CE 10224A - Science for CE (Biology) Flashcards
What are considered the building blocks of life?
Amino acids / proteins (catalysis, DNA replication, enzymes, transport)
Nucleic acids (code, transmit and express genetic info)
Carbohydrates (energy, structure, nutrition and genetic molecules)
Lipids (energy and structural appliances)
Lignin (in plants)
What are (3) types of microorganisms?
Cellular (bacteria, archaea and eukarya)
Viruses (non cellular microbes)
Prions (infectious molecules - aren’t organisms as they have no genetic material)
How do gram positive and negative bacteria differ?
Gram positive bacteria have many layers of peptidoglycan. This means they can retain the stain.
Gram negative have a few layers of peptidoglycan, and an outer membrane made up of lipopolysaccharides, lipoproteins and phospholipids.
It’s outer membrane is also permeable due to the presence of porins.
What is a hypotonic, isotonic and hypertonic solution?
Hypotonic - the solution has a lower amount of solutes
Isotonic - the solution has the same level of solutes
Hypertonic - the solution has a higher amount of solutes
What’s a uniporter?
A membrane carrier protein.
It binds to one substrate molecule at a time and is involved in facilitated diffusion.
What’s a symporter?
A membrane protein which allows molecules to be transported in the same direction at the same time.
This requires entropy
What’s an antiporter?
A membrane protein and cotransporter which transports two or more different molecules in opposite directions.
What does the nucleus do?
It contains genetic info - chromatin threads: DNA, RNA and protein.
Surrounded by porous nuclear envelope - contains importin and exportin pores.
What do ribosomes do?
Are site of protein synthesis.
Free ribosomes produce protein for the cytoplasm
Bound ribosomes produce protein for the membrane or for use outside of the cell.
They’re 15- 20 nm in diameter, comprising two sub-units: a large one (60S) and a small one (40S).
Each sub-unit contains rRNA and protein.
(S is the Svedberg unit – related to size and shape measures how fast a particle falls out of solution during centrifugation)
What’s does the endoplasmic reticulum do?
SER - lipid synthesis
RER - protein synthesis
What do lysosomes do?
They contain a range of digestive enzymes, called hydrolayses, which can break down all biochemicals.
What does the Golgi apparatus do?
Tag and package molecules, to send them where needed.
What do chloroplasts do?
Perform respiration in photo-synthetic eukaryotes – responsible for energy recovery from light.
Contain a characteristic internal membrane structure called the thyllacoids, which houses the photochemical reaction centres – chlorophylls.
What do vacuoles do?
Used for transporting and storing nutrients, metabolites and waste products. Act similarly to lysosomes.
Maintains cell shape and size through turgor pressure. (The osmotic pressure that stops the plant wilting.)
Major compartment inside a plant cell, surrounded by membrane called the tonoplast.
Typically occupy more than 30% of the volume of the cell
What are photoautotrophs?
Organisms that carry out photosynthesis.
They get their energy from light and (auto) get their CO2 from air.
What are photoheterotrophs?
Organisms that use light for energy, but cannot use carbon dioxide as their sole carbon source.
They use organic compounds from the environment to satisfy their carbon requirements
What are chemoautotrophs?
Organisms that obtain energy by the oxidation of electron donors in their environments.
Cells that create their own energy and biological materials from inorganic chemicals.
What’s a chemoheterotroph?
An organism which derives its energy from chemicals, and needs to consume other organisms in order to live.
What’s an exergonic reaction?
A reaction which gives off energy e.g. catabolism.
What’s an endogonic reaction?
Reactions which take in energy e.g. anabolism.
What acts as the electron donor and acceptor in photosynthesis?
H20 is the electron donor
NADP+ is the electron acceptor
What is used and produced in the Calvin cycle (photosynthesis)?
Used:
- 3 molecules of CO2
- 9 molecules of ATP
6 molecules of NADPH
Produced:
- 1 molecule of glyceraldehyde 3 phosphate
What is an electron donor?
Chemicals (reducing agents) which get oxidised and donate electrons to another compound (they’re typically organic molecules).
Examples include water, sugar fats.
What is an electron acceptor?
A molecule (oxidising agent) that gets reduced by accepting electrons from other molecules.
Examples include oxygen, nitrates, NAD+ and NADP+.
What are examples of chemoheterotrophs?
Aerobes
Animals
Fungi (yeasts)
Most heterotrophic bacteria
(Denitrifying bacteria and Methanogens under anaerobic conditions)
What acts as the electron donor and final electron acceptor under aerobic respiration for chemoheterotrophs?
Electron donor: organic substances such as fats, sugars and organic acids
Electron acceptor: oxygen
What acts as the electron donor and final electron acceptor under anaerobic respiration for chemoheterotrophs?
Electron donor: organic substances such as fats, sugars and organic acids.
Electron acceptor: CO2, nitrates (NO3-) and sulphates (SO4 2-)
What are examples of chemoautotrophs?
Bacteria
What acts as the electron donor and final electron acceptor under anaerobic respiration for chemoautotrophs?
Electron donor: hydrogen, nitrites (NO2 -), ammonium (NH4+), hydrogen sulphide (H2S), thiosulfate (S2O3 2-)
Electron acceptor: CO, nitrates (NO3-), sulfates (SO4 2-)
What is produced in one turn of the Citric Acid / Krebs cycle?
3 x NADH
1 x GRP
1 x FADH2
2 molecules of CO2 are also released.
What acts as the electron donor and electron acceptor during photosynthetic reactions in photoautotrophs?
Electron donor: water H2O
Electron acceptor: NADP+ (which then forms NADPH)
Where are the Citric acid cycle and Calvin cycle found?
Citric acid / Krebs cycle - in mitochondrial matrix for respiration
Calvin cycle - in chloroplasts for photosynthesis
What are metabolic pathways and what are their properties?
They’re a series of consecutive enzymatic reactions that produce specific products.
- They’re irreversible
- Catabolic and anabolic pathways MUST differ
- Each pathway has a first committed step
- They’re regulated
- They occur in specific locations (in eukaryotes)
What happens in the citric acid cycle (simplified)?
Pyruvate (formed via glycolysis) forms Acetyl CoA which is fed into the cycle.
This reacts with oxaloacetate to form citrate (6C).
During further reactions in the cycle, isocitrate (6C), CO2 and NADH are formed.
Then a 5C compound and NADH, followed by succinate (4C) , NADH and GTP, another 4C compound and FADH2.
Then malate (4C) and finally oxaloacetate and NADH; and the cycle repeats.
How is pyruvate formed?
Pump priming - glucose is phosphorylated.
2 molecules of ATP are used in this stage.
Stage 2 - Redox stages occur with the formation of ATP.
4 molecules of ATP are produced.
Thus there’s a net formation of 2 moles ATP per mole glucose.
What are industrial applications of citric acid (formed as citrate in the citric acid / Krebs cycle)?
Which organisms are used to obtain it?
Industrial global production around 2m tonnes
- Flavouring or preservative, E330
- Cleaning product, industrial chelating agent
- Pharmaceutical applications
Organism of choice:
Aspegillus niger
Fungus
Causes black mould
What can isocitrate be used for?
It can be reacted with ammonia to form alpha-ketoglutarate, which can form glutamate.
What are industrial applications of glutamate/glutamic acid (formed from isocitrate in the citric acid / Krebs cycle)?
Which organisms are used to obtain it?
- Flavouring for food industry (MSG)
- Pharmaceuticals – specialist fermentations
- Industrial global production around 1.5m tonnes
Organism of choice
- Corynebacterium glutamicum
- Bacteria
What is fermentation?
The formation of products from a reduced carbon source (glucose) in the absence of the electron transport chain.
It’s a process that produces molecules which are not used for cell growth or reproduction, e.g. ethanol or acetic acid.
What are the industrial applications of lactic acid / lactate?
Lactic acid fermentation is used to produce yogurt and other foods (2m tonnes US alone)
Industrial production of the pure product is around 300,000 tonnes a-1
Pure product is used to produce the biodegradable biopolymer: polylactic acid
What are the industrial applications of butanol?
Potential future fuel, produced alongside acetone
It is more energy dense than ethanol
and has a lower water absorbance
What must be regulated in metabolic pathways?
Environment: pH temperature oxygen nutrients (Conditions we must provide in bioreactor)
Structural:
Membranes and regulation of transport etc.
Molecular:
Cofactors / Coenzymes
Inhibition / induction
Genetic:
Induction / repression
what is compartmentalisation?
A characteristic of eukaryotes, which means they have specific membrane-regulated organelles to control the substrate level and chemical interactions.
What are multi-enzyme complexes?
Complexes formed when enzymes join together to do a number of steps in the same place.
For example in the synthesis of Acetyl Co-A from pyruvate
What are inhibition and repression? (feedback regulation)
Inhibition: It occurs because of direct interaction between the product and the enzyme. (Competitive and non-competitive)
Repression: a control mechanism where a protein molecule (repressor) prevents the synthesis of an enzyme by binding to the deoxyribonucleic acid that controls the enzyme synthesis.
It switches off synthesis of the enzyme protein.
What are the types of feedback regulation?
Inhibition Repression Concerted effects Co-operative effects Sequential control Regulation using isoenzymes
What is feedback regulation by concerted effects?
When there is more than one product, both of which are equally important and must be present to stop the activity of the first enzyme.
What is feedback regulation by cooperative effects?
When there is more than one product but each product has control over their own pathways.
One product alone can still have a small inhibitory effect.
What is feedback regulation by sequential control?
When the build up of final products results in a build up of previous products which then leads to inhibition.
What are isoenzymes?
Different enzymes that carry out the same reaction.
Multiple products may inhibit different the enzymes
What is saccharomyces cerevisiae?
A species of yeast, necessary for wine making, baking and brewing.
What can saccharomyces cerevisiae produce?
It’s used for wine making, baking and brewing.
However, it can produce farnesene. Farnesene can then be hydrogenated to form farnesane, which is a potential bio-jet fuel.
What is PLA, polylactic acid?
A biological polymer produced from lactic acid, which is formed during anaerobic respiration (using pyruvate and NADH).
What’s a genome?
The complete set of genetic material present in a cell or organism.
It’s encoded by DNA (or RNA for many viruses).
What are DNA and RNA?
Nucleic acid strands made up of a chain of nucleotides.
The nucleotides bond by phosphodiester bonds to form the sugar phosphate backbone.
What’s transcription and translation?
Transcription: process by which information in a strand of DNA is copied into a new molecule of single strand messenger RNA (mRNA).
Translation: the formation of a peptide chain from the mRNA template.
What are constitutively expressed genes?
Genes that are always expressed or ‘on’.
What are the types of selectively-expressed regulated genes?
Inducible - usually switched off, but switch on when an inducer is present
Repressible - usually switched on, but switch off when a repressor is present
What are operons?
Clusters of co-regulated genes transcribed as one mRNA, found in bacterial genes.
They usually contain extra regulatory sequences and can be repressible or inducible.
How does the lac operon function?
It has regulatory sequences and 3 structural genes.
It is switched of when there is no lactose present.
The lac regulator protein binds to the operator and prevents transcription.
Lactose prevents the lac regulator protein from binding to the operator.
However, the lac operon is only expressed when lactose is present AND glucose is absent.
What are the 2 approaches to genetic engineering?
Endogenous expression - manipulating genes/pathways already in the organism
Heterologous expression - introducing new genes/gene pathways
In what ways can endogenous expression (manipulating genes/pathways already in the organism) be manipulated?
Overexpression
Knock-out
Induce/Repress
Other/non-transcriptional mechanisms
What’s over-expression?
Genetic modification where a lot of the gene is expressed all of the time.
Specific promoters can be used which keep the gene switched on all the time.
What’s gene-knockout?
Genetic modification when the gene is removed/deleted, removing its function.
What’s GM by induction/repression?
When particular genes are expressed or repressed due to the presence of certain substances or enzymes.
How are favoured genes incorporated into cells for genetic engineering?
The cells are cloned - introduce new genes, extra copies of genes and new promoters.
1) Use PCR to amplify the target DNA
2) Restriction enzymes are used to cut bacterial plasmids and the genes are inserted (into the plasmid)
3) The plasmid (with target DNA) is placed into E.coli
4) The plasmid will also have genes which indicate if the target gene has successfully been uptaken (ampR and tetR)
5) The bacteria are cultured and those that are successful are able to grow
6) Positive colonies are further cultured on larger scales and the plasmids are finally extracted (containing the cloned target) and used downstream
How can gene expression be manipulated?
Overexpression
Knock-out
Induce/repress
Other, non-transcriptional mechanisms
What’s metabolic engineering?
Manipulation if metabolic pathways to optimise desirable products and cell processes.
What’s a template?
DNA containing the sequence you want to amplify
What are primers?
Short nucleic acid sequences that anneal to complimentary sequences in the template strand and provide starting points for DNA synthesis.
What’s DNA polymerase?
Thermostable enzyme that synthesises the new DNA strand
What are cycling conditions?
Multiple rounds of heating and cooling which vary depending on the primers, polymerase and target length
What is gel electrophoresis?
A method to see/identify PCR products.
What’s a lipid?
Give examples
An organic compound that’s soluble in organic/polar solvents, used for energy and insulation.
Examples: [Simple] Fats, oils and waxes [Complex] Phospholipids and Glycolipids [Derived] Fatty acids and alcohols [Other] Terpenes
What are prions?
Infectious molecules.
They can’t be called organisms because they don’t have genetic material.
