Metabolism Flashcards
Photoheterotroph
Use sunlight as the energy source and organic compounds as the carbon source
Describe the location and products of the light reactions of photosynthesis
The light reactions occur in the thylakoid membranes of eukaryotic chloroplasts. They oxidate water to Oxygen and reduce NADP+ to NADPH, simultaneously synthesising ATP. Otherwise known as the light-dependent energy transduction reactions.
What are some strategies for bacteria in saline/dessicating environments?
- Increase concentration of compatible solutes in the cytoplasm to reduce water loss
What are the 3 major types of stem cells and what are their characteristics?
- Pluripotent embryonic stem cells obtained from the inner cell mass of an early embryo
- Multipotent adult stem cells/tissue stem cells which can differentiate into any of the cell types of a specific tissue
- Induced pluripotent stem cells engineered by manipulating the expression of somatic genes back into a pluripotent state by reprogramming
What did Avery et al. do and what did they find?
Avery et al. pursued Griffith’s findings and isolated DNA as the transforming factor by isolating different cellular components including proteins, lipids etc and even used digesting enzymes to discover that it was only the removal of DNA that resulted in a lack of transforming factor.
Chemoautotrophs
Use inorganic chemicals as the energy source and CO2 as the carbon source
What are the four enzymes essential for gluconeogenesis?
- Pyruvate carboxylase
- Phosphoenolpyruvate carboxykinase
- Fructose-1,6-bisphosphatase
- Glucose-6-phosphatase
What are some strategies for bacteria in cold environments?
- Increase the number of unsaturated fatty acids to increase membrane fluidity
- Increase protein function by having less rigid protein cores and less interdomain interactions
What are the various ways muscle cells synthesise ATP for muscle contraction and why do they do this?
- There is a high demand for ATP during muscle contraction that would deplete cellular ATP reserves within 5 seconds, therefore ATP levels are maintained using creatine-phophate to replentish ATP
- CreatineP + ADP -> ATP + creatine
- However, these stores are also rapidly diminished, so ATP is synthesised rapidly via lactic acid fermentation
- The build up of ATP however results in fatigue, so ATP generated via aerobic respiration would be the major source beyond periods of 1-2 minutes of sustained muscle activity
Why does gluconeogenesis require three times more energy input than glycolysis?
- Glycolysis is an energy-releasing reaction, however not all of the energy released is captured as ATP.
- Therefore, to reverse the process, energy must be put back into the system.
What is euchromatin?
- Poorly staining, loose DNA found within the nucleus that is being actively transcribed
How are monosaccharides used as a fuel source?
- e.g. fructose and galactose
- Phosphorylated before being cleaved into DHAP and glyceraldehyde, which can then be phosphorylated into glyceraldehyde-3-P, which both can feed into the glycolytic pathway
What is a strict anaerobe?
Bacteria can only use anaerobic respiration (fermentation) and will die in the presence of oxygen
Photoautotroph
Use sunlight as the energy source and CO2 as the carbon source
Describe the location and function of the dark reactions of photosynthesus
Otherwise known as the Calvin Cycle, uses the NADPH and ATP generated from the light reactions to fix CO2 into CH2O within the stromal matrix of chloroplasts.
Describe the structure and function of the ribosome
Ribosomes consist of a small subunit and a large subunit.
- The small subunit binds to the mRNA to form a complex, which then binds to the aminoacyl-tRNA molecule
- The large subunit contains the enzyme peptidyl transferase and binds to the aminoacyl-tRNA complex to form peptide bonds between the amino acids, and also liberates polypeptide chains
What are the features of cancerous cells?
- Immortal (can divide indefinitely if nutrients allow)
- Not inhibited by density/over crowding
- Anchorage independent
- Can infiltrate into other tissues (metastise)
What is a lymphocyte and what is its function?
Lymphocytes are immunocytic agranulocytes of either one of two types:
- T Cells: function in mediated immunity against tumours and pathogens in the body
- B Cells: become metabolically active in the presence of antigens, differentiating into plasma cells to secrete antibodies specific to that antigen
Neutral sulphur containing aa’s
- Cysteine
- Methionine
What are some strategies for bacteria in acidic environments?
- Decrease membrane permeability to H+
- Implement plenty of proton antiporters to maintain pH close to neutrality/7
What is a transversion point mutation?
Purine replaces pyrimidine, pyrimidine replaces purine
What do the three types of RNA Polymerase synthesise?
RMT, 123
RNA Polymerase I = rRNA
RNA Polymerase II = mRNA
RNA Polymerase III - tRNA
Describe RNA Synthesis (Transcription)
- RNA Polymerase reads the DNA in a 3’ to 5’ direction so that RNA can be synthesised in a 5’ to 3’ direction, recognising the promoter region of the template strand.
- RNA Polymerase binds to the promoter region and sythesises RNA in a 5’ to 3’ direction, facilitating the binding of complimentary nucleoside triphosphates (UTP, GTP, ATP, CTP)
- The termination signal triggers the dissociation of RNA Polymerase from the DNA.
- Bacteria have one type of RNA Polymerase, but mammalian cells have three: RMT, 123
What is a missense mutation?
The substitution of a different amino acid for the original
What are the major processes using a source other than O2 as the final electron acceptor?
- Nitrogen reducing bacteria: Nitrate reducing bacteria NO3- > NO2- and denitrifying bacteria (2NO3- + 10e- + 12H+ -> N2 + 6H2O)
- **Sulfate-reducing bacteria: **SO42- -> H2S (less efficient than nitrate reduction)
- Methanogenic bacteria: CO2 -> CH4 (CO2 converted in water in the gut to CO3 which microbes use to convert to methane gas)
- Nitrogen-fixing bacteria: Rhizobia infect roots via root hairs into cortical cells, which divide to form nodules. Synthesise nitrogenase enzyme to fix atmospheric Nitrogen within the root nodules for plants (N2 + 8H+ + 16ATP -> 2NH3 + H2 + 16ADP + 16Pi)
What is a translocation mutation?
The movement of a segment of DNA to another region.
What are some strategies for bacteria living in pressure environments?
- Have an increased ratio of unsaturated fatty acids to maintain membrane fluidity
What is a strict aerobe?
Uses oxygen for respiration, and cannot grow anaerobically using fermentation
What is a eukaryotic enhancer site?
A DNA site that is able to bind regulatory activator proteins to activate and/or enhance transcription by increasing the rate. Some activator proteins must aggregate to form an enhanceosome to initiate transcription.
Appreciate how local depolarisation results in an action potential which is then transmitted down the nerve as a nerve impulse.
- The nerve is stimulated by a stimulus which causes the opening of voltage-gated Na+ channels causing local depolarisation
- If threshold is reached, an action potential is produced which moves from activated to inactivated areas ahead
- When an action potential reaches the end of an axon, acetylcholine is released from the synaptic vesicles
- Acetylcholine binds to specific receptors on the post-synaptic membrane, causing local depolarisation due to the opening of Na+ channels which may also create an AP if threshold is reached
- Acetylcholine dissociates from the postsynaptic receptors and is hydrolysed by choline sterase
- The products, acetate and choline, can diffuse back into the presynaptic axon and regenerate acetylcholine
What did Meselson and Stahl do and what did they find?
Meselson and Stahl relied on the isotopic distribution of Nitrogen in the DNA of Escerichia coli to determine the means of DNA replication by growing them in cultures of different Nitrogen weights. Across generations, the bacteria were found to exhibit semiconservative replication by possessing hybrid Nitrogen within their DNA.
What is a duplication mutation?
A nucleotide segment is duplicated
What does alpha amitin from Death Cap mushrooms do that is so toxic?
It inhibits transcription by preventing RNA Polymerase II from synthesising mRNA
ETC GO
Check ya notes and don’t forget that FMN thingy is the same as oxidoreductase apparently…
TCA CYCLE GO
Check your notes
What is a frameshift mutation?
A change in the reading frame of a gene
What is a nonsense mutation?
The insertion of a stop codon into the protein sequence
What is heterochromatin?
- Heavily staining condensed DNA usually associated with the nuclear envelope and nucleolus, not being actively transcribed
What is an inversion mutation?
A 180 degree rearrangement of a segment
What are the main components of plasma and their functions?
- Albumin: contributes to osmotic pressure by maintaining fluid balance
- Globulins: alpha and beta globulins are produced in the liver and carry fat soluble vitamins/lipids in the blood, and gamma globulins are the antibodies involved in immunity
- Fibrinogen: necessary for blood clotting, exists in soluble form and during a clotting cascade will be converted to insoluble fibrin to form a clot mesh with thrombocytes
How does the arrival of a nerve impulse at the NMJ lead to the muscle undergoing contraction?
- Acetylcholine binds to receptors on the muscle cell membrane (sarcolemma) triggering depolarisation
- This depolarisation causes the release of Ca2+ inside the cell, which allows myosin to interact with actin, causing contraction
- The Ca2+ pump requires ATP, which when hydrolysed causes the release and cocking of a myosin head
- The myosin head attaches to an actin binding site, sliding the thin filament along, which continues until there is no further neurotransmitter stimulation
- With no further stimulation, a Ca2+ pump returns Ca2+ levels to normal
GLYCOLYSIS GO
Check your notes
What are the main components of the ECM and their function?
- **Proteoglycans: **composed of glycosaminoglycan chains covalently bonded to a protein core forming hydrophilic moleules that form matrices able to withstand compressive forces
- Collagen: the main structural component providing tensile strength, regulating cell adhesion, chemotaxis/migration and direct tissue development
- Elastin: give tissues their elasticity due to the ability of the fibres to expand and contract
- Fibronectin: mediate cell attachment to fibrous proteins
- Laminin: anchors cells to the ECM
What is an INDEL Mutation, and what is the difference in gross vs point INDEL mutations?
Insertion/deletion of a codon in gross mutations, resulting in the insertion/deletion of an amino acid.
Insertion/deletion of a small number of bases in point mutations resulting in a specific affect on the protein sequence…
How are triglycerides used as a fuel source?
- Triglycerides are broken down into glycerol and fatty acids:
- Glycerol is phosphorylated into glycerol-3-phosphate which can enter the glycolytic pathway
- Fatty acids are converted via a series of steps into acetyl CoA, which can feed into the TCA Cycle via beta oxidation
What are the two effects on phenotype?
Lethal or non-lethal
Neutral aliphatic aa’s
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Proline
What did Hershey and Chase do and what did they find?
Hershey and Chase radioactively labelled bacterial viruses with either 32P DNA or 35S proteins and found that after centrifugation, the infected bacterial pellet contained more radioactive sulfur, meaning that DNA was the hereditary material.
Describe the activation and attachment of amino acids
- Aminoacyl-tRNA synthetase enzymes capable of recognising both a specific amino acid and tRNA molecule bind an amino acid to the 3’ -CCA end of a tRNA molecule to form an aminoacyl-tRNA molecule
- This occurs via a hydrolysis reaction using two high energy phosphate bonds from an ATP molecule to activate the amino acid so that it is able to form peptide bonds during translation
What is a basophil and what is its function?
Phagocytic granulocyte which store and secrete histamene for inflammatory reactions.
What is a neutrophil and what is its function?
Phagocytic granulocyte which actively ingest bacteria and are present in pus/infected wounds
What is a transition point mutation?
Purine replaces purine, pyrimidine replaces pyrimidine
How are polysaccharides used as a fuel source?
- e.g. cellulose, starch, glycogen
- Too large to cross the cell membrane therefore must be hydrolysed into its constituent monosaccharides.
- Amylase breaks down starch and glycogen
- Cellulase breaks down cellulose
What is aneuploidy?
A change within the chromosome set (more than/less than the usual number of chromosomes)
Describe the growth of bacteria
Bacterial growth occurs in four phases:
- The lag phase: the period of adjustment to the environment where bacteria are alive but not dividing
- The exponential phase: the period of growing and dividing at a constant rate. Growth can be measured using MGT. Rate of growth depends on the species, growth medium and environmental conditions
- The stationary phase: cell growth and reproduction stops as a result of changes in the environment
- Death phase: the point at which a population of bacteria begin to die due to environmental factors
What are some strategies for bacteria living in radiation-exposed environments
- Repair DNA damaged by radiation by synthesising radiation resistant repair proteins to reassemble damaged DNA
Neural hydroxyl containing aa’s
- Serine
- Threonine
What are some strategies for bacteria in hot environments?
- Increase the ratio of saturated fatty acids in the membrane to provide a higher melting point, and increase the number of branched fatty acids for fluidity
- Synthesise heat-stable enzymes and more molecular chaperones to aid in the correct folding of enzymes and denatured proteins
- Stabilise nucleic acids by using monovalent and divalent ions
When does DNA Replication occur?
In S (Synthesis) phase of interphase/the cell cycle
What will the charge be on a protein at a pH < pI and at a pH > pI, and why?
- At a pH less than its pI, where the protein is at its most soluble, the protein will be positively charged as the -NH2 group is accepting the excess H+ in solution to become -NH3+
- At a pH greater than it pI, a protein will be negatively charged, and the -COOH group will donate its H+ ion to become -COO- to attempt to restore the H+ concentration
What did Griffith find in his studies of DNA?
Griffiths isolated two strains of bacteria, a pathogenic S strain and non-pathogenic R strain and found that even when the S strain was inactivated, when co-innoculated there was a tranforming factor.
What labels the DNA 5’ and 3’ ends?
The 3’ strand terminates at the -OH group on the 3rd carbon, and the 5’ strand terminates at the 5th carbon.
What is a microaerophile?
Bacteria require low levels of oxygen of 5-10% for their respiration
What are the types of enzymes and what do they do?
- Oxidoreductases: redox reactions
- Transferases: transfer of a functional group from one molecule to another
- Lyase: removal/addition of a group by rearrangement of electrons
- Ligase: joining two molecules to form a single molecule
- Isomerases: isomerise a molecule (move a functional group within a molecule)
- Hydrolases: conduct hydrolysis reactions to split a molecule into two by removing water
What is a facultative aerobe?
Bacteria can grow aerobically using aerobic respiration in the presence of oxygen or anaerobically using fermentation
Chemoheterotrophs
Use organic compounds as the energy and carbon source
Neutral amide containing aa’s
- Glutamine
- Aspargine
Acidic aa’s
- Glutamate
- Aspartate
What did Okazaki do and what did he find?
Okazaki found that DNA Polymerase III could only occur in the 5’ to 3’ direction, resulting in the discontinuous production of a leading and lagging strand due to the antiparallel orientation of the DNA molecule.
The lagging strand synthesised RNA primers via transcription, which were converted to DNA by DNA Polymerase IIII. DNA Polymerase I then removes the RNA primers and replaces them with DNA, and DNA ligase connects the Okazaki fragments.
What is a thrombocyte and what is its function?
Thrombocytes are fragments of cells formed from megakaryocytes. They clump together to form a platelet plug to stop blood flow when blood vessels are damaged. They are anucleated and cannot undergo mitosis.
Basic aa’s
- Lysine
- Histidine
- Arginine
What is polyploidy?
More than two paired sets of chromosomes (could be three pairs, four pairs etc.)
What is a monocyte/macrophage and what is its function?
Monocytes are immature phagocytic granulocytes which travel to infected tissue and mature into macrophages which engulf target cells e.g. bacteria.
How are disaccharides used as a fuel source?
- e.g. lactose and sucrose
- Hydrolysed into their constitiuent monosaccharides which can be utilised.
- Bacteria can hydrolyse disaccharides within the cell however higher organisms must hydrolyse them prior to absorption via a specialised digestive system
What is an eosinophil and what is its function?
Eosinophils are phagocytic granulocytes which fight parasitic infections
What are the three enzymes bypassed in glycolysis?
- Hexokinase
- Phosphofructokinase
- Pyruvate kinase
How are amino acids used as a fuel source?
- The amine group must be removed via deamination, and the resulting keto acid is converted into intermediates of the TCA Cycle or Glycolysis
Neutral aromatic containing aa’s
- Tryptophan
- Tyrosine
- Phenylalanine
What is an aerotolerant anaerobe?
Bacteria do not use oxygen in their metabolism but can tolerate its presence
When is the best time to see condensed/structured chromosomes?
Metaphase
Describe initiation, translocation and termination of translation…
- Initiation: The initiator aminoacyl-tRNA (Met) binds to the Peptidyl (P) site according to complimentary base pairing between the codon of the mRNA and corresponding anticodon on the tRNA. The next aminoacyl-tRNA molecule then binds to the Aminoacyl (A) site, and peptidyl transferase forms a peptide bond between the adjacent amino acids, temporarily transferring the initiator amino acid to the next aminoacyl-tRNA molecule at the A site. The initiator tRNA is displaced from the ribosome.
- Translocation: the ribosome moves in a 5’ to 3’ direction of the mRNA, transferring the dipeptidyl aminoacyl-tRNA molecule to the P site as the next aminoacyl-tRNA molecule binds to the A site. Peptidyl transferase then transfers the polypeptide to the next aminoacyl-tRNA molecule and so on
- Termination: When the codon at the A site is a stop/terminator codon, peptidyl transferase is activated to become a polypeptide releasing enzyme which releases the polypeptide and displaces the last tRNA molecule.
- As translation occurs in a 5’ to 3’ direction, the polypeptide is synthesised from the amino group to the carboxyl group
What is a eukaryotic silencer site?
A DNA site capable of binding regulatory repressor proteins to inhibit transcription by preventing the binding of RNA Polymerase.
What is a silent mutation?
Point mutations that do not change the protein amino acid sequence
