MTM Flashcards
What is the plasma membrane?
Lipid bilayer in which proteins are embedded
What is a mitochondrion?
An organelle in which energy is extracted from food during oxidative metabolism
What makes up the cytoskeleton?
Micro tubules- tube of protein molecules
Intermediate filament- provide support and strength
Actin filament- twisted protein fibres responsible for cell movement
What does SER do?
Aids in the manufacture of carbohydrates and lipids
What is RER?
Membranes studded with ribosomes that carry out protein synthesis
What is the extracellular matrix?
Contains a network of macromolecules such as proteins and polysaccharides acts as a scaffold and stabilises the cell.
What does the centre some do?
Produces micro tubules and contains centrioles.
What is a peroxisome?
Filled with enzymes, enclosed in a single membrane and buds off the er. Breaks down lipids and destroys toxic substances via oxidation.
What are vesicles?
Transport of materials between organelles
Golgi apparatus?
Synthesises, packages and modifies molecules ready for secretion from the cell and routes new proteins to the correct compartment
Structure of mitochondria?
Double membrane and their own DNA, inner convoluted membrane forms cristae which increases the surface area for electron transport.
What are endocytosis, pinocytosis and exocytosis?
Endocytosis- the cell engulf large particles
Pinocytosis- eukaryotes ingest plasma mambrane as vesicles, type of endocytosis of soluble substances comes from ECM.
Exocytosis- vesicles fuse with the plasma membrane releasing contents into the external medium.
What are the 3 mechanisms of protein transport into organelles?
Nuclear pores- movement of RNA, proteins and ribosomes into and out of the nucleus.
Protein translocation- protein must unfold to get through the membrane, in the mitochondria, ER and peroxisomes, proteins enter the ER whilst being synthesised.
Transport vesicles- allow for the transport of substances between organelles
What is the role of endoplasmic reticulum?
Serves as an entry point for proteins destined for other organelles including, Golgi, endoscopes, lysosomes and the cell surface, enter er and are ferried in transport vesicles between organelles.
How are water soluble proteins moved?
Translocation across er membrane and released into the lumen
How do prospective cell membrane proteins move?
They partially translocate across the er membrane and become embedded
What is the cytoskeleton?
A system of crossed fine protein filaments either anchored to the plasma membrane or radiating from a central site next to the nucleus
How does the cytoskeleton move organelles?
Uses ATP to propel them along the filaments
What do the types of filaments in the cytoskeleton do?
Actin- thinnest, generate contractile forces, form a mesh beneath the plasma membrane and strengthen it.
Micro tubules- thickest, pull duplicated chromosomes and distribute them equally between daughter cells
Intermediate filaments- mechanically strengthen the cell
What is DNA?
A template, transcribed onto mRNA by RNA polymerase. 3mRNA form a codon corresponding to an amino acid.
What happens to mRNA after it has left the nucleus?
It is translated on a ribosome by tRNA onto a protein. Some of the code is redundant/ regulatory, degenerate means that the same amino acid is coded by different sets of nucleotides.
What is the primary structure of a protein?
Polypeptide chain, the sequence of amino acids. AA are lined by condensation reactions, the structure is flexible and various side chains with different properties such as polarity of hydrophilic/phobic groups determine folding.
Secondary structure
The folding of a primary structure into alpha helicopters or beta pleated sheets. Stabilised by van der waals forces, hydrogen bonds and electrostatic attraction. Alpha helices stabilised by h bonds.
Tertiary structure of a protein?
3D shape of the protein requiring the least energy to form.
Where are the different types of amino acids arranged to?
Non polar on the inside and polar on the outside
What happens when proteins don’t fold correctly?
They form aggregates and accumulate. This prevents their functioning, initiates an immune response which can damage cells and tissues.
What is the quaternary structure?
More than one polypeptide chain. Subunits ore honomers- the same polypeptide chain or heteromers- different
What are disulphides bonds?
Polypeptide chains are stabilised by covalent cross linkages, disulphides is the most common. Those stabilised in this was are transported out of the cell. The formation is catalysed in the er by an enzyme linking cysteine side chains.
What are the functions of fibrous and globular proteins?
Fibrous- collagen or keratin, supportive
Globular- secretory, can be enzymes, haemoglobin
What are the functions of proteins?
Catalysis- enzymes- specificity
Receptors- binding ligands
Switching- signalling pathways telling cell to differentiate and make enzymes
Structural- cytoskeleton element giving cell shape and helping the ,overextended of the organelles
How is the function of a protein regulated?
Synthesis- need signalling protein to produce protein when needed
Localisation- taken to the right cell and organelle
Modification- regulatory protein attached makes it inactive and detached to activate
Degradation- get rid of unnecessary or non functional proteins from inside the cell or store them in vesicles
What is feedback inhibition?
The catalytic activity of enzymes are often regulated by other molecules through feedback inhibition, an enzyme acting early in the pathway is inhibited by a later product
Where are proteins modified and how?
Disulphides bonds reinforce conformation, glycosylation occurs in endoplasmic reticulum. Further modification in the Golgi.
How is the protein conformation dynamic and how is it controlled?
Proteins can open and close depending on their regulation, conformation can shift to suit the function, open conformation is active and closed is inactive. It is controlled by phosphorylation, a phosphate group is covalently attached to amino acid side chains. Phosphorylase by kinase and dephosphorylated by phosphatase
What are the 2 types of secretion?
Constitutive- unregulated, continuous, no external signal required
Regulated- use secretory vesicles, need extracellular signalling
How do proteins get sorted to the correct site?
They have a sorting signal
Membrane structure?
Phospholipid bilayer and transmembrane proteins, prevent the passage of water soluble molecules. Phospholipid has a hydrophobic tail and hydrophilic head.
What does cholesterol do to the membrane?
Makes it more rigid and stabilised proteins for easier communication
Wher are glycol opioids found?
The noncytosolic half of the plasma membrane, form a carbohydrate later and acquire sugar in Golgi apparatus. Important for recognition
What are the types of protein association with the bilayer?
Transmembrane- through the membrane
Membrane associated- inner leaflet of bilayer in the cytosol
Lipid linked- anchored here
Protein attached- attached to integral membrane proteins
Actions of transmembrane proteins?
Receptors- bind ligands Anchors- link to intracellular matrix and actin Transporters- eg. Ion pump Signal transduction molecules Enzymes
Why does polypeptide chain cross the bilayer as an alpha helix?
Because the transmembrane segment has hydrophobic side chains and cannot form favourable interactions with water so hydrophilic polypeptide backbone forms h bonds with itself forming a helix in the absence of water
How do glycoproteins prevent cell damage?
They form a carbohydrate layer preventing chemical and physical damage. Sugars absorb water acting as a lubricant and are used in cell recognition and adhesion.
What is active transport and an example?
Requires energy from the hydrolysis of ATP and substances are moves against their concentration gradient. Sodium pump couples 3 sodium out and 2 potassium in.
Give an example of coupled active transport.
Na+ - glucose symporter.
What are the types of passive transport?
Simple diffusion- along a concentration gradient, no membrane proteins involved and no energy.
Facilitated diffusion- along the concentration gradient and channel proteins or uni porter carrier proteins involved, along a conc grad
What are channel proteins?
Pores which discriminate on size and charge, hydrophilic, allow rapid diffusion, non directional, some selectivity, controlled via gates.
What are carrier proteins?
Highly selective, molecule must bind, needed for small organic molecules such as glucose
Where is the cell cycle needed?
In embryogenesis, involves growth and tissue formation. Needs regulation
What are the signal proteins affecting cell proliferation?
Mitogens- stimulate cell division, overcome intracellular braking mechanisms
Growth factors- stimulate cell growth, promote protein synthesis and other macromolecules
Survival factors- promote cell survival by suppressing apoptosis
Why must the cell cycle be controlled?
To maintain genome integrity and ensure efficient and correct DNA replication, ensure identical daughter cells
What are the 5 phases of the cell cycle?
G0- quiescence, the cell is resting.
G1- the first growth phase, prepares the cell for replication. Cell grows in size, the mRNA and proteins needed are produced.
S- synthesis, copying of chromosomes to form 2 sets of genes connected at the centromere.
G2- second growth phase, increase in the number of organelles so they can be separated in cytokinesis and increase in the amount of cytoplasm
Room some segregation, cell division to form 2 identical cells.
When does proliferation begin?
When the appropriate signal is received
What are the checkpoints?
G1- ensures the cell is large enough to divide and has enough nutrients. If it receives the growth factor signal, cell cycle will continue, if not it will enter G0.
G1/S- a check of DNA to ensure it is not damaged, if damaged, auto lysis will occur.
G2- ensures successful DNA replication
Metaphase- ensures chromosomes are attached to the mitotic spindle correctly by kinetochore
How do cycling and cyclin dependent kinases work?
Fluctuations in the abundance and activity of these molecules pace the events of the cell. Kinases allow move,net through G1 and 2. They are activated by cyclins, the concentration of cyclin in the cell varies and is highest when the growth signal is received.
What types of cdk are there?
G1-CDK, drives through the G1 phase
G1/S CDK and S-CDK into S phase
M CDK to enter mitosis
What are the functions of CDKs?
Regulate the cell cycle checkpoint transitions and are regulated by feedback
How do CDKs work?
Cyclins accumulate during G1, S and G2 phases of the cell cycle and by G2 there is enough M- cyclin to form MCDK allowing the initiation of mitosis.
How is cdk regulated?
MCDK switches itself off and leads to the destruction of M cyclin inactivating CDK. CDK persists until cyclins can reactivity it.
How is the G1 checkpoint (restriction point) regulated?
Growth factors target surface receptors activating G1 CDK and G1/S CDK. These phosphorylate PRB causing it to release its binding of transcription regulators and activate genes for cell proliferation.
What happens in g1 in the absence of growth factors?
PRB binds transcription regulators preventing the continuation of he cell cycle.
What is PRB?
It is a tumour suppressor protein, mutation could lead to a tumour.
How is the G1/S checkpoint regulated?
P53.
Increased DNA damage will cause an increase in p53 activates the transcription of p21 which inhibits CDK and so prevents continuation into S phase. If DNA damage is too severe, p53 can induce apoptosis
What is apoptosis?
Programmed cell death, eliminates unneeded cells, shrinks and condenses.
What is necrosis?
Cell swells and bursts
What are the consequences of checkpoint failure?
Proliferation in the absence of a growth factor, replication of damaged DNA, segregation of incompletely replicated chromosomes and division of cells with the wrong number of chromosomes.
What is the growth factor signalling pathway?
An active receptor, growth factor binds and phosphorylates it. A Ras protein which binds GTP is phosphorylated this causes a kinase phosphorylation cascade and gene regulatory proteins are phosphorylated, unbending and expressing genes required.
What happens if receptors become oncogenic?
In the absence of growth factors continual phosphorylation occurs and the receptor is constitutively active, causes deregulated cell proliferation.
What types of oncogenic mutations can occur?
Oncogenic receptors, signalling proteins and regulatory proteins
What occurs in the printing stage of glycolysis?
1) Glucose is phosphorylated to glucose-6-phosphate by hexokinase. It uses energy from ATP, so produces ADP.
2) Glucose-6-phosphate is isomerise do to fructose-6-phosphate in a REVERSIBLE reaction by phosphoglucose isomerase.
3) Fructose-6-phosphate is phosphorylated to fructose-1,6-bis phosphate by 6-phosphofructokinase, using energy from the hydrolysis of ATP
What occurs in the splitting stage?
1) Fructose bisphosphate aldolase converts fructose-1,6-bisphosphate to dihydroxyacetonephosphate (DHAP) and glyceraldehyde-3-phosphate (GAP) REVERSIBLE REACTION
2) DHAP and GAP are converted in a REVERSIBLE REACTION by triode phosphate isomerase.
What happens in the oxidoreduction phosphorylation stage?
1) GAP is dehydrogenated to produce 1,3-bisphosphoglycerate by GAP dehydrogenase. This reduces an NAD+ to NADH.
2) 1,3-bisphosphoglycerate is converted to 3-phosphoglycerate by phosphoglycerate kinase, forming ATP.
3) 3-phosphoglycerate is converted to 2-phosphoglycerate by phosphoglycerate mutase.
4) 2-phosphoglycerate is converted go phosphoenolpyruvate by enolase, producing water.
ALL OF THESE REACTIONS ARE REVERSIBLE
5) PEP is converted to pyruvate by pyruvate kinase forming ATP.
What are the overall yields of glycolysis?
2x pyruvate
2x ATP
2x NADH
What may be the complications in glycolysis?
Arsenic poisoning may lead to a skip in the ATP generating step leading to no gain in ATP
Describe gluconeogenesis.
Lactate and pyruvate swap between eachother via lactate dehydrogenase.
2) pyruvate carboxylase catalysed the conversion of pyruvate to oxaloacetate, using CO2 and energy from ATP.
3) REVERSIBLE PEP carboxylase converts oxaloacetate to PEP, PRODUCING CO2 and GDP.
4) PEP to fructose-1,6-bisphosphate REVERSIBLE
5) fructose 1,6- bisphosphatase converts it to fructose 6 phosphate and produces Pi.
6) fructose 6 phosphate to glucose 6 phosphate REVERSIBLE
7) glucose 6 phosphatase converts glucose 6 phosphate to glucose, producing Pi.
What are the requirements and costs of gluconeogenesis?
Requirements: 2 pyruvate, 4ATP, 2GTP, 2NADH
Cost- 2 pyruvate, 2 ATP, 2 NADH as glycolysis makes less
Describe anaerobic respiration.
Pyruvate is converted to lactate which is converted to glucose and then 1,3 BGA and back to pyruvate.
Why is regeneration of NAD important?
To continue glycolysis and the TCA cycle. This explains lactate formation.
What is the cori cycle?
Lactate from anaerobic respiration is used by the liver to make glucose.
What are the carbon flux sources of acetyl CoA?
Amino acids, pyruvate and fatty acids(reversible)
How is pyruvate converted to acetyl CoA?
2 pyruvate move into the mitochondria. Pyruvate dehydrogenase catalysed the conversion, producing 2CO2 and using coenzyme A. Also producing 2 NADH
What is the role of acetyl CoA?
The TCA cycle requires acetyl CoA to release all the potential energy from the glucose.
What are catabolic and and anabolic reactions?
Catabolic- break down molecules through oxidative pathways and release energy.
Anabolic- generate complex molecules for the cell and use energy.
Why is oxygen needed for the TCA cycle to occur?
It is needed to regenerate NAD+ and FAD.
What does the TCA cycle yield?
2CO2, 3NADH, FADH2, GTP
What is substrate level phosphorylation?
When phosphate is transferred from a substrate to make GTP
What happens in the electron transport chain?
NADH dehydrogenase removes hydrogen and electrons. The electrons are passed along the chain via redox reactions to membrane bound carriers- cytochromes.
As the pass through the chain the elections lose energy and eventually bind with cytochrome oxidase.
Here, they combine with an O2 and H+ to form water. Oxygen is the final electron carrier.
How is ATP generated?
Energy is released from the electron transport chain and causes the active transport of ions across the inner membrane. this causes a build up of H+ in the intermembrane space, an electrochemical gradient builds up and hydrogen ions pass through the ATP synthase channel via chemiosmosis synthesising ATP.
When does uncoupled transport occur?
When H+ doesn’t go through the ATP synthase channel it leave through UCP1 and doesn’t produce ATP.
What happens to the energy from uncoupled transport?
It is dissipated as heat, it occurs in brown adipose tissue, important in babies as they lose heat quicker.
What are diseases resulting from mitochondrial defects?
Tarui- defect in phosphofructokinase, glycogen storage disease
Cancer- TCA cycle entered and produces lactate
Diabetes and glucosuria
Beriberi
Mercury and arsenic poisoning
What happens with s defect in pyruvate dehydrogenase?
It prevents the conversion of pyruvate to acetyl CoA so it cannot enter the Krebs cycle.
What does low lactate show?
Signals that it is now entering glycolysis due to an enzyme defect.
Where is metabolism controlled?
Primary- at the level of ATP
Major- via enzyme levels, enzyme activity and substrate availability.
Krebs- citrate synthase, isocitrate dehydrogenase and alpha ketoglutarate dehydrogenase complex
What are the stages of differentiation?
Stem cells, progenitor cells and terminal functional cells.
What are the functional stages in differentiation?
Self renewal (maintenance)- the stem cell remains in this state
Commitment- it commits and divides to become a progenitor
Expansion- cell division and differentiation
Differentiation- cell division and binary differentiation decision
What happens in the stem cell stage?
Indefinite self renewal, cells are pleuripotent, undergo commitment
What happens in the progenitor cell stage?
Intermediate cells which aren’t totally differentiated, important for tissue expansion and are multi potent
What happens in the terminal functional cells?
Terminally differentiated, only divide into identical cells and can no longer differentiate
What is the importance of cell differentiation?
During development to specialise and form organs and in an adult to allow for replacement of cells
What types of protein are found within a cell?
Metabolic, structural and regulatory
What do transcription factors do?
They allow for the control of proteins to be expressed
Where do transcription factors bind?
Bind to the promoter region of a gene, this is upstream of the gene to be transcribed, they can inhibit or allow for the transcription of mRNA by RNA polymerase and may be done through transcriptional activators.
What are transcriptional activators?
Modular, have a DNA Binding domain and interact with RNA polymerase
What is the role of transcription factors in differentiation?
Regulate every step towards differentiation, lead to different genes being transcribed and lead to different proteins being formed.
What does Epo do?
Stimulates stem cells in bone marrow, a change in oxygen changes the levels and stimulates or inhibits RBC production.
What is a cell niche?
Microenvironment where a stem cell can divide indefinitely, asynchronous division occurs as a response to the environment and results in one committed cell.
What is post transcriptional control?
Additional points of control after DNA to protein, operate after synthesis of RNA and can destroy RNA to prevent excess gene expression,
What are the different classifications of gene disorders?
Single gene, multifactorial, Christmas imbalance, mitochondrial and somatic.
Examples of single gene disorders?
Autosomal dominant- heterozygous with one copy of the gene have the condition.
Autosomal recessive- homozygous with 2 copies with the gene will have the condition
X Linked recessive- males with one copy of the altered gene will have the condition
What is an autosomal dominant condition?
Any trait expressed in a heterozygote, distinctive pattern of segregation within families.
What is variation in expression?
Family members have different symptoms and signs of the same disorder, the severity varies. Eg. Everyone with the NF1 mutation shows signs and symptoms but these vary
What is penetrance?
Complete penetrance is where everyone with the mutation shows at least one clinical sign, there can be reduced or incomplete penetrance.
Give an example of age dependent penetrance.
Huntigton’s- there is a delay in the onset of genetic disease.
What are new mutations?
New changes in the DNA that may cause a disease. They increase with paternal age and it is due to a greater number of germ cell divisions.
What is anticipation?
Results in diseases occurring earlier in age or increasing in severity through the family tree. Severity or age correlates with the repeat length, numbers above the normal limit. It worsens the symptoms.
How do you recognise an autosomal recessive disorder?
1) you can’t follow the disease through the pedigree
2) there is horizontal transmission where siblings are affected
3) may be evidence of consanguinity
What are the risks to the offspring of each of the 3 genotypes?
Affected- 25%
Carrier- 50%
Unaffected- 25%
What is the CF mutation?
Change in the F508 gene
What are the symptoms of CF?
Chronic lung disease secondary to recurrent infection, secondary cardiac failure, impaired pancreatic function, malabsorption due to thick secretions, diabetes, cirrhosis, sterility in males
What is the genetic cause of CF?
A mutation in the CFTR gene linked to enzyme polymorphism on chromosome 7q, encodes cf transmembrane conductance regulator, CTT bp deletion at 508
What is genetic heterogeneity?
A single phenotype of genetic disorder may be caused by a multiple number of alleles or mutations at a number of different loci.
What is pseudodominance?
It is where an autosomal recessive disease appears in subsequent generations because there is a 50% chance of being affected due to homozygous (aa) and heterozygous (Aa) gametes meeting.
What is the Hardy Weinberg principle used for?
To estimate the carrier frequency of an AR disease in a population.
Hardy Weinberg principle equations?
p + q = 1 Frequency of A= p and frequency of a= q.
AA= p^2, aa= q^2, Aa=2pq.
What is segregation analysis?
Study of how a disorder is inherited in families to establish the mode of inheritance.
What is a summary of the Hardy Weinberg theory?
Carrier frequency = 2(F)1/2
How do you estimate the frequency of an AD allele n a population?
F=2q where q is the diseased allele and AD diseased alleles are very rare.
What determines genotype frequency in a population?
Mutation rate and heterozygous advantage.
What is heterozygous advantage?
It is where the heterozygote for the recessive allele holds an advantage over homozygotes because having half the gene dosage for a certain receptor or enzyme decreases susceptibility to certain diseases.
Segregation analysis for AD disease?
Compare the number of affected children born to affected parents, penetrance varies.
Segregation analysis for AR disease?
More difficult as some carrier parents will have no affected offspring.
What are the applications of clinical genetics?
Prenatal screening and diagnosis, risk counselling, prenatal risk assessment.
What are the forms of prenatal diagnosis of genetic disease?
Chorionic villus sampling, amniocentesis, study foetal cell in the mother’s blood.
What are the methods of genetic analysis?
Linkage analysis (risk not given), direct mutation analysis, using PCR.
What is an X linked recessive disease?
A gene coded for on the X chromosome contains a mutant allele and encodes a recessive trait. Disorder usually only affects homozygous males.
How do you identify an X linked recessive pedigree?
More than 1 generation involved, usually only males, no male to male transmission.
What are examples of X linked recessive diseases?
Red green colour blindness, fragile X syndrome, mental retardation, DMD
What are the signs and symptoms of DMD?
Presents in infancy, delayed walking, waddling gait, Gower’s sign, calf pseudo hypertrophy, develop progressive weakness, cardiac muscle involvement, intellectual impairment.
What are the investigations for DMD?
Serum muscle enzymes, high levels of creatine kinase, muscle biopsy- lack of antibodies to dystrophin gene, molecular genetic analysis via PCR.
What are the types of mutation in DMD?
- Deletions
- Point mutations
- Premature stop codons
- Altered splice site mutations (lose splicing of exons or add exons that shouldn’t be
there) - Promoter mutations
How can females show X linked recessive traits?
- Skewed X inactivation
- Turner’s syndrome
- Homozygous for recessive trait eg. XaXa
- Chromosomal rearrangement with an autosome, the translocated X is preferred so not inactivated.
What happens in each stage of X inactivation?
Initiation- The Xic- X inactivation centres are counted and half chosen to remain active.
Spreading- the inactivated X has an Xist gene in the Xic which compacts the chromosome and encodes RNA to coat it and compact to form a Barr body.
Maintenance- This X remains inactive in all cells produced from this cell.
When does X inactivation occur?
In the inner cell mass early in the embryo stage.
What is clonal and random?
X inactivation
What is sex limitation?
The appearance of only some symptoms in individuals of only one sex.
What evidence is there for complex disease?
-Familial clustering
-Twin studies
-Adoption studies
-Population and migration studies
Can estimate the proportion of the aetiology ascribed to genetics.
