Exam 😈 Flashcards
what are prokaryotic cells
cells within prokaryotes that lack a membrane-bound nucleus
what are eukaryotic cells
cells within eukaryotes that have a membrane-bound nucleus and other membrane-bound organelles
what is nucleic acid made up of?
sub-units / monomers called nucleotides
what are nucleotides?
basic building blocks or sub-units of DNA and RNA consisting of a phosphate group, a base and a five-carbon sugar.
what are the types of sugar in RNA and DNA nucleotides?
DNA = deoxyribose, RNA = ribose
what are the 5 types of bases?
adenine, thymine, uracil, cytosine and guanine
what are the (main) 3 types of RNA?
transfer RNA (tRNA), messenger RNA (mRNA) and ribosomal RNA (rRNA)
what does mRNA do?
Carries the genetic message from the DNA from the nucleus to the ribosomes (to be translated)
what does rRNA do?
together with particular proteins, makes the ribosomes found in cytosol
what does tRNA do?
carry amino acids to ribosomes that are free in the cytoplasm, where they are used to construct proteins
what is it meant by the genetic code is degenerate
the property of the genetic code in which more than codon of bases can code or one amino acid
what are the steps of gene expression
Transcription
RNA processing
Translation
transcription definition
process of copying the genetic instructions present in DNA to messenger RNA
RNA processing definition
occurs after transcription and involves modifying pre-mRNA to form mature mRNA
translation definition
process of decoding the genetic instructions in mRNA into a protein (polypeptide chain) built of amino acids
what are the 3 steps of transcription
- The DNA is unwound by the RNA polymerase binding to the promoter region as well as DNA helicase assisting
- This base sequence of DNA gained acts as a template for a mRNA strand to be made by RNA polymerase continuing moving along (3’ to 5’) bring complimentary nucleotides as it goes
- A pre mRNA strand is made and released from the templated.
what are the 3 main steps in RNA processing?
Capping
Adding a tail
splicing
What happens during capping? (RNA processing)
The 5’ end of the pre-RNA has its G’s modified with a methyl cap (methyl guanosine). This capping protects the pre-RNA from enzyme attack and assists with stability, allowing it to attach to the ribosome.
what happens during adding a tail? (RNA processing)
A poly-adenine (A) tail with up to 250 A’s is also added to the 3’ end. The tail contributes to the stability of the mRNA and facilitates mRNA export from the nucleus
what happens during splicing (RNA processing)
the introns from the pre-RNA are spliced out allowing the exons to join together. This is done by spliceosomes which recognise the base sequences at the 5’ (GU) and 3’ (AG) that are the end of the introns.
what is alternate splicing?
exons can be removed enabling one gene to produce a multitude of proteins if required.
where does translation take place?
cytosol
what are the 4 steps of translation
- mRNA moves to the ribosome where it is read in codons.
- the amino acids are then brought to the mRNA by the tRNA. At one end of the tRNA it makes an anticodon, and at the other end it attaches to a specific amino acid.
- The ribosome then continues to make more amino acids and they are joined by peptide bonds.
- A codon that tells the ribosome to stop production is reached and the polypeptide is released from the ribosome.
what is the start codon
AUG
what are the 3 stop codons
UAA, UAG or UGA
what is the coding region?
the part of the gene that gives the information for making proteins
what is the flanking regions?
parts of the gene that isn’t the coding region
what is the coding region made up off?
exons and introns
what are the 2 flanking regions known as?
upstream and downstream
what are exons?
the part that contain the instructions for the synthesis of the protein and are both transcribed and translated
what are introns?
parts in the coding region that are transcribed but are cut out during RNA processing and therefore are not translated
what are the 3 sections of the upstream region?
promoter
operator
leader
what happens in the promoter region?
The promoter is where transcription factors and RNA polymerase binds to initiate transcription
what happens in the operator region?
It is a binding site for repressor proteins, which are proteins that prevents RNA polymerase binding to a promoter, and thus transcription cannot be initiated
what are the 4 parts of the leader region?
TrpL (1), then three attenuator regions (2, 3, 4)
what happens in the leader region?
further regulation of transcription
what is an operon?
group of linked structural genes with a common promoter and operator that is transcribed as a single unit
what are the two types of regulation of the trp operon?
repression and attenuation
what happens when trp is present in repression (3 steps)
- trp binds to the repressor protein causing a configurational change in its shape, allowing it to be active
- This allows the repressor to bind at the operator
- RNA polymerase is unable to bind to the promoter and transcription does not occur. Thus the operon is OFF
what happens when trp isn’t present in repression (2 steps)
- the repressor is unable to bind to the operator (as it is still in an inactive form)
- RNA polymerase can bind to the promoter and start transcription of the structural genes; thus, the operon is ON
when there is trp present what happens in attenuation (4 steps)
- trpL can be quickly translated. When the ribosome translates this region quickly (to the leader peptide), it will quickly detach from the mRNA
- This allows a hairpin loop to form between the mRNA produced in regions 1 and 2.
- A terminator hairpin loop between the mRNA in regions 3 and 4 is also able to form.
- the RNA polymerase detaches from the DNA, transcription is stopped
when there isn’t trp present what happens in attenuation (5 steps)
- trpL is translated slowly
- As the ribosome translates the gene, the ribosome pauses at the trp codon to wait for enough tryptophan to be available to produce the leader polypeptide
- the ribosome stays attached to region 1, and therefore no hairpin loop can form between the mRNA in regions 1 and 2, but one will form between 2 and 3
- this hairpin loop does not cause the RNA polymerase to detach and prevents the terminator hairpin of regions 3 and 4 forming
- RNA polymerase continue remains attached to the trp operon, transcription and translation can occur
what are polypeptides?
large molecules made up of amino acids
what are amino acids made up of
an amino group and a carboxyl group. The difference between amino acids are the R group
what are the 4 levels of protein structure?
primary, secondary, tertiary, quaternary
what is a primary protein structure?
linear sequence of amino acids, each protein has a different primary structure and therefore different functions
what is a secondary protein structure?
folded amino acid sequences depending on the R group
what are the 3 types of secondary protein structures
- Alpha helix
- Beta-pleated sheet
- Random coiling
what is an alpha helix (protein)
secondary structure in proteins that appears as a tight twist
what is a beta-pleated sheet? (protein)
secondary structure in proteins that appears as folded sheets, with a change in direction of the polypeptide chain
what is random coiling? (protein)
secondary structure in proteins that does not fit in as either a alpha helix or beta-pleated sheet
what are tertiary structures?
total irregular 3D folding held together by ionic or hydrogen bonds forming a complex shape
what is a quaternary structure?
A structure in which two or more polypeptide chains interact to form a protein
what is the basic function of enzymes?
increase the rate of almost all the chemical reactions and to do this within the prevailing conditions of temperature and pH within cells
What is a proteome
The complete array of proteins produced by a single cell or an organism in a particular environment.
what happens at the ribosome?
translation (in cytosol ribosomes)
what happens in the rough endoplasmic reticulum?
transporting some of the proteins to various sites within a cell
what does the Golgi apparatus (complex) do?
packages proteins into vesicles for export from the cell through exocytosis
what do vesicles outside of the golgi apparatus do?
move to the plasma membrane of the cell, where they fuse with it and discharge their protein contents to the exterior through exocytosis
What is reverse transcription?
the process in cells by which an enzyme makes a copy of DNA from RNA
when is reverse transcription used?
when only specific genes or small sections of DNA are required to be synthesised, we use mRNA instead of DNA
what are the 5 steps in reverse transcription
- mRNA is isolated from cytosol
- Poly-A tail is added to the mRNA
- a primer is added and binds to this tail, then the DNA lengthens from nucleotides being added
- polymerase is added, catalysing the building of the complementary DNA strand
- the double stranded DNA is produced
what enzyme is used to use mRNA as the template to build the single stranded DNA in reverse transcription?
reverse transcriptase
what are restriction enzymes?
cleave (cut) DNA at specific recognition sequences known as restriction sites, splitting DNA into smaller fragments
what is a restriction site
a particular order of nucleotides
what do restriction enzymes create when cutting? (ends)
blunt and sticky ends
how are blunt ends cut?
at points directly opposite each other
how are blunt ends rejoined together (ligated)
the DNA fragments are joined directly together through the use of DNA ligase
how are sticky ends cut?
cut one strand at one point but cut the second strand at a point that is not directly opposite, leaving over hanging ends.
how are sticky ends joined together (ligated)
The DNA ligase enzyme connects the single-stranded DNA together via the sugar-phosphate backbones
where does ligase join DNA together?
sugar–phosphate backbones
what is polymerase chain reaction (PCR)
is a technique used to amplify a segment of DNA accurately and quickly
what is the main enzyme used in PCR and why is it used over others
Taq polymerase, because it can withstand great heat needed for the breakdown of DNA (heat resistant)
what are the 3 main steps in PCR?
- Denaturing
- Annealing
- Extension
what are the 2 steps involved in denaturing (PCR)
- DNA is heated to 94 degrees
- separation happens by raising the temperature of the PCR mixture, the hydrogen bonds between the complementary DNA strands break
what is the optimal temperature for denaturing to occur at and for how long
around 94 for a minute
What happens in annealing (PCR)
Short segments of single-stranded DNA, known as primers, are added, binding to the 3’ ends (target DNa sequences) initiating DNA synthesis. These primers bind to their complementary sequences on the single-stranded template DNA
what is the optimal temperature for annealing to happen and for how long
55 for 2 mins
What happens in extension (PCR)
The polymerase (Taq polymerase) uses the primers as a starting point and extending the primers, synthesising the new strands of DNA by adding nucleotides
what is the optimal temperature for extension to happen and for how long
72 for one minute
what is the difference between DNA and RNA polymerase
DNA polymerases synthesise DNA strands by adding (DNA) nucleotides (deoxyribose, ACTG)
RNA polymerases synthesise RNA strands by adding (RNA) nucleotides (ribose, AUCG)
what is gel electrophoresis
a technique for sorting a mixture of DNA fragments through an electric field on the basis of different fragment lengths
what are the 6 steps in gel electrophoresis
1.The DNA sample (fragments) is combined with DNA loading dye
2. it is then placed in a well at one end of a slab of aragose gel
3. This agarose gel is immersed in a buffer (salt) solution
4.The gel is then exposed to an electric field with the positive (+) pole (anode) at the far end and the negative (−) pole (cathode) at the starting origin. The DNA is attracted to the positive pole
5. Smaller fragments move through the agarose gel faster compared to larger fragments
6. fragments appear as bands on a gel which can be interpreted in various ways
why do smaller fragments move further in gel electrophoresis
the smaller fragments are able to better move and weave through the porous agarose gel compared to larger fragments
what is DNA profiling
a technique for identifying DNA from different individuals based on variable regions known as short tandem repeats (STRs)
what are STRs
short tandem repeats, sequences of just two to seven base pairs are repeated over and over
how are STRs used in DNA profiling
The number of repeats of an STR marker can vary between people and each variation is a distinct allele, so people with the same amount of repeats will match with certain DNA that is found
what is a plasmid
a small, circular, double-stranded DNA molecule, separate from the cell’s chromosomal DNA that exist naturally in bacterial cells
what is a recombinant plasmid
plasmids that carry foreign DNA
what are the 4 steps in making recombinant plasmids
- DNA of the plasmid is cut using a specific cutting enzyme in order to create sticky ends
- foreign DNA fragments are prepared using the same endonuclease so that the foreign DNA has sticky ends complementary to the cut plasmid (mostly done through reverse transcription)
- foreign DNA fragments and the plasmids are mixed, and, in some cases, their ‘sticky ends’ pair by using weak hydrogen bonds. A recombinant plasmid has been created
- The joining enzyme, ligase, is added and this makes the joins permanent through covalent bonding
what needs to happen after making a recombinant plasmid
needs to be transferred into a bacterial cell (bacterial transformation)
what is bacterial transformation
process in which bacterial cells take up segments of foreign DNA that become part of their genetic make-up
what are selectable markers
genes carried by plasmids for certain traits, often for antibiotic resistance
what are screening markers
A marker inserted into a plasmid that will change colour based on if the DNA has been taken up by the bacteria, lacZ is an example
what is a main thing we create using recombinant plasmids
insulin
what type of protein structure is insulin, therefore what does that mean
quaternary, meaning multiple peptide chains
how is insulin prepared before undergoing recombinant plasmid construction
reverse transcription, because don’t have to splice out introns
what are the 5 simple steps in creating insulin separately
- cut with endonucleases
- add insulin genes using ligase
- transformations of bacteria with plasmids and expression of proteins
- extract protein (insulin + B-galactosidase) from bacteria
- purify both A and B and combine each to each other
how can the success rate of bacterial transformation be increased
by heat shock or electroporation
why is heat shock and electroporation used
to increase the chance of bacteria to take up the recombinant plasmid as chances are low
what happens in electroporation
Cells are briefly placed in an electric field that shocks them and appears to create holes in their plasma membranes, allowing the plasmid entry
what is a vector
an agent or vehicle used to transfer pathogens or genes between cells and organisms
what happens in heat shock
The bacterial cells are suspended in an ice-cold salt solution and then transferred to 42 °C for less than one minute. This treatment appears to increase the fluidity of the plasma membranes of the bacterial cells and increases the chance of uptake of plasmids
what is gene cloning
the process which a gene of interest is located and cloned to produce multiple copies
what is recombinant DNA
DNA that is formed by combining DNA from different sources, often from different kinds of organisms
what are recombinant proteins
proteins that are expressed by recombinant DNA present in an organism
CRISPR Cas9 definition
a tool for precise and targeted genome editing that uses specific RNA sequences to guide an endonuclease
what is Cas9
a restriction enzyme, that will cut at the right positions based on the gRNA (guide) also known as sgRNA (synthetic/single guide RNA)
what is CRISPR
short, repeated segments of DNA, with each repeated segment being separated by a length of spacer DNA.
what are spacers?
a region of non-coding DNA between genes
what are the 4 main steps that CRISPR Cas9 uses when cutting DNA
- Targeting
- binding
- cleaving
- DNA repair
What happens in the targeting step? (CRISPR-Cas9)
Cas9 will locate and bind to a common sequence in the genome known as the PAM sequence
what is the PAM sequence
a sequence of bases (NGG, N is any nucleotide) that is in the genome
what happens in the binding step (CRISPR-Cas9)
Cas9 unwinds the DNA, and if the DNA at that location matches with the 20 strands of gRNA then it will bind together with complimentary base pairing
what happens in the cleaving step? (CRISPR-Cas9)
Binding triggers Cas9 to change shape and gives the signal to cleave both strands of DNA upstream of PAM.
This disables the viral DNA
what happens in the DNA repair step? (CRISPR-Cas9)
the cell will try and repair the DNA, leading to mutation (error prone). Disabling the gene
Or scientists will add another sequence or modify the specific sequence allowing for knocking out genes or replacing faulty ones with healthy ones
what are GMOs (genetically modified organisms)
are organisms that has had their genome altered using genetic engineering technology
what are transgenic organisms
sub-group of GMOs, that contain genetic material from different species
what may GMOs involve (2)
- addition of gene segment
- silencing of gene
what are some uses for GMOs for plants (3)
- increased photosynthesis efficiency
- greater crop yield
- faster growth rates
what are biomechanical reactions
reactions occurring in cells that lead to the formation of a product from a reactant.
what are biomechanical pathways
a series of linked biomechanical reactions
what are the types of biomechanical pathways
- anabolic pathways
- catabolic pathways
what is metabolism
The total activity of the reactions of all biochemical pathways in a living organism
what are substrates
a compound on which an enzyme acts
what happens to the energy levels in the anabolic pathways
anabolic pathways are energy-requiring or endergonic
what are anabolic pathways (anabolism)
These pathways turn simple molecules into more complex ones
what are catabolic pathways (catabolism)
These pathways break down complex molecules into more simple ones
what happens to the energy levels in catabolic pathways
Catabolic pathways are energy-releasing or exergonic
example of anabolic pathway
Photosynthesis, where glucose molecules are synthesised from carbon dioxide and water using radiant energy from the Sun
example of catabolic pathway
Aerobic cellular respiration, where glucose molecules are broken down into carbon dioxide and water molecules
what are catalysts
factors that increase rate of reaction
are enzymes specific to reaction?
yes, each different reaction will be catalysed by a specific enzyme
are all catalysts enzymes?
no, enzymes are all catalysts but not all catalysts are enzymes
what is activation energy
minimum amount of energy required to initiate a chemical reaction
what is the active site
region of an enzyme that binds temporarily with the specific substrate of the enzyme
how do enzymes lower activation levels (2)
- Influence the stability of bonds in the reactants
- Providing an alternative reaction pathway;
what do enzymes do to speed up a reaction
lower activation levels
how do enzymes bind to substrates (2 steps)
- the enzyme and substrate with join to form the E-S complex (when it binds to the active site)
- the substrate forms weak bonds with particular amino acid residues (in the protein) at the active site.
what are coenzymes
an organic molecule that acts with an enzyme to alter the rate of a reaction
what are cofactors
a non-protein molecule or ion that is essential for the normal functioning of some enzymes
are cofactors and coenzymes the same
no, coenzymes are cofactors but not all cofactors and coenzymes
what are inorganic cofactors
cofactors that do not contain carbon and include metal ions such as magnesium or copper
what are organic cofactors
small non-protein organic molecules that are essential for the function of particular enzymes
what are the 2 types of organic cofactors
- prosthetic groups
- coenzymes
prosthetic groups are ……
cofactors that are tightly bound to an enzyme and are essential for it to function as a catalyst.
what is the difference between prosthetic groups and coenzymes
prosthetic groups are tightly bound to an enzyme, whereas, coenzymes are loosely bound
what are the 5 main coenzymes we focus on
- NAD
- NADP
- FAD
- ATP
- CoA (coenzyme A)
what are the 2 roles of coenzymes to assist enzymes
- transfers of atoms or groups of atoms, such as hydrogens, phosphate groups and acetyl groups
- energy transfers
loaded coenzymes main info
they are high in energy and have a group that can be transferred. In simple they are electron donors
unloaded coenzymes main info
they have low energy, and accept groups. In simple they are electron acceptors
what are the 3 factors that impact enzyme activity
- temperature
- pH
- substrate concentration
why does a temperature that it close to an enzymes (or reactions) optimum have an increased reaction rate
there is more movement of particles, therefore more collisions possible with substrate and enzyme
summary of what happen with varied pH for enzyme activity (rate of reaction)
As pH increases or decreases from optimum pH, the rate of reaction and the activity of an enzyme decreases.
summary of what happen with varied substrate concentration for enzyme activity (rate of reaction)
the rate of reaction increases with increasing substrate concentration — but only up to a point. Beyond this, any further increase in substrate concentration produces no significant change in reaction rate (active sites are all occupied)
what are enzyme inhibitors
substances that prevent the normal action of an enzyme and therefore slow the rate of enzymes-controlled reactions
what are the 2 types of inhibition
reversible inhibition
irreversible inhibition
what are the 2 types of reversible inhibition
- competitive inhibition
- non-competitive inhibition
what is competitive inhibition
inhibition in which a molecule binds to the active site of a molecule instead of the usual substrate
what is non-competitive inhibition
inhibition in which a molecule binds to the allosteric site of an enzyme causing a conformation change in the active site
why does competitive inhibition slow down reaction rate
inhibitor molecules prevent the formation of the E–S complexes (as active site is partially occupied)
why does non-competitive inhibition slow down reaction rate
as the binding of the inhibitor to the allosteric site changes the shape of the enzyme’s active site the E-S complex cannot form
what is irreversible inhibition
occurs when a specific molecule can form a strong covalent bond with an enzyme at its active site, so that the normal substrate is permanently blocked from accessing the active site
what are common irreversible inhibitors?
Heavy metals
what are 3 things that the regulation of rates of reaction does
- prevent waste, such as would occur if pathway products were made in excess of cell requirements
- prevent the build-up in cells of products to potentially harmful levels
- prevent depletion of substrates
what are the 2 types of regulation
- allosteric regulation
- feedback regulation
what is allosteric regulation
control of the reaction rate of enzymes through conformational changes in enzymes. This occurs when a regulator molecule binds to the allosteric site
what can the regulator molecules be (allosteric regulation)
- allosteric inhibitors
- allosteric activators
what does allosteric inhibitors do
their binding produces a change of shape in the enzyme that stops enzyme activity; they act like an OFF switch
what does allosteric activators do
the shape change resulting from the binding produces an increase in enzyme activity; they act like an ON switch
what is feedback regulation
the end product of a metabolic pathway acts as an inhibitor of the key enzyme that catalyses the first step in a pathway.
what is photosynthesis
the process by which plants use the radiant energy of sunlight trapped by chlorophyll to build carbohydrates (glucose) from carbon dioxide and water.
what are the 2 stages of photosynthesis
- light-dependent stage
- light-independent stage
what is the photosynthesis equation
6 carbon dioxide + 6 water = glucose + 6 oxygen (gas)
what is the function of the light dependent stage
to transform sunlight energy that is captured by chlorophyll into the chemical energy of loaded coenzymes
what is the function of the light independent stage
to assemble simple inorganic carbon dioxide molecules into more complex organic glucose molecules
what is another name for the light independent stage
Calvin cycle
where does photosynthesis occur
chloroplasts, in the chlorophyll pigment inside (in the cytosol of plants)
what does chloroplasts enable a plant to do
capture the radiant energy of sunlight, bringing it into cells as the starting point of photosynthesis
what are the 3 main things inside the chloroplasts (not including chlorophyll)
thylakoids
grana
stroma
what are thylakoids
flattened membranous sacs in chloroplasts that contain chlorophyll
what is the grana
stacks of thylakoids are known as grana, where a singular stack is a granum
what is stroma
fluid inside the chloroplasts, containing the enzymes that are involved in calvin cycle
what does the light dependent stage involve
involved in the capture of sunlight and the transformation of its energy to the chemical energy of loaded coenzymes, NADPH and ATP.
where is the light dependent stage occur (c3)
thylakoid (within the grana)
what are the 3 inputs in the light dependent stage
- water
- ADP + Pi
- NADP+
what are the 3 outputs of the light dependent stage
- oxygen
- ATP
- NADPH
summary of what happens in light dependent stage
the energy caught by the chlorophylls make the electrons have high energy (excited) and the splitting of water molecules gives H+ ions (protons).
This then allows NADPH to form as well as ATP
what do the chloroplasts have after the light dependent stage
a supply of high-energy loaded ATP molecules
a supply of high-energy loaded NADPH coenzymes that can act as donors of hydrogen ions and electrons
light dependent equation
water + 18ADP + NADP into 6O2 + 18ATP + NADPH
what happens in the light independent stage
inorganic carbon dioxide molecules (CO2) are built into energy-rich reduced organic molecules, such as glucose (C6H12O6).
where does the light independent stage occur
the stroma
what is required for the light independent stage
Rubisco, and the NADPH (donate H and e-) and ATP (energy source) from the previous stage
what are the 3 inputs of the light independent stage
- ATP
- NADPH
- CO2
what are the 3 outputs of the light independent stage
- ADP + Pi
- NADP+
- Glucose
summary of what happens in light independent stage
inorganic carbon is converted in organic CO2 thru carbon fixation
NADPH donate hydrogens and electrons as molecules are reduced to higher energy levels
ATP supplies energy for anabolic steps
why are there different types of plants
they are categorised into how they fix carbon into glucose
how do C3 plants carry out the Calvin Cycle
These plants carry out the original Calvin Cycle, using Rubisco, and are prone to photorespiration
what are optimal conditions for C3 plants
moist and cool conditions
how do C3 plants use RuBisco
use the Rubisco enzyme to fix inorganic carbon dioxide from the air and it enters the Calvin cycle joined to a carrier molecule (RuBP)
where does the Calvin Cycle take place in C3 plants
in the stroma of the leaf mesophyll cells
Photorespiration definition
a process in which plants take up oxygen rather than carbon dioxide in the light, resulting in photosynthesis being less efficient. (Rubisco takes up O2 instead of CO2)
what does rubisco normally do
the critical enzyme in C3 plants that brings carbon dioxide from the air into the Calvin cycle where the glucose is made
when does photorespiration occur
rubisco binds oxygen rather than carbon dioxide
why will Rubisco bind to oxygen instead of carbon dioxide
the active site can readily accommodate the oxygen molecules as well as the carbon dioxide molecules, so the two different molecules are in competition for the active site of Rubisco.
2 ways photorespiration arise in C3 plants (increase amount)
- temperature increases
- conditions dry out
why does photorespiration increase as temperature increases
the ability of the Rubisco enzyme to distinguish between carbon dioxide and oxygen decreases and, as a result, Rubisco will increasingly bind oxygen.
why does photorespiration increase as conditions dry out
C3 plants close their stomata to prevent water loss. This closure blocks the entry of carbon dioxide needed as input to the Calvin cycle and limits the exit of oxygen produced
creating a high oxygen low CO2 environment inside the mesophyll cells
how do C4 plants carry out the Calvin Cycle
carry out an adapted Calvin cycle, in which carbon fixation and glucose production occur in different cells
what are optimal conditions for C4 plants
These cells will thrive in warm and tropical regions
what anatomy changes are present in C4 plants (compared to C3 and CAM)
- bundle sheath cells have chloroplasts
- mesophyll cells that are arranged in a close association around the bundle sheath cells
where do the two processes (stages) occur in C4 plants
leaf mesophyll cells and bundle sheath cells
what happens in the first process in C4 plants (light dependent stage)
Carbon dioxide is converted into malic acid, in the mesophyll cells
PEP carboxylase catalyses the binding of carbon dioxide to an acceptor molecule (malic acid) (this is called carbon fixation)
what enzyme is used in the first step of C4 plants in photosynthesis
PEP carboxylase
what happens in the second process of the C4 plants (light independent stage)
Calvin cycle (glucose production) occurs in the bundle sheath cells
produce a steady supply of carbon dioxide from the breakdown of malic acid that raises the carbon dioxide concentration in their leaves. This allows the RuBisco in the bundle sheath cells to bind only to CO2
how do CAM plants carry out the Calvin Cycle
two stages of the Calvin cycle occurring at different times
what are optimal conditions for CAM plants
thrive in hot and arid environments, that are exposed to droughts
when does carbon fixation happen in CAM plants
at night (stomata are open)
when does the Calvin cycle happen in CAM plants
in the day (when the stomata are closed)
where do photosynthesis processes occur in the CAM plants
mesophyll cells
does CAM plants use PEP carboxylase or Rubisco initially
PEP carboxylase
what happens to the malic acid produced in CAM plants when it is night time
it is stored in vacuoles waiting for the stomata to close (day time)
what 3 things will make RuBisco work most efficiently
- carbon dioxide levels in leaves are high
- oxygen levels are low (as happens when water is freely available)
- when temperatures are moderate.
what are 2 examples of CAM plants
- cacti
- pineapples
what are 3 examples of C3 plants
- wheat
- rice
- potato
what are 2 examples of C4 plants
- maize/corn
- sugar cane
what are the 4 main factors that affect the rate of photosynthesis
- the amount of light reaching their leaves
- the temperature of the environment
- the availability of water
- the concentration of carbon dioxide
what is a limiting factor
any environmental condition that restricts the rate of biochemical reactions in an organism.
what happens to the rate of photosynthesis as light intensity increases
increases as light intensity increases, until it reaches a maximal point.
what is the light saturation point
the point where further increases in light intensity have no effect and the rate of photosynthesis stays constant
why does increased light intensity increase the rate of photosynthesis
more chlorophylls are energised
what does too little or too much water do to the rate of photosynthesis
rate of photosynthesis declines and then stops because closed stomata prevent the uptake of carbon dioxide needed for the Calvin cycle
what does waterlogging do to the rate of photosynthesis
the rate of photosynthesis will also decline and stop because the lack of oxygen for cellular respiration in root cells stops water uptake
what happens to the rate of photosynthesis as temperature increases
As the ambient temperature is increased, the rate of photosynthesis also increases due to an increase in collisions between the reactants and the enzymes involved in photosynthesis. Eventually, as the heat passes a certain threshold, the enzymes start to denature, in which the tertiary structure of an enzyme is lost. This causes the rate to again decrease.
what happens to the rate of photosynthesis as CO2 concentration increases
the rate of photosynthesis will increase until it levels off due to limiting factors
does CO2 concentration impact the light dependent stage and why
no, because CO2 is not apart of the reaction
what is cellular respiration
the process of converting chemical energy into a useable form by cells, typically ATP.
what are the 2 types of cellular respiration
- aerobic
- anaerobic
what is the equation for aerobic cellular respiration (without coenzymes)
glucose + oxygen → carbon dioxide + water + ATP
how many ATP does aerobic respiration make
30-32, 36-38 in optimal conditions
what are the 3 steps of aerobic cellular respiration
- glycolysis
- Krebs cycle
- electron transport chain
what is the main (broad) thing that happens in glycolysis
glucose is broken down into pyruvate
what is the main (broad) thing that happens in Krebs cycle
makes a supply of energy-rich loaded coenzymes
what is the main (broad) thing that happens in the electron transport cycle
transfers energy from electrons supplied by loaded coenzymes to make ATP.
where does glycolysis occur
cytosol
how much ATP is produced from glycolysis
2
what are the 3 inputs in glycolysis
glucose, 2x (ADP + Pi) and 2x (NAD+)
what are the 4 outputs in glycolysis
2x (pyruvate), 2x ATP, 2x (NADH) and two hydrogen ions (protons)
where does the Krebs cycle and electron transport chain occur
mitochondria
where specifically does the Krebs cycle occur
the matrix
what is the matrix of the mitochondria
gel like solution within their inner membrane
where specifically does the electron transport chain happen
the cristae
what does cristae do
It folds in the inner membrane of the mitochondria, it holds enzyme
what happens in between glycolysis and Krebs cycle
pyruvate oxidation
what in summary happens in pyruvate oxidation
pyruvate loses a C and an H atom, forming a 2C acetyl group that is delivered to the Krebs cycle by coenzyme A.
what are the 2 coenzymes that are becoming high in energy in the Krebs cycle
FAD+ and NAD+
what are the 4 inputs in Krebs cycle and pyruvate oxidation
2 x (acetyl CoA (acetyl groups)), 6 x (NAD+), 2 x (FAD) and 2 x (ADP + Pi)
what are the 4 outputs in Krebs cycle and pyruvate oxidation
4 x (CO2), 6 x (NADH), 2 x (FADH2) and 2 x (ATP)
detailed electron transport chain info
Electrons are transferred along enzyme complexes
The first input of high-energy electrons to the ETC comes from loaded NADH coenzymes.
FADH2 also donates its high-energy electrons to an acceptor, but further down the chain.
Oxygen accepts electrons and hydrogen ions, forming water
how is so much ATP produced in the ETC
As electrons transfer from one enzyme complex to the next, the energy released is ultimately used to power the production of ATP from ADP and Pi.
what are the 4 inputs of ETC
- 6 (oxygen)
- 26-28 (ADP + Pi)
- 10 (NADH)
- 2 (FADH2)
which process of aerobic cellular respiration needs oxygen
electron transport chain
what is anaerobic respiration/fermentation
processes that occur without the presence of oxygen, producing a net of 2 ATP molecules
when does anaerobic fermentation occur in humans
occurs in human skeletal muscle cells when the supply of oxygen to the cells by aerobic cellular respiration cannot keep up with their demand for ATP.
where does anaerobic fermentation take place
the cytosol
is the rate of ATP production in anaerobic fermentation higher lower or similar to aerobic respiration
much faster, this is why it is able to produce enough ATP
what are the 2 anaerobic fermentation pathways
- alcohol (ethanol) fermentation
- lactic acid fermentation
what are the 2 processes that occur in both anaerobic fermentation pathways
glycolysis
short add on stage
is glycolysis the same in aerobic and anaerobic cellular respiration
yes
what happens in the add on stage for lactic acid fermentation
pyruvate, ADP and NADH is turned into ATP, lactic acid and NAD+
what happens in the add on stage for alcohol fermentation
alcohol and carbon dioxide is created, NAH+ is regenerated for glycolysis again
what fermentation does yeast and animals use (anaerobic fermentation)
animals use lactic acid
yeast uses alcohol
what 3 factors affect the rate of cellular respiration
- temperature
- oxygen concentration
- glucose concentration
glucose concentration affecting cellular respiration summary
an increase in glucose concentrations leads to an increase in the rate of cellular respiration. This rate eventually levels off from rate-limiting factors
what is biomass
the organic material from plants and animals; it is a renewable source of energy.
what is biofuel
Biofuels are any fuel source derived from biomass.
what is the 4 general processes of creating biofuel from biomass
- deconstruction of biomass to increase surface area
- hydrolysis (breaking down) of biomass by enzymes
- yeast fermentation to produce ethanol
- purification and dehydration to remove debris and water
what could CRISPR-Cas9 be used for to improve plants for humans (3)
- increase photosynthetic efficiency
- crop yield
- crop quality
how could CRISPR-Cas9 be used to improve photosynthetic efficiency
could improve the Rubisco, by knocking out parts of genes that result in rubisco binding to O2
What are antigens
molecules or parts of a molecule that stimulate immune response through the adaptive immune response.
antibodies definition
proteins produced by plasma cells in response to antigens and which react specifically with the antigen that induced their formation
immunoglobulins definition
They are another term for antibodies
inflammation definition
an innate reaction by the immune response to foreign particles or injury resulting in redness and swelling
Cytotoxic T cell definition
T cells that are activated by cytokines to bind to antigen–MHC-I complexes on infected host cells and kill infected body cells
what are the 2 ways antigens can be classified as
self or non-self
self antigens are:
those that are not foreign and are thus usually tolerated by the immune system
non-self antigens definition
Non-self antigens can be identified as invaders and can be attacked by the immune system.
what is the main way for an immune cell to tell self and non-self antigens apart
the cell surface receptors that tell them if they are self or non-self (MHC)
what is the major histocompatibility complex
receptor proteins on the surface of cells that identify the cells as ‘self’
where are MHC-l markers found
all nucleated cells
what do MHC-l markers do
provide a site for binding of antigens to occur, that allows cells to be recognised as ‘self’ so they will not be attacked
Where are MHC-II markers found
- mainly on specific white blood cells, including antigen-presenting cells (macrophages and dendritic cells)
- and helper T cells.
what do MHC-ll markers do
the antigen presenting cells present antigens on their surface on these MHC-II markers, which bind to helper T cells to help activate the adaptive immune response.
what is a pathogen
A pathogen or infectious agent is a biological agent that causes disease or illness to its host
what are the 2 subtopics of pathogens
- cellular
- and non-cellular
what are the 4 main cellular pathogens
- bacteria
- parasites
- fungi
- protozoa
what are protozoans (cell info)
single-celled eukaryotic cells
what are bacteria (cell info)
They are singular chromosome and double stranded DNA, prokaryotic cells
cellular pathogens definition
any disease-causing agent made up of cells that can reproduce independently without relying on the host machinery
what type of cell are cellular pathogens
can be both eukaryotes or prokaryotes
what is a major reason why bacteria is a pathogen (what do they produce)
toxins
what do bacteria toxins do
damage particular tissues of their host organism and cause disease
what are the 2 main non-cellular pathogens
- viruses
- prions
virus definition
non-cellular pathogens that use the host cell in order to replicate their genetic material
what are viruses called outside of the host cell
virions (viral particle)
what are virions
the extracellular form of a virus that can transfer between hosts
prions definition
infectious particles made of protein that lack nucleic acids (folded proteins)
what do all viruses have (structure)
- genetic material, either DNA or RNA, organised as a single molecule or as several molecules
- a protein shell, known as a capsid, that surrounds the genetic material.
what is lysis
destruction of cells by rupturing the membrane of the cell
how do viruses spread (release particles from cell)
The mode of release of viral particles from an infected cell may be by budding or by cell lysis.
what do prions do
triggers normal proteins in the brain to fold into an abnormal structure
what is an incubation period
the time period between infection and the first appearance of the symptoms of a disease
what pathogen has a long incubation period
prions
what is an allergen
an antigen that elicits an allergic response
what systems are involved in an allergic response
cells from both the innate and adaptive system
innate immunity definition
the type of immunity that is present from birth, is fast acting but not long lasting, and produces non-specific (generic) responses against classes of pathogens
adaptive immunity definition
an immune response that is specific to a particular antigen and develops through contact with an antigen
immunological memory definition
ability of the adaptive immune response to remember antigens after primary exposure
what are the 2 types of actions that the immune system uses to protect against infection (types of immunity)
- cell-mediated immunity
- humoral immunity
cell-mediated immunity definition
immune response that is mediated by immune cells
humoral immunity definition
immune response mediated by soluble molecules in the blood, lymph and interstitial fluid that disable pathogens
what kinds of cells are all cells in the immune system
white blood cells
lymphocytes definition
class of white blood cells found in all tissues including blood, lymph nodes and spleen, and which play a role in specific immunity
B cells (B lymphocytes) definition
white blood cells that recognise antigens or pathogens and produce a large number of antibodies specific to an antigen
T cells (T lymphocytes) definition
white blood cells that mature in the thymus and participate in the adaptive immune response
what happens in the lymph nodes
B cells and T cells are activated and adaptive immune responses occur
what is apart of the 1st line of defense
a physical, chemical and microbiological barriers to prevent pathogens from gaining entry to the body
what is apart of the 2nd line of defense
the actions of immune cells and soluble proteins mounting a rapid but non-specific attack against pathogens that gain entry to the body.
what is apart of the 3rd line of defense
the recognition of specific antigens by lymphocytes
what type of immunity do the 1st and 2nd line of defense use
innate immunity
what type of immunity does the 3rd line of defense use
adaptive immunity
physical barriers definition
innate barriers that act to prevent the entry of pathogens into the body
What are the 3 barriers that prevent the entry of pathogens into an organism (1st line)
- physical barriers
- chemical barriers
- microbiological (microbiota) barriers
what is 1 example of a physical barrier in plants
stomata (close to prevent pathogen entry)
what is 1 example of a physical barrier in animals
intact skin
chemical barriers definition
a innate barriers that use enzymes to kill pathogens and prevent invasion into a host
what is 1 example of a chemical barrier in animals
sweat (with lysozyme)
what is 1 example of a chemical barrier in plants
caffeine (Toxic to fungi and insects)
microbiological barriers definition
innate barriers involving normal flora in the body
how to chemical barriers (sweat and tears) kill pathogens
by an enzyme called lysozyme that kills the pathogens
when does the second and third line of defense start to work
when pathogens have entered the body (cut in skin)
phagocytosis definition
bulk movement of solid material into cells where the cell engulfs a particle to form a phagosome
what are the 3 key aspects of innate immunity (2nd line)
- soluble proteins
- inflammation
- immune cells
what are the 6 main white blood cells (immune cells)
- natural killer cells (NK cells),
- mast cells,
- eosinophils
- macrophages
- neutrophils
- dendritic cells
what are two other names for immune cells
white blood cells
leukocytes
which of the 6 immune cells are phagocytes
- neutrophils
- dendritic cells
- macrophages
where are neutrophils, eosinophils and NK cells found
in the bloodstream
what are granulocytes
a type of white blood cell that has small granules inside their cytoplasm
what are the 2 granulocytes (WBC’s)
eosinophils, neutrophils
which immune cells are antigen presenting
- dendritic cells
- macrophages
simple overview of steps in phagocytosis
- pathogen recognised by pattern recognition receptor
- pathogen engulfed by phagosome
- Lysosomes fuse with the phagosome
- pathogen is destroyed by toxic chemicals and lysosome
- material is discharged by exocytosis
In these antigen presenting cells what is on their surface (specifically MHC-ll markers) once phagocytosis happens
some antigens or sub-units from the digested pathogen on the MHC-ll markers (activating adaptive immune system)
what is a pattern recognition receptor
protein receptors present on phagocytic cells of the innate immune system that enable these cells to recognise and bind to pathogens, with recognition being at a generic leve
macrophage info (brief)
they identify eliminate and engulf pathogens by phagocytosis and clear dead cells and debris. Also antigen presenting (can activate adaptive immune response)
Neutrophils info (brief)
Neutrophils are abundant immune cells that are usually the first to the site of an infection, engulfing and destroying pathogens.
dendritic cells info (brief)
Dendritic cells are professional antigen-presenting cells, engulfing pathogens and presenting their antigens to T cells to activate the adaptive immune response.
eosinophils info (brief)
assist in defending against larger parasitic agents that are too large to be engulfed by phagocytosis. They contain granules with toxic chemicals and histamine
NK cells info (brief)
lymphocytes that kill virus-infected cells through apoptosis
degranulation info for NK cells
There granules contain granzymes and perforin. The perforin makes holes in the cells plasma membrane allowing the granzymes to enter. This enzymes induces apoptosis
degranulation definition
the process by which immune cells release various chemicals (such as histamine and antimicrobials) stored within secretory vesicles known as granules
mast cells info (brief)
they are vital in the inflammatory response. As well as releasing histamines that increase vascular permeability, they also release cytokines that attract other immune cells to help destroy the pathogen. (out of granules) (also contain heparin)
histamine definition
a substance involved in inflammation and allergic reactions that causes blood vessels to dilate and become more permeable to immune cells
what is the cell-mediated immunity for the second line of defense
the immune cells attacking the pathogen
what is the humoral immunity for the second line of defense
complement proteins and cytokines
what are complement proteins
proteins that assist other innate immune cells and can destroy bacterial cells by lysis
what are cytokines
signalling molecules of the immune system
what is an important cytokine in the innate immune system and definition
interferons,
proteins secreted by some cells, in response to a virus infection, that helps uninfected cells resist infection by that virus
where are complement proteins found
dissolved in blood plasma
what are the 3 things that complement proteins do
- opsonising pathogens
- recruiting immune cells involved in an inflammatory response (chemotaxis)
- destroying bacterial pathogens by lysis
opsonisation definition
the coating of the surface of pathogen cells by complement proteins, making the pathogens more susceptible to phagocytosis
Why does opsonisation make pathogens more susceptible to phagocytosis
phagocytes have receptors for complement proteins on their plasma membranes, and these bind to the opsonised microbes. Allowing for direct binding to the pathogen
what is chemotaxis
movement of a cell or organism in response to a chemical substance
what is the membrane attack complex (MAC)
one of the defence mechanisms resulting from activation of complement proteins that destroys pathogen cells by osmotic shock
how does chemotaxis work for complement proteins
Small complement peptides that diffuse from the pathogen surface act as chemical signals, attracting immune cells involved in the inflammatory response
how are complement proteins activated (cascade attached)
The activation of a complement protein occurs when the protein is cut (cleaved) into two fragments — a larger activated protein and a smaller peptide fragment. This sequence of reactions starts a cascade that can neither be stopped nor reversed.
Or C3 makes direct contact with molecules on the surface of a pathogen
how do infereons work
Once a body cell is infected with viruses, the cell secretes interferons. That cell is doomed, but the interferons that it secretes into its surroundings act as warning signals to nearby cells so that they can prepare in advance for a possible virus infection
how does lysis work
The MAC inserts into the plasma membrane of the pathogen and produces a pore that allows fluid to enter, causing the pathogen cell to swell and burst — explosive death by osmotic shock
what are the 5 main symptoms of inflammation
- redness
- pain
- heat
- swelling
- pus
what are the 3 stages of inflammation
- vascular stage
- cellular stage
- resolution stage
what are 2 things that happen in the vascular stage of inflammation
- chemical signals (such as histamine) are released to attract phagocytes
- dilation and increased leakiness of capillary (vasodilation)
what are 2 things that happen in chemical stage of inflammation
- phagocytes consume bacteria and cell debris
- phagocytes migrate to area
what are 2 things that happen in resolution stage of inflammation
- platelets move out of the capillary to seal wound
- an abscess forms, containing pus, with dead phagocytes and cell debris
what are the 4 functions of the lymphatic system
- production and maturation of immune cells
- the removal of excess fluids from body tissues
- absorption and transportation of fatty acids to the digestive system
- allowing for the process of antigen recognition by T and B lymphocytes
what 4 things does the lymphatic system have in it (structure)
- lymph
- lymphatic vessels
- primary lymphoid organs
- secondary lymphoid organs
what are the primary lymphoid organs
bone marrow and thymus
what are the secondary lymphoid organs
lymph nodes and spleen
what happens in the bone marrow
- source of pluripotent stem cells (where immune cells originate)
- and site of maturation of B cells
what is lymph
is the fluid in the lymphatic system that gets squeezed out of blood vessels
what happens in the thymus
site where T cells mature after being released from the bone marrow
what happens in the spleen (3)
- filters the blood passing through it, clearing the blood of bacteria and viruses as well as worn-out red blood cells
- contains T cells and B cells that detect and respond to infectious agents in the blood
- contains other immune cells
what are lymph nodes
Lymph nodes are the sites in which antigen recognition occurs
what is antigen recognition
This is where antigen-presenting cells display their antigens to their specific T and B lymphocytes, leading to expansion of the appropriate lymphocytes for adaptive immunity
what do the helper T cells cytokines do to other cells
These can initiate either the humoral adaptive immune system (through stimulating the clonal selection and clonal expansion of B cells) or the cell-mediated immune system (through stimulating the clonal selection and expansion of cytotoxic T cells).
6 steps involved with antigen presenting and initiation of immune response (adaptive immune response)
- pathogen is engulfed by APCs
- pathogen is degraded into fragments (my fusion with lysosome)
- some of the fragments are presented on MHC-II markers
- They present these fragments to helper T cells by moving to the lymph nodes (antigen presentation)
- Helper T cell binds to the antigen (via receptors) and activates the helper cell
- Helper T cells release cytokines (interleukins) that activate B or T cells
where does antigen presentation happen
lymph nodes
what are the 3 functions of helper T cells
- activate cytotoxic T cells
- activate B cells into becoming antibody-producing plasma cells
- activate macrophages to remove - antibody-coated pathogens by phagocytosis
what is the two main features of the adaptive immune response
- specificity
- Immunological memory
what is specificity (adaptive response)
the ability to recognise and respond to specific antigens
3 key components of adaptive immune response
- T cells and B cells
- antibodies, also known as immunoglobulins
- lymph nodes, organs where B cells and T cells meet foreign antigens and are activated
what are the 2 types of B cells
- B plasma cells
- B memory cells
what is the humoral immune response for the adaptive response
Involves the actions of antibodies that identify and bind to extracellular pathogens, to toxins and to other extracellular foreign antigens. Antibodies are products of special B plasma cells.
where do B cells develop
bone marrow
what is the cell-mediated immune response for the adaptive response
involves various actions of T cells. Cytotoxic T cells eliminate body cells that are infected by pathogens or have abnormal or missing self markers. They eliminate intracellular pathogens.
where do T cells develop
thymus
what are the 5 steps of activation of humoral response
- After the helper T cell activates the interleukins they naive B cells are activated
- The B cells undergo clonal expansion to produce clones of B cells
- These clones differentiate into plamsa B cells or memory B cells
- plasma B cells secrete antibodies to the antigen, memory B cells remain in the lymphoid tissue
- then PIANO occurs via antibodies
what are naive B and T cells
B and T cells that haven’t been activated
what is precipitation (antibodies)
they bind to soluble antigens, making them insoluble, causing them to precipitate out of the solution, creating a solid (more visible)
what is clonal selection
when the correct (specific) naive B or T cell binds to the antigen
what is in clonal expansion
when the naive B or T cell differentiates
what are the chains of an antibody
light and heavy chains (light short, heavy long)
what are the 2 regions of an antibody
- variable region (ends that bind to antigens)
- constant region (most of the antibody)
what is acronym to remember what antibodies can do to pathogens and what does it stand for
PIANO
precipitation
inflammation
agglutination
neutralisation
opsonisation
what is agglutination (antibodies)
they bind to the surface antigens on pathogens to form antigen–antibody complexes, causing them to clump together (more visible)
what is inflammation (antibodies)
they release histamine, triggering inflammation
what is neutralisation (antibodies)
they bind to surface antigens on pathogens and form a coating that neutralises pathogens by blocking their receptors so that the pathogens cannot attach to healthy body cells and infect them
what is opsonisation (antibodies)
they bind to the surface antigens on pathogens to form antigen–antibody complexes and tag the pathogen for destruction. This activates phagocytes and complement proteins
cell-mediated adaptive response definition
a specific response in which cytotoxic T cells destroy virus-infected cells using perforin and granzyme B
how do cytotoxic T cells recognise and bind to infected cells
the MHC-I marker
what happens in the 4 steps of activating the cell-mediated adaptive response
- After the helper T cells release interleukins it will activate naive T cells
- They then undergo clonal expansion to produce these T cell clones
- These clones differetiate into cytotoxic T cells and memory T cells
- The cytotoxic T cells release perforin and granzyme B, destroying the infected cell via it intiating apoptosis
how do cytotoxic T cells do apoptosis
- release perforin, making a hole in the cell
- secrete granules (granzyme B) enter the cell and initiate apoptosis
what are the two ways we can gain immunity depending on the source of the antibody
- actively (active immunity)
- passively (passive immunity)
what happens in active immunity
antibodies are produced by a person’s own adaptive immune system
why and how does natural immunity occur
occurs naturally, without deliberate intervention
what are the two means of gaining immunity
- naturally
- artificially
how does artificial immunity occur
is induced through a deliberate intervention
what is natural active immunity
a type of immunity in which the body produces antibodies in response to a normal infection by a pathogen
what does artificial active immunity involve
the deliberate and artificial introduction of a disabled pathogen or its toxin to the body (vaccination)
what happens in passive immunity
antibodies are acquired by a person from an external source
what is natural passive immunity
a form of immunity in which an individual receives antibodies from a natural source, such as through breastfeeding
what is artificial passive immunity
the injection of antibodies, providing immediate response, (antivenom)
disease definition
a condition in a living animal or plant body that impairs the normal functioning of an organ, part, structure or system
what are the 2 way diseases can be
- non-infectious
- infectious
what are emerging diseases
a disease caused by a newly identified or previously unknown agent
what is re-emerging disease
reappearance of a known disease after a significant decline in incidence
what are pandemics
a situation when, over a relatively short time, many people worldwide contract a specific disease as it spreads from a region of origin
what are epidemics
the widespread occurrence of an infectious disease in a community or in a restricted geographic area at a particular time
what can we identify to quickly stop the spread of the disease
the host or the pathgoen
what are the 2 modes of transmission (of diseases/illnesess)
- direct transmission
- indirect transmission
what is direct transmission (of a diseases)
mechanism of transmission of pathogenic agents that involves direct person-to-person contact, such as by kissing or sexual contact
what is indirect transmission (of a diseases)
mechanism of transmission of pathogenic agents that does not involve direct person-to-person contact, such as by airborne droplets or by ingestion of contaminated food
what are asymptomatic carriers
a person with an infectious disease showing no symptoms but able to infect others
what is the R0 value?
the basic reproduction number that identifies the expected number of individuals a person with a certain disease will infect
what are the 6 methods of disease control
- prevention
- vaccination
- medication
- surveillance
- modification of environment
- infection control standards
example of modification of environment (disease control)
spraying chemicals to eliminate breeding of the pathogens
example of infection control standards (disease control)
washing hands
what are antibiotics
a class of antimicrobial drug used in the treatment and prevention of bacterial infections that act either by killing pathogenic bacteria or by inhibiting their growth
what are vaccination programs
mandated programs that set a schedule in which vaccinations against specific diseases should be administered
what is herd immunity
indirect protection, at the population level, against an infectious disease; the protection is created by the presence in the population of a high proportion of individuals who are vaccinated against the particular disease
how much percent of a population has to be vaccinated for herd immunity to be viable
95%
what are 2 ways to identify pathogens
- ELISA
- microscope
elisa definition
a technique known as enzyme linked immunosorbent assay, which can detect specific antigens or antibodies
what are monoclonal antibodies
specifically designed antibodies used in the treatment of some diseases such as cancer and autoimmune disease
how are mAbs made
- a mouse is injected with antigens, allowing for their B cells to produce and antibody which is withdrawn (from spleen)
- then they are fused with collected tumor cells in suspension
- they make hybrid cells (hybridomas)
- these cells are isolated to grow separately
- they then grow many of these mAbs
what can mAbs be used for
- treat cancer
- treat autoimmune disease
what are the types (forms) mAbs can be in
- naked
- conjugated
what is a naked mAbs
mAbs that dont have any molecules attached
what is a conjugated mAbs
mAbs that have other molecules attached
what are the 4 modes that mAbs can be used to treat cancer
- stop growth of blood vessels
- signal immune attack
- block growth factors
- deliver anticancer or radioisotopes to the cancer cells
what 3 things can naked mAbs do to treat cancer
- block signalling to prevent growth by inhibiting blood vessels (bind to growth factor)
- they block signals for cell division (cant replicate cancer cells)
- they can bind to tumor cells to signal attack from immune system
what does conjugated mAbs do to treat cancer
they bring the anticancer and radioisotopes to the cancer cells (kill the cells)
what is autoimmune disease
a disease where antibodies attack self cells
how can mAbs be used to help treat autoimmune disease
alter the course of an autoimmune disease by directing the antibodies against major histocompatibility antigens to prevent them triggering an autoimmune response
population definition
members of one species living in one region at a particular time
gene pool definition
sum total of genetic information present in a population
genotype definition
The total set of this genetic information in an individual
phenotype definition
the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.
genetic diversity definition
the amount of genetic variation there is within a population’s gene pool
allele frequency definition
the proportion of a specific allele in a population
how to calculate allele frequency
- times the # of organisms by 2 (for 2 alleles) to gain total number of alleles in the pool
- write the number of alleles for each type (10 of a, 6 of A)
- divide each # of alleles by the total alleles in the pool for the allele frequency of that allele.
what are the 3 agents that can cause allele frequency changes
- changes in environmental selection pressures leading to natural selection
- genetic drift
- gene flow
what are environmental selection pressures
external agents which influence the ability of an individual to survive in their environment
what are the 3 categories of environment selection pressure
- physical agents
- chemical agents
- biological agents
example of physical agents (selection pressures)
climate change
example of biological agents
predation
example of chemical agents
pollutants in soil or water
what is natural selection
a process in which organisms better adapted for an environment are more likely to pass on their genes to the next generation
what is ‘fitness’
the ability to survive and pass genetic material on to the next generation
what is selective advantage
relative higher genetic fitness of a phenotype compared with other phenotypes controlled by the same gene
what are the 4 mechanisms of natural selection (steps of natural selection)
- There is variation within the population’s gene pool.
- struggle for all individuals in the gene pool to survive. Environmental selection pressures act upon the population
- Individuals that are better adapted to their environment are more likely to survive and reproduce, passing their alleles on to the next generation
- The alleles that allow for survival will be inherited by subsequent generations and they can increase in frequency in the gene pool over time
what is genetic drift
random changes, unpredictable in direction, in allele frequencies from one generation to the next owing to the action of chance events
what are the 2 subtopics of genetic drift
- bottleneck effect
- founder effect
what is bottleneck effect
chance effects on allele frequencies in a population as a result of a major reduction in population size
what is founder effect
chance effects on allele frequencies in a population that is formed from a small unrepresentative sample of a larger population
what are the 2 ways gene flow can happen
- immigration
- emigration
what is emigration
the movement of individuals and their alleles out of a population, and thus out of a gene pool
what are 3 examples of ways bottleneck effect can occur
- a natural disaster
- a new disease to which the population has not previously been exposed
- human activity, such as destruction of habitat or large scale poaching.
gene flow definition
the movement of individuals and their genetic material between populations
what is immigration
the movement of individuals and their alleles into a population, and thus into a gene pool
what does gene flow do to genetic diversity
increases it
what does genetic drift do to genetic diversity
decreases it
what does natural selection do to genetic diversity
decreases it
what does founder effect do to genetic diversity
decreases it
what does bottleneck effect do to genetic diversity
decreases it
what does mutations do to genetic diversity
increases it
what is a mutation
a permanent alteration in the DNA sequence of a gene that leads to the formation of new alleles
what are mutagens
chemical or physical agent that can cause mutation in DNA
what are 3 examples of causations of mutations
- radiation (x-rays)
- chemicals (benzene)
- pathogenic (bacteria)
what has to happen to the mutation for it to come about (and in future populations)
it is first necessary that the mutation occur in the germline of an organism so that it may be passed to the next generation.
what are the 3 types of traits mutations can give
- advantageous
- neutral
- disadvantageous
what are point mutations
a mutation that affects a single nucleotide
what are the 2 types of missense mutations
- conservative
- non-conservative
what are the 2 types of point mutations
- substitution (silent, nonsense, missense)
- frameshift (insertion, deletion)
what are the 2 types of point frameshift mutations
- insertion
- deletion
what are the 3 types of point substitution mutations
- silent
- nonsense
- missense
what is a non-conservative missense mutation
a type of missense mutation in which the substituted amino acid is very different in properties to the initial amino acid
why are silent mutations possible
because DNA is degenerate
what are silent mutations
a type of mutation in which a single base change does not change the amino acid and final protein expressed
what are nonsense mutations
a type of mutation in which a single base change leads to a STOP signal being received, resulting in a truncated protein
what are missense mutations
a type of mutation in which a single base change leads to the change in the amino acid translated in the protein chain
what is a conservative missense mutation
a type of missense mutation in which the substituted amino acid is similar in properties to the initial amino acid
what are frameshift mutations
type of mutation in which, as a result of insertion or deletion of a base, all codons from that point are affected
what is a deletion mutation
A nucleotide deletion also causes a frameshift with all bases from the point of the deletion being moved back by one position to compensate for the deletion
what are insertion mutations
An insertion mutation occurs when one nucleotide base is added to a DNA strand
what happens in translocation of homologous chromosomes
part of the chromosome will join to another one
what is polyploidy
the entire genome is replicated (so instead of 2 of each chromosomes there may be 3 of every chromosome).
what are the 4 types of block mutations
- deletion of part of a chromosome
- duplication or gain of part of a chromosome
- translocation between non-homologous chromosomes
- inversion (when a segment of a chromosome rotates through 180 degrees)
what are some reason for why having low genetic diversity is not favourable (2)
- limit the population’s ability to adapt to changing environmental conditions,
- can make them vulnerable to becoming susceptible to disease and even to becoming extinct
what is artificial selection
the process by which humans breed animals or plants in such a way to increase the proportion of chosen phenotypic traits
what is aneuploidy
the loss or gain of a single chromosome
what are the 3 consequences of rapid genetic change of pathogens
- bacterial resistance
- antigenic drift (viruses)
- antigenic shift (viruses)
what is bacteria mainly becoming resistant to (that is not good)
antibiotics, because of the selection pressure of the antibiotics being present
what are the 4 steps in the mechanism of artificial selection (steps)
- There is variation within the population’s gene pool.
- Humans select individuals with a desirable trait.
- These individuals breed and pass their alleles on to the next generation.
- The alleles that lead to the desired phenotype will be inherited by subsequent generations and they can increase in frequency in the gene pool over time.
what is a selective breeding program
a process of mating that is not random, but uses parents chosen by the breeder on the basis of particular phenotypic characteristics that they display
what can artificial selection do (negatively)
can favour features that are disadvantageous for survival and reproduction and would be selected against in the wild (causing difficulty to survive)
what are 3 examples of why bacterial resistance increases
- poor hygiene (more bacteria present)
- not finishing antibiotic course
- over-prescribing of antibiotics
what are the consequences of bacteria becoming resistant of antibiotics
Diseases which could once be treated with a dose of antibiotics can now be life-threatening to individuals with an antibiotic-resistant strain of infection because the bacteria can continue to reproduce in the body.
what is antigenic shift
Antigenic shift occurs when two or more strains of a virus combine to form a new strain of the virus with antigens from each of the original strains.
what is antigenic drift
Antigenic drift is when a point mutation alters a virus’s nucleic material, resulting in small changes to its antigens.
what are the consequences of antigenic drift occurring to a virus
there will be a partial immune response (because of the memory B cells, creating antibodies)
what are the consequences of antigenic shift
Organism has no memory of pathogen so time will be required for adaptive response (illness is given)
why cannot vaccines be given to things such as influenza virus
because of antigenic shift and drift occurring changing the genetic material, so the vaccine needs to be changed regularly to combat this
what are the 3 types of fossils
- physical
- trace
- biosignatures
what are physical fossils
the remains of all or part of the structures of organisms, such as bones, teeth or leaves
what are 3 ways physical fossils are commonly formed as
- mineralised fossils
- fossils impressions
- preserved organism
what are fossil impressions
a physical fossil formed when the organic matter has disappeared but the organism has left an impression of its structure
what are mineralized fossils
a physical fossil formed when the organic material of the structure is replaced by minerals
what are preserved organisms
a physical fossil formed when an organism is completely preserved in a substance such as amber, ice or tar
what are biosignatures (fossils)
chemical or physical traces that can be inferred to have resulted from the action of life forms
what are trace fossils
preserved evidence of the activities of organisms, such as footprints, tooth marks, tracks, burrows and coprolite
what is an example of biosignatures
corrosion pits in rocks caused by chemosynthetic microbes
what are the 3 broad conditions to allow fossilisation to occur
- the remains are rapidly buried in sediments after death
- continued deposits of sediments bury it more and more deeply
- Over time the rock is eroded, uplifted through the movement of tectonic plates or excavated by palaeontologists so that the fossil is exposed
what is fossilisation
process of preserving parts of organisms that lived in the geological past
what are good climate conditions for fossils
- very cold environment
- low oxygen environments
what is faunal succession
the principle that fossilised fauna and flora in sedimentary rock strata are arranged vertically in a specific order
what are index fossils
fossils of geologically short-lived species that are widely distributed but are found in a restricted depth of rock strata
what are index fossils used for
to define a period of geological time
what are transitional fossils
the fossilised remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group
what are the 2 dating methods for fossils
- absolute dating
- relative dating
what are 2 methods to gain the relative age of fossils
- use of index fossils
- use of stratigraphic method (or faunal succession)
what is the most important method for estimating the absolute age of fossils
radiometric dating technique
what is the stratigraphic method
the method of obtaining the relative age of an object by its position within a given sequence of rock strata
what is the radiometric dating technique
a technique for obtaining an absolute age that depends on the known rate of decay of a radioactive parent isotope to a stable daughter product
what are isotopes
the different forms of an element which differ in the number of neutrons
how does the radiometric dating technique work?
- The radioactive isotopes, which can be called ‘parents’, spontaneously decay or break down over time to form stable ‘daughter’ products.
- The rate of the decay is specific for each radioactive isotope. This is usually measured in terms of half-life, the time taken for half the original radioactive isotope to decay.
what is an example of radiometric dating
carbon-dating
what is speciation
process of formation of new species
what is half life
the time taken for an amount of radioactive isotope to decay to half of its initial amount
what is post-zygotic isolation
barriers that prevent a fertile offspring developing after mating
what are the 2 methods of isolation
- pre-zygotic isolation
- post-zygotic isolation
what is pre-zygotic isolation
barriers that prevent an organism from finding and securing a mate
what are 2 examples of prezygotic isolation
- geographic isolation
- temporal isolation (active at night or day)
what 4 processes must occur to allow for speciation
- variation
- isolation
- selection
- genetic divergence
what are 2 examples of post-zygotic isolation
- incompatibility of gametes
- sterility of hybrid (hybrid produced is sterile)
what is genetic divergence
when two or more populations accumulate genetic changes, leading them to eventually be reproductively isolated
what is variation
differences exhibited among members of a population owing to the action of genes
what is selection
the process in which a variant is more advantageous under certain selective pressures, enhancing its chance of survival and reproduction
what are the 7 steps for speciation to occur (steps)
- variation appears in population
- breeding in population becomes isolated
- different characteristics emerge (from genetic drift, mutation or environmental pressure) to gain genetic divergence
- the environment changes and the organisms that are best suited survive
- survivors reproduce these traits to offspring
- the frequency of these genes rise
- the isolated population becomes quite different (new population)
what are the 2 types of speciation
- allopatric
- sympatric
what is allopatric speciation
speciation that occurs between two populations that are geographically isolated
what is sympatric speciation
speciation that occurs between two populations that have no geographical barrier between them
what are the 3 steps in allopatric speciation
- physical barrier separates the population (geographically isolated), and no gene flow occurs (begin to mutate differently)
- different environmental selection pressures appear (different phenotypes being selected by natural selection or genetic drift)
- over time they become new species and reproductively isolated
what is an example of allopatric speciation
Galapagos finches
what is an example of sympatric isolation
Howea palms trees
what are the 3 steps in sympatric speciation
- population isolated by pre-zygotic isolation barrier (other than geographic isolation, such as temporal or behavioural isolation) and some gene flow occurs
- Over many generations, genetic divergence occurs. Eventually the isolated populations respond differently to environmental selection pressures
- change significantly over time. become reproductively isolated and new species
what is reproductively isolated
the inability of species to breed and produce fertile offspring
how did the Howea palm trees become sympatrically isolated
The trees where different in when they flowered
Also in the soil they grew in (one prefered volcanic soil)
what are the 4 types of evidence to show relatedness
- structural morphology
- molecular homology
- biogeography
- developmental biology
what is structural morphology
the process of comparing similarities in body structures to infer relatedness
what is molecular homology
the process involved in comparing similarities in molecular structures to infer relatedness, with a particular focus on DNA and amino acid sequences
what is developmental biology
the process of comparing embryos of different species to infer relatedness
what is biogeography
geographical distribution of species
what are homologous structures
structures of organisms that have evolved from a common ancestor to have possible differences in form and function but retain similarities in structure
what are vestigial structures
non-functional structures that are remnants of functional structures in ancestral species
what are 2 examples of vestigial structures in humans
- goosebumps
- tailbone
what is a orthologous protein
gene or proteins derived from a shared ancestor in which the primary function is conserved
what is 2 examples of orthologous proteins
- cytochrome c
- haemoglobin
are species that have more amino acid differences more or less related
less related, as they have had more mutations to their amino acid sequences
what are the 2 ways to compare DNA
- direct comparison of DNA base sequences
- comparison of whole genomes
what is comparative genomics
the comparison of DNA or genes between different species to identify evolutionary relationships
what are phylogenetic trees
a branching diagram showing inferred evolutionary relationships between life forms based on their observed physical and genetic similarities and differences
what is the root (phylogenetic trees)
the common ancestor of all taxa on a phylogenetic tree (starting point)
what are the 5 features of a phylogenetic tree
- sister taxa
- root
- branches
- nodes
- tips
what is the sister taxa (phylogenetic trees)
two groups with a common ancestor that is not shared with another taxa
what is the node (phylogenetic trees)
shows an ancestor of two or more descendants on a phylogenetic tree (where the species split)
what are branches (phylogenetic trees)
a section of the phylogenetic tree which indicates a speciation event (coming off the node)
what are 5 main characteristics of mammals
- warm blooded
- milk-producing mammary glands
- three bones in the middle ear
- a lower jaw made of a single bone
- fur or hair over their body surface
what are tips (phylogenetic trees)
the terminal point of a phylogenetic tree, representing a particular species
what is the 7 level of hierarchy (groups of animals)
- kingdom
- phylum
- class
- order
- family
- genus
- species
what are primates
a group of mammals with opposable thumbs, flat nails and binocular vision
what are 4 groups of primates
- old world monkeys
- new world monkeys
- prosimians (lemurs)
- apes
what are 4 characteristics of primates
- opposable thumbs
- flat nails
- binocular vision
- large brain related to body size
what are hominoids
a superfamily of primates that lack a prehensile tail, including apes and humans
what are 4 characteristics of hominoids
- shoulder joints that permit arms to be rotated
- distinctive molar teeth in the lower jaw with five cusps
- larger and more complex brains
- no tail
what are hominins
modern human species and our extinct close relatives that could walk with a bipedal locomotion
what is bipedalism
a form of locomotion involving routine movement on two feet
what are 5 structures that are vital for bipedalism
- position of the hole (foramen magnum) in the base of the skull
- arrangement of the femur and tibia
- shape of the pelvis
- shape of the spine
- size of the heel bone and subsequent heel arch
what is the carrying angle
the angle formed between the femur and the vertical
where does the foramen magnum need to be positioned for bipedalism
the centre of the cranium (skull)
what is foramen magnum
a hole at the base of the skull in which the vertebral column attaches
does there need to be a carrying angle for bipedalism
yes between 8 and 11 degrees
shape of spine for bipedalism
more S shaped, compared to C
what are the 4 main genus that are classified as hominins
- Australopithecus
- Paranthropus
- Homo
- Ardipithecus
what are the 3 main trends observed from Australopithecus to Homo
- increase in the size of the cranium, including the height and the width of the skull, indicating that brain size also was increasing
- an increase in the length of feet with more developed arches
- an increase in leg length (a larger leg : arm ratio)
what are the 4 trends in limb structure of hominins (what changed)
- length of the legs (increase)
- angle of the legs (bipedal position)
- shape of the pelvis (long and narrow)
- shape of the foot (flat foot, with curved toes)
what is mitochondrial DNA (mtDNA)
DNA located on the mitochondria in cells that is usually inherited maternally
what are 3 differences between mtDNA and whole genome analysis
- mtDNA is only inherited by mother, genome is both parents
- mtDNA has fewer bases
- mtDNA has faster mutation rate
what are 2 advantages of using mtDNA for analysis
- constant rate of mutation
- high copy number per cell
what is interbreeding
breeding between two species
what are 3 advantages of using nuclear DNA for analysis
- more bases (more info)
- from both parents so can see if interbreeding occured
- introns are there so can reveal more inherited mutations
what is mtDNA’s non coding region called
D loop
what is a haplotype
a region of DNA in the D-loop of mtDNA that varies between individuals
what are the 3 ethical approaches
- consequences-based
- duties or rules-based
- virtues-based
what is the consequence based approach
this approach places important on the consideration of the consequences of an action, with the aim to get the most positive outcomes and least negative ones
what is the rules/duties-based approach
places importance on the idea that people have duty to act in a particular way (follow the rules)
what is the virtues-based approach
consideration is given to the virtue or moral character of the person carrying out the action (did they try to do the right thing)
what are the 5 ethical concepts
- integrity
- non-maleficence
- justice
- beneficence
- respect
what is integrity
commitment for searching for knowledge and understanding that they have to share all their results
what is justice
moral obligation to ensure that there is fair consideration of all competing claims; no unfair burden on specific group
what is beneficence
maximising benefits and minimising risks
what is non-maleficence
involves avoiding the causations of harm
what is respect
consideration that all living things have intrinsic value (need to consider everything, animals, plants, etc.)
what are independent variables
the variable that is changed or manipulated by an investigator
what are dependant variables
the variable that is influenced by the independent variable and is measured by an investigator
what are controlled variables
variables that are kept constant across different experimental groups
what is aim (of an experiement)
a statement outlining the purpose of an investigation, linking the dependent and independent variables
what is a hypothesis
a tentative, testable and falsifiable statement for an observed phenomenon that acts as a prediction for the investigation
what is it meant my ‘tentative’ hypothesis
not fixed or certain, may be changed with new information
what is it meant my ‘falsifiable’ hypothesis
able to be proven false using evidence
what is it meant my ‘testable’ hypothesis
able to be supported or proven false through the use of observations and investigation
is what a control group
a group that is not affected by the independent variable and is used as a baseline for comparison
what is precision
how close multiple measurements of the same investigation are to each other
what is accuracy
how close an experimental measurement is to a known value
what is primary data
direct or firsthand evidence obtained from investigations or observations
what is secondary data
comments on or summaries and interpretations of primary data
what is qualitative data
data that has labels or categories rather that numberical quantities; also known as categorical data
what is the two types of qualitative data
- nominal
- ordinal
what is nominal data
a type of qualitative data that has no logical sequence
what is ordinal data
a type of qualitative data that can be ordered or ranked
what is quantitative data
numerical data that examines the quantity of something (e.g. length or time); also known as numerical data
what are the 2 types of quantitative data
- continuous
- discrete
what is continuous data
a type of quantitative data that can take on any continuous value
what is discrete data
a type of quantitative data that can only take on set values
what is repeatability
how close the results of successive measurements are to each other in the exact same conditions
what is reproducibility
how close results are when the same variable is being measured but under different conditions
what is reliability
the consistency of a measurement across multiple trials
what is validity
credibility of the research results from experiments or from observation; a measure of how accurately and precisely results measure what they are intending to measure through fair testing
what are the 3 types of errors (for an experiment)
- personal
- random
- systematic
what are personal errors
human errors or mistakes that can affect results but should not be included in analysis
what are random errors
chance variations in measurements
what are systematic errors
errors, usually due to equipment or system errors, that affect the accuracy of a measurement and cannot be improved by repeating an experiment.
