
x axis = 1/[s]
what is seen in a lineweaker Burk plot of a competeitive inhibition
- binds to active site
- Vmax remains the same
- Km varies
what is seen in a Lineweaker Burk plot of a non competative inhibition
- bind to other side than active site
- Km stays the same
- Vmax varies
where is Vmax on a Lineweaker Burk plot
the point at which the line crosses the Y axis
what is allosteric control and what does it show on a graph
Allosteric control refers to a type of enzyme regulation involving the binding of a non-substrate molecule, known as the allosteric effector, at locations on the enzyme other than the active site
shows a sigmoidal relationship
what are the functions of lipids
Cholesterol
- present in cell membranes
- component of the mylein sheath
- precursor molecule for: steroid hormone, Vit D, bile acid
Triglycerides
- present in all cell membranes - lipid bilayer
- highly concentrated energy stores
what enzyme of the TCA cycle is not present in the matrix
succinate dehydrogenase in the inner mitochondrial membrane
what is phosphoryl transfer potential
free energy change for ATP hydrolysis
what is electron transfer potential
measured by redox potential of the compound
what is standard redox potential of a substance
measure of how readily it donates an electron
- Negative = reduced form of X has a lower affinity for electrons than hydrogen
- Positive = reduced form of X has higher affinity for electrons than hydrogen
what is glycolysis
initial pathway for the conversion of glucose to pyruvate
- per glucose there is a net gain of 2 ATP
- Hexokinase phosphorylates glucose
- Phosphofructokinase phosphorylates fructose-6-phosphate
- Pyruvate kinase converts phosphoenolpyruvate to pyruvate
explain aerobic metabolism of pyruvate
Enters mitochondria matrix
Converted to acetyl-coA (catalysed by Pyruvate Dehydrogenase Complex PDC)
explain the TCA cycle
- Pyruvate has been converted to acetyl-coA (catalysed by Pyruvate Dehydrogenase Complex PDC)
- Condenses with 4C compound to form 6C compound
- 6C compound decarboxylated twice – yields CO2
- 4 oxidation reactions – yield NADH + H+ and FADH2
- GTP formed
- 4C compound recreated
what is produced form each cycle of the TCA cycle from one acetyl-coA
- 3 NADH + H+
- 1 FADH2
- 1 GTP
- 2 CO2
explain oxidative phosphorylation
It is the coupling of respiration to ATP synthesis
2 stages:
- Electron transport
- Respiratory chain – electrons from NADH enter at complex I, electrons from FADH2 enter at complex II (TCA cycle), electrons are handed down from higher to lower redox potentials, transferred onto O2 to form H2O
- Transfer of electrons through respiratory chain is coupled to H+ transport from mitochondrial matrix to intermembrane space
- 3/4 complexes pump H+ (1,2,4)
- Electrochemical gradient – more protons in intermembranous space than matrix, matrix side more negative, protons attracted to matrix – coupled to ATP synthesis - ATP synthesis
what inhibits oxidative phosphorylation
cyanide, azide, CO inhibit the transfer of electrons to O2
what is the essence of oxidative phosphorylation
- electrons from NADH and FADH2 used to reduce O2 to H20
- Their energy used to pump protons from mitochondrial matrix to intermembrane space
- Protons flow back across the membrane
- Energy of proton flow used to phosphorylate ADP to ATP
what is the final balance of the breakdown of glucose
- Glycolysis - 2 ATP
- TCA cycle (2GTP) - 2ATP
- Glycolysis, PDH, TCA cycle (10 NADH + H+) - 25 ATP
- TCA cycle ( 2 FADH2) - 3 ATP
- 1 glucose molecule yield 30-32 ATP molecules
what makes up a chromosome
DNA strands associates with proteins (including histones)
when does DNA synthesis occur
S phase of the cell cycle
what is an overview of transcription and translation
- DNA transcribed to pre-mRNA
- Pre-mRNA spliced to mRNA
- mRNA translated to protein
- Protein is modified and moved around the cell
what are sequence variations within a gene
- change in promotor sequence
- change in exon sequence
what are sequence variations in DNA between genes
- SNPs (single nucleotide polymorphisms)
- larger duplications or deletions
what are polymorphisms
- Any variation in human genome which has a population frequency >1%
- Does not cause disease in own right
- May predispose to common disease
what does aneuploidy mean
whole extra or missing chromosome
what are some translocation examples
Rearrangement of chromosomes 47 XY +21 – Down syndrome, trisomy 21 47 XY +14 – Miscarriage, trisomy 14 47 XY +18 – Edward Syndrome, trisomy 18 45 X – Turner syndrome 47 XXY – Klinefelter syndrome
what is robertsonian translocation
Two acrocentric chromosomes stuck end to end
Increases risk of trisomy in pregnancy
what is microarray CGH
1st line chromosome test
Detects any missing or duplicated piece of chromosome
Find polymorphisms
what is penetrance
the likelihood of you having the disease if you have the gene mutation
what is expression
variation in disease severity if you have the mutation
what is aCGH (microarray competative genomic hybridisation)
1st line for paediatric referrals, checks for deletions/ duplications.
what is a polymorphism
A genetic variation that is prevalent in the population and not, in itself, disease causing.
what is a mutation
(Genetic variation that causes a disease)
Promotor and splice site sequence changes
Stop transcription or cause abnormal splicing
Base changing causing amino acid change
Change in protein sequence
May or may not reduce protein function
Base change causing premature stop codon
Insertion or deletion of bases
what is a mendelian disorder
a disease that is caused by a change in a single gene
is X linked inheritance dominant or recessive
recessive eg haemophilia
‘Only having one working copy is not enough’ mutation
haploinsufficiency
‘Abnormal protein interferes with normal protein ‘ mutation
dominant negative
‘mutation activates gene’ mutation
gain of function mutation
what is Angelman syndrome
Neuro-genetic disorder Developmental delay Intellectual disability Ataxia Epilepsy Happy demeanour Frequent laughing and smiling Chromosome 15
what are the characteristics gained by cells on progression to cancer
Proliferation Evasion of immune response Acquire a vascular supply Avoid apoptosis Metastasis
what genes are involved in cancer
- Oncogenes – switch these on for cell division
- Tumour suppressors – switch these on to stop cell division
- DNA repair genes – repair DNA damage
- Drug metabolism – genes that metabolise carcinogens
what is FISH
Fluorescence in situ Hybridisation
Can light up specific bit of chromosome if you know which bit to light up
where is the mutation in breast cancer
BRCA1 gene
what makes up a eukaryotic cell
- Outer membrane
- Inner cytosol – solution of proteins, electrolytes and carbohydrates
- Cytoskeleton – determines shape and fluidity of the cells
Made from thin, intermediate filaments and microtubules - Membrane bound organelles within the cytosol
what are the components of the cytoskeleton
Microfilaments – 7nm – composed of actin
Intermediate filaments - >10nm – composed of proteins
Microtubules – 25nm – composed of tubulin
- Originate from organising centre called centrosome
- Polar
- Dynein and kinesin attach to them and move along them
what are occluding junctions
Link cells to form diffusion barrier
Prevent diffusion
Also known as tight junctions
what are anchoring junctions
Provide mechanical strength
Adherent junctions – link submembrane actin bundles of adjacent cells
Cadherin molecules bind to each other in extracellular space and to actin of cytoskeleton
what are hemidesmosomes
Hemidesmosomes link submembrane intermediate filaments of cells to extacellular matrix through transmembrane proteins
what are desomsomes
Desmosomes link submembrane intermediate filaments of adjacent cells
what are communicating junctions
- Allow movement of molecules between cells
- Often termed gap junctions
- Each junction is circular patch studded with pores (produced by connexion proteins)
- Found in epithelium, but also in smooth muscle and cardiac muscle
what are endocrine cells and their features
- product secreted towards basal end of cell
- Distributed by vascular system
- Ductless glands
what are exocrine cells and their function
- product secreted towards apical end of cell
- Ducted glands
what are the 3 types of connective tissue
- soft
- hard
- blood and lymph
what are features of soft connective tissue
Tendons, ligaments, mesentery, stroma of organs, dermis of skin
Loose
Dense regular if fibres aligned
Dense irregular if fibres run in many directions
what are features of hard connective tissue
- Bone and cartilage
- Strong, flexible, compressible, semi-rigid tissue
3 types of cartilage
- Hyaline – articular surface, tracheal rings, costal cartilage, epiphyseal growth plates
- Elastic
- Fibrocartilage
- Bone
Outer shell of cortical bone makes up shaft – diaphysis
Cancellous/trabecular bone occupies ends – epiphyses
what cells are in connective tissue
- fibroblasts
- adipose cells
- oesteocytes
- chondrocytes
what are the 3 types of muscle
Smooth – involuntary and non-striated
Skeletal – voluntary and striated , multinucleated
Nuclei are elongated at located at the periphery, just internal to cell membrane (sarcolemma)
Cardiac – involuntary and striated
Have intercalated discs – contain multiple intercellular junctions to maintain mechanical integrity
what nervous tissue surrounds the CNS and PNS
CNS = meninges PNS = epineurium
what are astrocytes
support and ion transport
what are oligodendrocytes
produce mylein
what are microglia
provide immune surveilance
what are schwann cells (PNS)
produce myelin and support axons
where are non-keratinised stratified squamous epithelium found in the GI tract (protective)
- oral cavity
- pharynx
- oesophagus
- anal canal
where are simple columar epithelium with villi and tubular glands found (absorptive mucosa)
small intestine
where are simple columnar epithelium with extensive tubular glands found (secretory)
stomach
where are simple columar epithelium with tubular glands found (protective and absorptive)
large intestine
In the large intestine, the outer longitudinal smooth muscle is not continuous – found in 3 muscular strips called
teniae coli
immunonology on other
brainscape
gram positive stains
purple
gram negative stains
pink
what is a commensal
organism that is part of the normal flora
what is an opportunistic pathogen
probably only cause infection in immunocomprimised individual
what is virulence
degree of pathogenicity of an organism
how does bacterial growth divide
binary fission
what is an exotoxin
- usually gram positive
- produced inside cell and exported from it
what is endotoxin
- usually gram negative
- part of gram negative bacterial cell wall
features of mould
produce spores and hyphae
- Aspergillus
features of yeasts
- single cells that reproduce by budding
- Candida
what are features of streptococcus
gram positive cocci
- Aerobic
- Cocci chains
- Alpha haemolysis (partial) – Strep pneumoniae (pneumonia, meningitis), Strep viridans (endocarditis)
- Beta haemolysis (complete) – Group A Strep (throat, skin infection), Group B strep (neonatal meningitis)
features of enterococcus
gram positive cocci
- Aerobic
- Cocci chains
- Non-haemolytic
- Normal gut commensal and cause of UTIs
features of staphylococcus
gram positive cocci
- Cocci clusters
- Coagulase positive (golden) – Staph aureus – wound, skin infections
Flucloxacillin antibiotic of choice
Common cause of bacteraemia (bacteria in the blood) - Coagulase negative (white) – Staph epidermidis – normal skin commensal, IV line infections
features of gram negative cocci
- Diplococci
- aerobic
- Neisseria gonorrhoea
- Neisseria meningitidis
features of coliforms
Gram negative bacilli
- Aerobic but can also be anaerobic
- Gut commensals
E coli, Klebsiella, Proteus - Gut pathogens
Salmonella, Shigella, E coli O157 - Gentamicin is first line antibiotic
features of strict aerobes
- Gram negative bacilli
- Pseudomonas aeruginosa
- Legionella pneumophilia
what are spiral or curved gram negative bacilli
Campylobacter – food poisoning
Helicobacter pylori – gastritis
what is haemophilus influenzae
Small gram negative bacillus
Common cause of chest infection, especially in COPD exacerbations
features of gram positive anaerobic bacilli
- Clostridium spp.
- Part of normal bowel flora
- Produces spores
- Produce exotoxin that cause severe tissue damage
features of gram negative anaerobic bacilli
- Bacteroides spp.
- Normal gut commensals, only pathogenic when found in other sites
- Metronidazole is first line treatment for infections caused by anaerobes
what is Mycobacteria
- TB
- thick waxy outer coat
- acid fast bacilli or ziehl neelson stain
what is transformation gene transfer
DNA from dead bacteria taken up by living bacteria and incorporated in plasmids or the bacterial chromosome
what is conjugation gene transfer
Sex pilus (fimbria) produced by one bacteria through which plasmid DNA can be transferred
what is transduction gene transfer
Viruses infecting bacteria can transfer bits of DNA from one bacterium to another
what antibiotics work on the cell wall
- penicillin
- cephalosporins (ceftriaxone)
- glycopeptides (vancomycin)
what antibiotics prevent protein synthesis
- macrolides (erythromycin, clarithromycin, azithromycin)
- tetracyclines (doxycycline)
- aminoglycosides (gentamicin)
antibiotics that act on bacterial DNA
- metroniadazole
- trimethoprim
- fluoroquinolones
what is a side effect of gentamicin
renal and VIII nerve damage
what is a side effect of ciprofloxacin
tendonitis
what is a side effect of metronidazole
interacts with alcohol
