everything? Flashcards
At what organelle does anaerobic cellular respiration occur?
Anaerobic cellular respiration doesn’t occur in any organelles, it occurs in the cytosol
Explain what happens when lactic acid builds up in muscles due to anaerobic respiration.
Lactic acid lowers the pH of cells which can reduce enzyme function. Once oxygen is present again, lactic acid is metabolised back into pyruvate and used for aerobic cellular respiration.
What is the equation for aerobic respiration?
Glucose + Oxygen → Carbon dioxide + Water + 30 or 32 ATP
or
C6H12O6 + 6O2 → 6CO2 + 6H2O + 30 or 32 ATP
Where does each stage of aerobic respiration take place?
Glycolysis -cytosol
Kreb’s cycle - mitochondria matrix
Electron transport chain - cristae of the mitochondria
What are the 3 key coenzymes involved in aerobic respiration?
ATP, NAD+, FAD
What factors influence enzymes?
- Temperature
- pH level
- concentration
Why are enzymes used in biological reactions?
Enzymes catalyse and speed up reactions by providing a lower energy, alternate pathway for the reaction to take place.
Explain the ‘induced fit’ model.
The induced fit model explains how enzymes are flexible and change shape slightly when a substrate binds to them, which causes a reaction to occur.
What are the inputs and outputs of glycolysis?
Inputs:
* 1 Glucose
* NAD+ + 2 H+
* 2ADP + 2Pi
Outputs:
* 2 Pyruvate
* NADH
* 2 ATP
What are the inputs & outputs of the Krebs cycle?
Inputs:
* 2 acetyl-CoA
* 2 ADP + 2 Pi
* 6 NAD+ + 6 H+
* 2 FAD + 4 H+
Outputs:
* 2 ATP
* 4 CO2
* 6 NADH
* 2 FADH2
What are the inputs & outputs of the electron transport chain?
inputs:
* 6 O2 + 12 H+
* 2 FADH2
* 10 NADH
* 26 or 28 ADP + Pi
outputs:
* 26 or 28 ATP
* 6 H2O
* 10 NAD+ + 10 H+
* 2 FAD + 4 H+
Explain why the rate of cellular respiration increases when the temperature was increased from 0 to 33°C.
The rate of cellular respiration increased due to more frequent enzyme-substrate collisions between rubisco and CO2, thus increasing the rate of fixing CO2 into organic glucose and increasing photosynthetic rate.
Why do enzymes in the cytoplasm and mitochondrial matrix have different optimal pH levels.
The pH levels of different locations vary due to the cycling of H+ ions through FAD and NAD+, and thus the enzymes that support those functions have evolved to also have the same optimal pHs as their environments.
What are two reasons why a light-saturation point can be reached?
- Enzymes within chloroplasts are operating at full capacity.
- There is another limiting factor, such as CO2 availability, temperature, water availability, light colour or etc that is restricting the rate of photosynthesis.
Plants absorb light mostly at the:
short (blue) and long (red) wavelength ends of the visible light spectrum.
when does photorespiration occur
Photorespiration occurs in hot weather when Rubisco has a greater affinity for O2 than CO2
or when the concentration of O2 is greater than CO2
how does C4 photosynthesis work
- This separation allows for higher concentrations of CO2 than O2 around RuBisCO, which increases the chances for it to bind to CO2 which reduces photorespiration and increases photosynthesis.
how does CAM photosynthesis work
- In dry habitats plants lose their turgor due to water loss via transpiration, which causes the stomata to close.
- O2 from the light-dependent stage of photosynthesis builds up, and increases the likelihood that rubisco binds to O2 rather than CO2 and initiate photorespiration.
- CAM plants open their stomata at night to bring in CO2, and store fixed CO2 in vacuoles within mesophyll cells. During the day the stomata
What are the inputs & outputs of the light-dependent stage of C3 photosynthesis?
inputs:
* 12 H2O
* 12 NADP+
* 18 ADP + 18 Pi
outputs:
* 6 O2 molecules
* 12 NADPH
* 18 ATP
What are the inputs & outputs of the light-independent stage of C3 photosynthesis?
inputs:
* 6 CO2(g) molecules
* 12 NADPH
* 18 ATP
outputs:
* C6H12O6
* 6 H2O
* 12 NADP+
* 18 ADP + 18 Pi
What is chlorophyll?
Chlorophyll is the green pigment, found in thylakoid disks within chloroplasts, that absorbs light energy for use in photosynthesis.
Where do the stages of C3 photosynthesis occur?
light-dependent - On thylakoid membranes
light-independent - In the stroma within chloroplasts
What are the factors that affect the rate of photosynthesis?
- Light intensity
- Light colour
- Water availability
- Temperature
- CO2 concentration
- O2 concentration
What are C3 plants?
C3 plants are plants that conduct photosynthesis normally and have no evolved adaptations to minimise photorespiration.
What is the equation for photosynthesis?
Carbon dioxide + water → glucose + oxygen gas
or
CO2 + H20 → C6H12O6 + O2(g)
What are the two ways water availability can affect the rate of photosynthesis?
- Water is required as an input for the light dependent stage of photosynthesis.
- Dehydrated plants lose their turgor and stomata close, which increase conc. of O2 from light dependent reactions and thus increases likelihood of rubisco binding to O2 and initiating photorespiration.
What is the role of Rubisco in photosynthesis?
Fixes inorganic CO2 into glucose
Explain C3 photosynthesis
Explain why above 33°C the rate of photosynthesis decreases significantly with reference to rubisco.
rubisco is an enzyme that denatures above 42ºC but after 33ºC it is no longer at it’s optimum working temperature thus anything above or below is less efficient or entirely ineffective
* extreme temps = denature
CRISPR-Cas9 in bacteria functions as a:
primitive adaptive immune system
temps of each step of PCR
Denaturation: occurs at 94°C
Annealing: occurs at 54°C
Elongation: occurs at 72°C
Repetition
Generally explain how CRISPR-Cas9 would be used to disrupt a gene
- Using a vector, add the CRISPR-Cas9 complex to a cell that contain the target gene.
- Guide the RNA that is manufactured to anneal to the target DNA so that it binds to the target gene.
- Cut the target gene to disrupt it.
Outline the process CRISPR-Cas9 uses to cut specific DNA
- a bacteriophage attaches to the outside of bacterial cell and injects its VIRAL DNA into the cell (reinfection)
- previously, a segment of the viral DNA has been stored as a spacer in the CRISPR region - the CRISPR sequence is TRANSCRIBED resulting in CRISPR RNA (crRNA)
- tracer RNA (trcrRNA) has a complementary sequence to the repeat DNA (NOT the spacers) - role: helps hold the gRNA in place in the Cas9 enzyme
- the specific spacer of the crRNA binds to the trcrRNA to form single guide RNA (sgRNA) - sgRNA then binds with the Cas9 enzyme → forms a Cas9-gRNA complex
- Cas9-gRNA complex scans bacteriophage (target DNA) to look for complementary bases
- once it is found, the DNA is unzipped and Cas9 cuts/cleaves the DNA the viral DNA cannot reproduce as the DNA has been disrupted
What are the two types of primers used in PCR?
Forward primer - is the primer that binds to the start codon at the 3’ end of the template strand.
Reverse primer - is a primer that binds to the stop codon at the 3’ end of the coding strand.
What is the purpose of a reporter gene in plasmid vectors?
Reporter genes create an easily identifiable phenotype to help distinguish between transformed bacteria with and without the gene of interest.
What is the ORI of a plasmid?
The origin of replication is the sequence in prokaryotes that signals the starting site for DNA replication.
What are two social implications of GM crops?
- Increased crop productivtiy means that more food can be produced and increase food security.
- Strict packaging and marketing regulations for GM crops may not be complied with if producers or consumers are not educated on the regulations.
What are proteases vs restriction enzymes vs endonuclease?
Proteases - Enzymes that cut polypeptides
What are Cas1 and Cas2 enzymes used for?
Cas1 and Cas2 form a Cas1-Cas2 complex which cuts out sections of bacteriophage DNA which can be introduced into CRISPR genes and become a spacer.
What are some factors that can influence the distance that DNA fragments travel during gel electrophoresis?
- Buffer concentration (more ions in buffer=more electrical current conducted through gel=DNA fragments move further down)
- Gel composition(More viscous and denser agarose concentrations increase difficulty for large fragments to pass through)
- Current voltage (The stronger the electric force, the further DNA travels to the positive cathode)
- Fragment size (Smaller fragments travel quicker through the gel than large fragments)
- Time (Longer periods of time allow fragments to travel further)
What are the three types of enzymes that manipulate DNA?
DNA polymerase, DNA ligase, Restriction endonuclease
What is the ‘region of interest’ in PCR?
The region of interest is the sequence of DNA that is wished to be amplified or replicated.
What occurs in the denaturation stage of PCR?
During the denaturation stage, the DNA is heated up to approximately 90-95 degrees Celsius to break the hydrogen bonds between complementary DNA strands, which causes the DNA to separate into single-stranded DNA.
What occurs in the annealing stage of PCR?
The single-stranded DNA is cooled to approximately 50-55°C so that primers can bind to their complementary sequences in the single-stranded DNA.
What occurs in the elongation stage of PCR?
During the elongation stage, DNA is heated to 72 degrees Celsius (which is the optimal temperature for Taq polymerase) so that Taq polymerase can use primers as starting points to build a complementary DNA strand from free-floating DNA nucleotides.
Why can’t human DNA polymerase be used in PCR?
- High temperatures are required to keep single stranded DNA separate during PCR.
- Human DNA polymerase has an optimal temperature of 37 degrees Celsius, and would denature at the temperatures required and thus is not suitable.
- Taq polymerase has an optimal temperature of 72 degrees Celsius, and this is suitable and used instead of human DNA for PCR.
What are the components of the solution that is placed in the thermocycler for PCR?
Buffer, DNA with the region of interest, Primers, Taq polymerase, DNA nucleotides.
What are the two main methods of promoting recombinant plasmid uptake?
Heat shock and electroporation
What does making a recombinant plasmid require?
- Gene of interest
- Plasmid vector
-> Restriction enzyme sites
-> Antibiotic resistance gene
-> A reporter gene
-> An origin of replication - Restriction enzymes
- DNA ligase
What are short-tandem repeats?
Short-tandem repeats (STRs) are short sections of repeated nucleotides that vary in length between people and are found in non-coding DNA regions.
What are the stages of DNA profiling?
- Obtain DNA sample
- Amplify DNA sample using PCR
- Sort DNA fragments by length in a gel
What are spacers in CRISPR?
What is a protospacer?
- Spacers are short DNA sequences, from invading bacteriophages, that are interleaved between short palindromic repeats in CRISPR.
- A short sequence of bacteriophage DNA extracted by a Cas1-Cas2 complex that has not yet been incorporated into the CRISPR gene.
What is a PAM?
- A sequence of 2-6 nucleotides that is searched for by CRISPR-Cas9 and Cas1-Cas2 complexes to increase their efficiency in detecting viral, bacteriophage DNA.
- The PAM sequence is searched for by the Cas9 enzyme to increase its efficiency in detecting viral DNA and allows sgRNA to bind to the Cas9 enzyme.
—> finish
What is viral recombination?
Viral recombination is the combination of surface antigens from two or more different viral strains to form a new virus subtype.
What is the function of the Cas9 enzyme in CRISPR?
The Cas9 enzyme unzips double-stranded DNA and cleaves the phosphodiester bonds between nucleotides on both DNA strands.
Outline how natural killer cells detect and destroy pathogenic cells
- Killer activation receptors on natural killer (NK) cells bind to cellularly stressed cells.
- Killer inhibitory receptors examine the cell’s surface for MHC I markers to bind to.
- If there are insufficient MHC I markers on the cell, killer inhibitory receptors cannot bind and cell death is initiated via apoptosis.
What are the cellular components of the second line of defense?
Neutrophil, macrophage, dendritic cell, natural killer cell, mast cell, eosinophil cells
What are eosinophils?
Eosinophils are large immune cells found in tissues and contains enzymes such as DNases, RNases, and proteases to help destroy invading pathogens.
brief outline of the humoral immune response.
- Antigen presenting cells display pathogenic antigens on their cell surface to activate helper T-cells and initiate the humoral immune response.
- Helper T release cytokines activating B cells which bind to the same antigen in secondary lymphoid tissues and express them via MHC II markers on their surface.
- The selected Helper T-cells recognise and bind to the selected B cell and release cytokines to make the B cell undergo clonal expansion and differentiate into either plasma or B memory cells.
- Plasma cells produce antibodies specific to the selected antigen, and are secreted into the bloodstream to defend against the pathogen.
- Memory B cells remain in lymphoid tissues and can divide into plasma cells if reinfection occurs.
How is the adaptive immune response initiated?
The adaptive immune response is initiated by:
- the selection of T-helper cells
→ phagocytosis occurs and the antigen-presenting cell displays the specific pathogenic antigens on their surface via MHC II markers to activate corresponding T-helper cells
- This can lead to either the humoral or cell-mediated immune responses.
What is a complement cascade?
A complement cascade is activated when they make direct contact with molecules on the surface of pathogens
- it is a series of complex reactions where complement proteins interact with each other to deal with pathogens, and can result in opsonisation, chemotaxis, or lysis
Outline the cell-mediated immune response.
- Antigen presenting cells display pathogenic antigens on their surface via MHC II markers to activate helper T-cells, while simultaneously they encounter a naive T-cell with matching antigens.
- The selected T-cell is stimulated by cytokines to undergo clonal expansion and differentiate into cytotoxic T cells and memory T cells.
- Cytotoxic T cells can recognise abnormal proteins on infected cells, destroying them by secreting chemicals to induce apoptosis.
- Memory T cells provide long lasting immunity and remain in lymphoid tissues and can rapidly divide into helper and cytotoxic T cells if the pathogen is re-encountered for a faster adaptive immune response.
Outline the process of fossilisation.
- Remnants of a dead organism are rapidly covered by sediment, decreasing exposure to oxygen, weathering, microorganisms, and other factors that would increase its rate of decomposition.
- Over time sediment layers build upon each other and compact to form sedimentary rock, resulting in a fossil.
- The fossil can take forms such as a permineralised, mould, or cast fossil.
What is the order of the fossil record?
- prokaryotes
- first unicellular eukaryotes
- Development of multicellularity (600 mya)
- first invertebraes
- first vertebraes (jawless fish)
- first insects
- first land plants
- first amphibians
- first reptiles
- first dinosaurs
- mammals (200 mya)
- flowering plants (125 mya)
- Humans
How do fossils form? [steps]
- An organism dies and is:
*Rapidly buried/frozen
*Protected from scavengers - Prevented from decomposition by
*Low oxygen levels
*Low temperatures - Over time, the molecules in the organism** are replaced by minerals from groundwater
**usually the hard parts - 10,000 yrs+ old
Explain why the proteome is more diverse than the genome.
- The entire complement of proteins expressed by a cell or organism at a given time.
- The genome is the entire complement of genetic information of a cell or organism.
- Each gene encodes roughly 10-40 different functional proteins, thus there are more proteins than genes in an organism.
What is the role of rRNA, tRNA, mRNA?
rRNA reads mRNA codons and binds specific amino acids, that were delivered by tRNA molecules, together in the correct order
- works with other proteins to make ribosomes in the cytosol [fluid; cytoplasm is entire cell contents]
tRNA delivers a specific amino acid to ribosomes after recognising complementary mRNA codons.
mRNA acts as a template for the synthesis of proteins; mRNA carries genetic information from the DNA to the ribosomes for the translation of proteins.
fix??
Outline the process of attenuation in the trp operon.
- Occurs when there are high levels of bound trp in the cell otherwise repression will occur
- High levels of tryptophan bound to tRNA molecules allow the leader to be translated quickly and not pause at trp codons.
- This causes a terminator hairpin loop to form between domains 3 and 4 in the leader, which causes the mRNA attenuator to rip away from DNA which sends the RNA polymerase flying and ribosome detaches
- Prevents transcription of structural E-A genes, no tryptophan is produced
Outline the process of repression in the trp operon.
Outline the steps of translation.
- Ribosome will come along and bind to the mRNA strand which is read by a ribosome until a start codon is reached.
- tRNA anti-codons that are complementary to mRNA codons deliver individual, specific amino acids to the ribosome.
- Amino acids in adjacent tRNA molecules bind together via condensation polymerisation reactions, and form peptide bonds.
- This continues until a stop codon is reached, and then the ribosome releases the polypeptide chain and translation is complete.
Outline the stages of transcription.
- RNA polymerase attaches to promoter region
- DNA unwinds/unzips and the 3’ to 5’ DNA strand is used as a template strand
- RNA polymerase reads template strandand creates a complementary pre-mRNA sequence by joining free complementary RNA nucleotides.
- The resulting pre-mRNA sequence is identical to the coding strand except uracil takes the place of thymine.
how recombinant insulin is made
Isolate genes for two different insulin polypeptides (1) and ligate/use DNA ligase to insert into two different plasmids into the β -galactosidase gene (1) and transform into two separate bacteria (1). Plate on agar containing X gal and ampicillin – those transformed bacteria turn blue (1). Once the genes are expressed and the fusion proteins are produced by each bacteria, these fusion proteins are then purified (1), and the insulin polypeptides are removed and then combined together to produce functional insulin (1).
Outline the process of the formation of different Galapagos finch species in the Galapagos islands.
- Each Galapago island is separated by the ocean, a geographical barrier that limits gene flow between islands
- There is heritable phenotypic variation between finches on each island.
- Each island has different food sources, which act as environmental selection pressures selecting for different phenotypes (such as beak shape).
- Over time genetic and phenotypic differences accumulate until finch populations cannot interbreed between islands to form fertile viable offspring.
- A new species of finch has been formed and allopatric speciation has occurred.
Outline the process of sympatric speciation in Howea Palms on Lord Howe Island.
- Difference in soil nutrients between two regions on Lord Howe Island, one region having calcareous soil and the other having volcanic soil which has more nutrients.
- The difference in soil nutrients acts as an environmental selection pressure, selecting for different phenotypes.
- Over time genetic differences accumulate, eventually leading to pre-zygotic isolation (different flowering times, which decreases the chances of interbreeding) and the formation of a new species that cannot interbreed to form fertile and viable offspring.
(volcanic soil has more nutrients allowing plants to grow more quickly/flower earlier)
Outline the steps involved in natural selection.
- There is heritable phenotypic variation between members in a population.
- A specific environmental selection pressure causes a struggle for survival, members with advantageous alleles have increased chances of surviving and reproducing.
- These ‘fitter’ organisms thus have higher chances of passing on their advantageous alleles to their offspring, increasing those allele frequencies over successive generations.
Outline the process of how antibiotic resistance occurs.
- Heritable phenotypic variation exists between bacterium in a population, with some having advantageous alleles that confer antibiotic resistance and others not.
- An antibiotic acts as an environmental selection pressure, antibiotic resistant bacteria have a selective advantage and increased chances of surviving and passing on their advantageous alleles via binary fission or bacterial conjugation while those without will die.
- Allele frequencies of those advantageous alleles increase over successive generations and an antibiotic resistant bacterial population has formed.
Outline the process of allopatric speciation.
- A geographical barrier has isolated a population of the same species from each other, thus preventing gene flow and interbreeding between populations
- Heritable phenotypic variation [specify the kind] exists within the population.
- Different environmental selection pressures act on the isolated populations selecting diff advantageous phenotypes and allowing for genetic differences to accumulate.
- Once sufficient genetic differences accumulate, reproductive isolation occurs, and the two populations cannot interbreed to form fertile viable offspring, allopatric speciation has occurred.
What is allopatric vs sympatric speciation?
Allopatric speciation is the divergence of a new species from a parent species due to a geographical barrier that separates the two populations.
In sympatric speciation there is no physical barrier to prevent gene flow between populations, rather another type of pre-zygotic isolation barrier such as a temporal or behavioural isolation mechanism.
Outline the process of selective breeding.
- The species’ population has heritable phenotypic variation.
- As [trait] is desirable to humans, humans act as an artificial selection pressure and only allow organisms with [trait] to breed together.
- The selected trait is heritable, and so the allele frequency of [trait] increases over time as only individuals with [trait] are allowed to breed.
Outline how monoclonal antibodies are created.
- Mice are immunised with an antigen
- This activates the production of B cells, which produce antibodies against the antigen
- B cells that are specific to the antigen are isolated and extracted from the mouse’s spleen
- Those B cells are then fused with myeloma cells to form hybridoma cells.
- The hybridoma that produce the desired antibody are identified and cloned
- Cloned hybridoma are immortal and are used to produce monoclonal antibodies.
How can monoclonal antibodies be used to treat autoimmune diseases?
Monoclonal antibodies (mAbs) can suppress the immune responses to self-cells by inhibiting cytokines or binding to antigens on autoreactive B and T cells and inhibiting or depleting the autoreactive B and T cells.
How can monoclonal antibodies be used to treat cancer?
Monoclonal antibodies (mAbs) can be used to treat cancer as they can activate the immune system by binding to antigens on cancerous cells thus activating complement proteins, blocking cell division, or blocking growth of blood vessels to tumours and killing them.
how is biofuel produced from biomass?
- Yeast or bacteria is added to the biomass waste. (1 mark)
- Yeast or bacteria breaks down the starch into glucose. This glucose undergoes glycolysis and is broken down in two molecules of pyruvate. (1 mark)
- The pyruvate is broken down further through ethanol (or alcohol) fermentation, leading to the production of ethanol. (1 mark)
