Cell Biology Flashcards
What are the general properties of biological membranes?
- Flexible
- Self repairing
- Continuous
- Selectively permeable
What are the role of lipids in biological membranes?
- Phospholipids - fatty acid tails are hydrophobic and consist of saturated or unsaturated - creates kinks in tail
- Cholesterol - poor head group, non polar hydrocarbon tail
What are the role of proteins in biological membranes?
- Peripheral membrane protein - bound to lipids which insert into the membrane
- Integral membrane proteins - protein its self is in phospholipid bilayer
What are the role of carbohydrates in biological membranes?
- Glycoproteins
- Glycolipids
Cell recognition
What is the role of phospholipids in membrane structure?
- Provide the structure and permeability barrier of membranes
- Have important roles in cell signalling and membrane interactions
What are integral membrane proteins?
- Proteins that directly insert in the membrane by a hydrophobic domain
- The transmembrane domain of proteins usually form alpha helix because there is a high conc. of hydrophobic acid
- Can also from beta barrels
What are peripheral membrane proteins?
- Covalently bound lipids which insert into the membrane and associate with integral membrane proteins or directly bind lipids
- Attach to membrane via covalently bound fatty acid or phenyl group
What are the advantages of peripheral membrane proteins?
Mobility at the cell surface
Rapid release into the extra cellular space
What is the role of peripheral proteins in red blood cells?
Cell shape determination - cytoskeleton
What peripheral proteins are present in red blood cells?
- Spectrin - forms dimers - mutation can cause certain types of haemolytic anaemia
- Actin - junctional complex with tropomyosin - Ankyrin
What integral proteins are present in red blood cells?
- Glycophorin
- Band 3
- They are restrained by the cytoskeleton of red blood cells
Where can phospholipids move?
Can rotate or exchange on the lateral plane but move slowly between leaflets
Do saturated or non saturated phospholipids make the membrane more fluid?
Saturated as it means that the membrane is less densely packed
Cold blooded animals have more saturated phospholipids so that the membranes are fluid at lower temperatures
What is the role of cholesterol in biological membranes?
- Lowers permeability - makes it less fluid in the area it is present but doesn’t affect the whole membrane
- Stops crystallisation
Why are membranes asymmetric?
Proteins
- Enzymes and transport proteins take up substances from one side to the other
- Receptors are orientated so they can bind to extracellular ligands
Phospholipids
- Maintains electrochemical gradient as inner surface is negatively charged
- Can lead to different fluidity in the leaflets
- Some proteins involved in cell signalling need to interact with inner leaflets
How is asymmetry of the membrane maintained?
- New phospholipids move into the membrane creating gaps which are filled by scramblase which ensures equal growth on both halves
- Flipase ensure asymmetry is maintained
What is the function of carrier proteins?
- Carrier proteins undergo conformational changes to transport solute
- Carrier mediated diffusion has higher rate of transport than simple diffusion
What are the three types of carrier mediated transport?
- Uniport - 1 molecule transported
- Symport - coupled transport - transport molecule and co -transported ion pass through
- Antiport - coupled transport - transport molecule and co -transported ion pass in opposite direction
How is the blood group of an individual is determined?
By the structure of the oligosaccharides attached to sphingomyelin and proteins in the red blood cell membrane
What sugars do the different blood groups have on the oligosaccharide chains?
O - no extra sugar
A - Has GALNAC
B - Galactose
AB - both
What are the electrical properties of membranes?
- Voltage difference across cell because excess positive ions on one side and negative on the other
- Combination of membrane potential and concentration gradient gives an electrochemical gradients
- Inner surface of plasma membrane os neg and outer is pos
- Created by carriers and pumps
How do ion channels allow transport across membranes?
- Form narrow hydrophobic pores through the membrane
- Specific to different ions
- Allow rapid movement of ions down conc gradient
- Regulated by binding of ions
- Often target for many toxins and medicines
How does active transport allow transport across membranes?
- Coupled carriers
- ATP and light driven pumps
- Driven by Na+ gradients in mammals and by H+ gradients in bacteria
What are the uses of liposomes?
- Drug delivery
- Delivery of DNA and RNA into cells
- Cosmetic industry
How is the cytoskeleton of RBC’s purified?
- Solubise in detergent
- proteins analysed by Gel electrophoresis
Why is important for phospholipids to be asymmetric?
Coagulation
- Scotts disease - lack of scramblase - stops the efficient movement of phosphatidylserine causing the inhibition of coagulation
Cell recognition and apoptosis
- Receptors on plasma membrane of macrophages recognise those on old red blood cells
- Signals phagocytosis
Give the structure of the nuclear envelope
- Formed from two membranes
- Membranes enclose perinuclear space
- Outer membrane is continuous with the endoplasmic reticulum
- Perinuclear space can fill with newly synthesised proteins
Give the structure and function of the nucleoplasm
Nuclear lamina
- Layers of filaments lying close to inner membrane of the nuclear envelope
- Polymerisation and dephospho rylation makes the lamina stronger
- Involved in regulation of genetic activity
Also contains ions, enzymes and nucleotides
What disease can mutations in the lamina cause?
Hutchinson - Gilford progeria syndrome which prevents cleavage and can cause premature ageing
Give the structure and function of the nucleolus
- Most obvious structure in the nucleus - is an organelle but is not membrane bound
- Site for processing ribosomal RNA to produce ribosomes
- Contains rRNA genes, ribosomal subunits, mRNA and tRNA
Give the basic structure of chromosomes
DNA wraps around histone molecules to allow effective packaging
DNA is loosely packed in non dividing cells -chromatin
In cell division packaging tightens and chromosmes become visible
What is the structure of the nuclear pore?
Consists of 50 proteins and 8 subunits 4 building blocks - Column subunit - Annular subunit - Lumenal subunit - Ring subunit https://micro.magnet.fsu.edu/cells /nucleus/nuclearpores.html
What is the function of the nuclear pore?
- Moving substances across the nuclear envelope
- Histone molecules pass through when new DNA is needed to be packaged
- Ribosomal subunits pass through
- weights up to 5000 are freely diffusible
- Active transport - signal can cause them to open to 26nm, signal is a peptide sequence
What is the basic structure of the mitochondria?
Outer membrane - encloses organelle
Inner membrane - highly folded - critsae
The inner matrix contains the enzymes responsible for energy production
What is the evolution of the mitochondria?
An aerobic prokaryotic cell and anaerobic pre-eukaryotic cell formed a symbiotic relationship - allowed them to survive in the environments
How can we track the evolution of the mitochondria?
Mitochondria have their own DNA which is passed on from the mother
- Mitochondrial DNA mutates much quicker than normal DNA so it can be tracked - out of Africa theory
Why do mitochondrial diseases affect so many areas?
- The area that is effete is the area with the mutant mitochondria
- They don’t produce enough ATP to meet cells need
Name some mitochondrial disorders
Leber hereditary optic nerve neuropathy - Visual loss begining in you adulthood - Conduction problems with heart Mitochondrial encephalomyopathy, lactic acidosis and stroke-like syndrome (MELAS) - Cognitive impairment - Dementia - Strokes
What is the basic structure and function of the chloroplast?
Do not have double membrane - have thylakoids
Uses CO2 to produce O2
- ATP and NADPH produced in light reaction
- They provide energy to convert CO2 to carbohydrates
What is the structure of peroxisomes?
- Only have a single membrane
- Do not contain DNA or ribosomes
- Found in all eukaryotic cells
- Thought to be remnant of an organelles found in ancestors
What is the function of peroxisomes?
Remove hydrogen atoms from various organic compounds
RH2 + O2 –> R + H2O2
H2O2 + R’H2 –> R’ + 2H2O
Used to detoxify alcohol in liver
What are the two phases of glycolysis?
Preparation phase - consumes 2 molecules of ATP Payoff phase - Production of 4 ATPs - Starts at step 7
What is required in the conversion of glucose to Glucose-6-Phosphate (reaction 1)?
Hexokinase
ATP consumed
What is required in the conversion of Glucose-6-Phosphate to Fructose-6-phosphate (reaction 2)?
Phosphoglucose isomerase
It is an isomerisation reaction
Freely reversible
What is required in the conversion of Fructose-6-phosphate to Fructose-1,6-bisphosphate (reaction 3)?
Phosphofructokinase
ATP consumed
What is required in the conversion of Fructose-1,6-bisphosphate to Glyceraldehyde-3-phosphate and dihydroxyacetone phosphate (reaction 4)?
Adolase
What is required in the conversion of dihydroxyacetone phosphate to Glyceraldehyde-3-phosphate (reaction 5)?
Triose phosphate isomerase
What is required in the conversion of Glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate (reaction 6)?
Glyceraldehyde-3-phosphate dehydrogenase
NAD–>NADH
What is required in the conversion of 1,3-bisphosphoglycerate to 3-phosphoglycerate (reaction 7)?
Phosphoglycerate Kinase
ATP formed
What is required in the conversion of 3-phosphoglycerate to 2-phosphoglycerate (reaction 8)?
Phosphoglycaro mutase
What is required in the conversion of 2-phosphoglycerate to phosphphenylpyruvate (reaction 9)?
Enolase
Releases water
What is required in the conversion of phosphphenylpyruvate to pyruvate (reaction 10)?
Pyruvate Kinase
ATP produced
Draw the glycolysis pathway
http://biochem.co/2010/02/glycolysis/
What are the end products of glycolysis?
2pyruvate, 2ATP, 2H20, 2NADH
What happens to pyruvate under anaerobic conditions?
Converted to lactate
Using lactate dehydrogenase
NADH to NAD
Allows glycolysis to continue with the NAD
Why is arsenate poisonous?
- Arsenate can substitute fro phosphate in step 6 of glycolysis producing 1-arseno,3-phosphoglycerate
- This dissociated to 3-Phosphoglycerate skipping step 7
- Means no ATP produced in that step so net production in 0 ATP molecules
What is Tarui disease?
Defect in muscle phosphofructokinase
- causes build up of glycogen
- Cause pain and weakness
What does pyruvate kinase deficiency in erythrocytes lead to?
Lack of enzyme activity
Short half life
What mechanisms are involved in regulation of glycolysis?
Hexokinase - Regulated by glucose-6-phosphate Phosphofructokinase - Inhibited by ATP - Regulated by fructose-2,6-bisphosphate as it stimulates phosphofructokinase 1 to increase glycolysis - Phosphofructokinase 2 increases fructose-2,6-bisphosphate Pyruate kinase - Inhibited by ATP and acetyl coA - Activated by fructose-1,6-bisphosphate
What is the net link reaction?
Pyruvate + CoA + NAD+ —-> Co2 + Acetyl CoA + NADH + H+
What is the PDH complex?
- 20-30 copies of pyruvate dehydrogenase
- 60 copies of dihydrolipoly transaceylase
- 6 copies of dihydrolipoly dehydrogenase
Regulates the link reaction
How does the PDH complex regulated the link reaction?
PDH complex is activated normally and deactivated when phosphorylated
Ensures that there is not a build up of acetyl CoA
What stimulates and inhibits the PDH complex?
Stimulates
- NADH, ATP, Acetyl CoA, Ca2+, Mg2+
Inhibits
- Pyruvate, NAD+, CoASH, ADP
How does sodium fluoroacetate affect the Krebs cycle?
Bind to aconite enzyme causing citric build up and stops Krebs cycle, causes nausea and vomiting
No antidote
What is required in reaction 1 of the Krebs cycle?
Acetyl CoA is added to Oxaloacetate
Citrate synthase enzyme
Froms citrate
What is required to convert citrate to isoscitrate in the Krebs cycle (Reaction 2)?
Aconitase
What is required to convert isoscitrate to alpha-ketoglutarate in the Krebs cycle (Reaction 3)?
Isocitrate dehydrogenase
NAD+ —> NADH
CO2 released
What is required to convert alpha-ketoglutarate to succinyl-CoA in the Krebs cycle (Reaction 4)?
Alpha-ketugluterate dehydrogenase
NAD+ —> NADH
CoA-sh —> Co2
What is required to convert succinyl-CoA to succinate in the Krebs cycle (Reaction 5)?
Succinate thiokinase
GTP to GDP
What is required to convert succinate to fumerate in the Krebs cycle (Reaction 6)?
Succinate dehydrogenase
FAD to FADH2
What is required to convert fumerate to L- Malte in the Krebs cycle (Reaction 7)?
Fumerase
H20 released
What is required to convert L- Malte to oxalocetate in the Krebs cycle (Reaction 7)?
Malate dehydrogenase
NAD+—-> NADH
What are the end products of the Krebs cycle?
6NADH, 2FADH2, 2GTP, 4CO2
What electron carriers are involved in oxidative phosphorylation?
- NAD and FAD
- Ubiquinone
- Cytochrome C
- Iron - sulphur proteins
What is complex 1 in oxidative phosphorylation?
NADH dehydrogenase
What happens at complex 1 in oxidative phosphorylation?
- Transfers electrons from NADH to ubiquinone forming ubiquinol
- Complex 1 pumps out 4 protons into the inner membrane space
What is complex 2 on oxidative phosphorylation?
Succinate dehydrogenase
What happens at complex 2 in oxidative phosphorylation?
- Transferes 2 electrons from FADH2 to ubiquinone
- No protons pumped across
What is complex 3 in oxidative phosphorylation?
Cytochrome bc1 complex
What happens at complex 3 in oxidative phosphorylation?
- Ubiquinone passes electron to cytochrome C (cytochrome C can only carry one electon)
- Other electron forms semi ubiquinone and then transferred to cytochrome C
- 2 protons released into inner membrane space
What is complex 4 in oxidative phosphorylation?
Cytochrome oxidase
What happens at complex 4 in oxidative phosphorylation?
Electrons pass from cytochrome C to oxygen (final acceptor) to form water
- 4 protons consumed in making H20 - amplifies proton gradient
- 4 Protons pumped into inner membrane space
What happens at ATP synthase complex in oxidative phosphorylation?
- Protons move through enzyme causing y subunit to rotate inside F1 unit
- This causes change in B subunit which has ADP and Pi
- Froms ATP molecules
What are the end products of aerobic respiration?
36 ATP molecules
10 NADH
2 FADH2
How is oxidative phosphorylation regulated?
ADP/ATP determine rate of electron transfer
- At rest - Hugh ATP levels - minimal proton flow through synthase, low transfer of electrons
- During exercise - ATP consumed, ADP high, increased proton movement, increase electron transfer
Name some molecules that inhibit oxidative phosphorylation
Cyanide - Electron transport inhibitor - Site of action of complex IV Carbon Monoxide - the same Oligomycin - Inhibits ATP synthase - OSCP fraction of ATP synthase effected
What is Leigh syndrome?
A fatal neurodegenerative disorder, early onset
Results in bilateral lesions in the brainstem, basal ganglia, thalamus and spinal cord
Causes psychomotor retardation and brainstem dysfunction
Due to mutation in ATP synthase?
What are the differences in structure between DNA and RNA?
DNA - Deoxyribonucleic acid - Thymine as a base - Double stranded - H group instead of OH RNA - Ribonucleic acid (RNA) - Thymine replaced with uracil - Single stranded - OH group
What is the structure of a tRNA molecule?
- Amino acid attached
- Has multiple anticodon loops
- Anticodon loop is complementary to the RNA coding for that amino acid
How do tRNA and mRNA interact in protein synthesis?
mRNA does not bind directly to an amino acid so it needs tRNA with the corresponding anticodon to attach amino acids
What is the structure of a ribosome?
Has three binding sites - Aminoacyl - tRNA (A) - Peptidyl - tRNA (P) - Exit (E) Has a large subunit and small subunit
What happens at a ribosome in protein synthesis?
- An incoming amino acid - tRNA binds to vacant A site
- The original AA-tRNA moves to the P site to allow new tRNA molecule to bind
- Large and small subunits undergo relative conformational change as a new peptide bond forms between amino acids
- mRNA moves 3 nucleotides through small subunit and the used tRNA moves to E and is ejected
How is correct base pairing ensured in tRNA ribosome part of protein synthesis?
- Amino acid - tRNA is associated with elongation factor EF-tu-GTP (a hydrolysing protein)
- Correct base pairing activates this protein allowing it to dissociate from the complex
- Incorrect base pairing then no GTPase
What promotes the movement of tRNA molecules to the next binding sites in a ribosome?
Elongation factor EF-G in GTP-bound form promotes movement of tRNA molecules to the next binding site
How is protein synthesis initiated?
- Translation begins with AUG
- Initiator tRNA carries methionine
- Initiator factor - eLF 2
- Meets 5’ capped mRNA
- Ribosome subunits bind to capped mRNA
- eLF dissociate and large subunit associates
How is protein synthesis terminated?
- Stop codons not recognised by tRNAs
- Release factors bind to A site on ribosome with stop codon in
- Pepitdyl transferase catalyses transfer of water to C terminus - causes dissociation from ribosome
What immediate modifications occur to proteins after they have been synthesised?
- Removal of targeting signal sequences
- Folding e.g.. to hide hydrophobic regions
- Modifications can completely change the function of the protein (e.g. different hormones often have the same precursor
Name some consequences of protein misfolding
- Can lead to aggregation
- Abnormal folding can lead to plaques causing alzhiemers
- Can lead to perversion - e.g.. abnormal cellular prion proteins resist protease action - recruits normal prion proteins and proliferates and infects the organism