Module 2 notes Flashcards
(182 cards)
1
Q
light microscope
A
- poor resolution, long wavelength
- living samples, colour image
2
Q
TEM (transmission electron microscope)
A
- high magnification & resolution
- electrons pass through specimen
3
Q
SEM (scanning electron microscope)
A
- high magnification & resolution
- electrons bounce off surface of specimen
4
Q
laser scanning confocal microscope
A
- high resolution, 3D imaging
- laser light
5
Q
resolution
A
minimum distance between 2 objects in which they can still be viewed as separate
6
Q
magnification
A
how many times larger the image is compared to the object
7
Q
slide preparation for light microscopes
A
- dry mount- slices or whole specimens viewed, with just coverslip placed on top, e.g. plant tissue or hair
- wet mount- water or stain added to specimen before lowering coverslip with mounted needle to prevent air bubbles forming, e.g. aquatic organisms
- squash slide- wet mounts which you push down on the coverslip to squash sample and get thin layer, e.g. root tip squash- mitosis
- smear slide- placing a drop of sample at one end of slide and using edge of another slide at angle to smear sample across slide- coverslip placed on top, e.g. blood cells
8
Q
eye piece graticule
A
used to measure the size of objects you are viewing under the microscope
9
Q
magnification calculation
A
magnification = size of image/size of real object
10
Q
differential staining
A
many chemical stains used to stain different parts of a cell in different colours
11
Q
examples of stains
A
- crystal violet or methylene blue- positively charged so stain negatively charged materials
- nigrosin and congo red- negatively charged so cannot enter cells as cytosol repels them- creates stained background so unstained cells stand out
12
Q
electron microscopes
A
- a beam of electrons has a very short wavelength which gives high resolution- meaning that small organelles and internal structures can be visualised
- image created using electromagnet to focus beam of negatively charged electrons
- electrons absorved by air- EM must be in vacuum to prevent this- therefore can’t examine living specimens
- image black and white
13
Q
TEM
A
- thin specimens stained and placed in vacuum
- electron gun produces beam of electrons that passes through specimen
- some parts of specimen absorb electrons- appear darker
- image produced is 2D- detailed images of internal structure of cells
14
Q
SEM
A
- specimens don’t need to be thin as electrons beamed onto surface and scattered in different ways depending on contours
- produces 3D image of surface of specimen
15
Q
structure of nucleus
A
- nuclear envelope- double membrane
- nuclear pores
- nucleoplasm- granular, jelly-like material
- chromosomes- protein-bound, linear DNA
- nucleolus- smaller sphere inside which is site of rRNA production and makes ribosomes
16
Q
function of nucleus
A
- site of DNA replication and transcription (making mRNA)
- contains the DNA for each cell
- site of ribosome synthesis
17
Q
structure of flagella
A
- whip like structure
18
Q
function of flagella
A
- for mobility, and sometimes as a sensory organelle for chemical stimuli
19
Q
stucture of cilia
A
- hairlike projections out of cells
20
Q
function of cilia
A
- can be mobile or stationary
- mobile help move substances in sweeping motion
- stationary are important in sensory organs such as nose
21
Q
structure of centrioles
A
- made of microtubules
- occur in pairs to form centrosome
22
Q
fucntion of centrioles
A
- involved in production of spindle fibre and organisation of chromosomes in cell division
23
Q
stucture of cytoskeleton
A
- network of fibres found within the cytoplasm all over a cell
- consists of microfilaments, microtubules and intermediate fibres
24
Q
function of cytoskeleton
A
- provides mechanical strength to cells, helps maintain the shape and stability of a cell
- many organelles are bound to cytoskelton
- microfilaments are responsible for cell movement
- microtubules are responsible for creating a scaffold-like structure
- intermediate fibres provide mechanical strength
25
structure of endoplasmic reticulum
- rough and smooth both have folded membranes called cisternae
- rough have ribosomes on cisternae
26
function of endoplasmic reticulum
- RER- protein synthesis for proteins destined to leave cell, proteins transported through RER and into secretory vesicles
- SER- synthesis and store lipids and carbohydrates
27
structure of golgi apparatus and vesicles
- folded membranes making cisternae
- secretory vesicles pinch off from cisternae
28
function of golgi apparatus and vesicles
- add carbohydrates to proteins to form glycoproteins
- produce secretory enzymes
- secrete carbodhydrates
- transport, modify and store lipids
- form lysosomes
- molecules 'labelled' with their destination
- finsihed products are transported to cell surface membrane in secretory vesicles where they fuse with membrane and contents are released
29
structure of lysosomes
- bags of digestiv enzymes- can contain 50 different enzymes
30
function of lysosomes
- hydrolyse phagocytic cells
- completely break down dead cells (autolysis)
- exocytosis- release enzymes to outside of cell to destroy material
- digest worn out organelles for reuse of materials
31
stucutre of mitochondria
- double membrane
- inner membrane called the cristae
- fluid centre called the mitochondrial matrix
- loop of mitochondria DNA
32
function of mitochondria
- site of aerobic respiration
- site of ATP production
- DNA to code for enzymes needed in respiration
33
stucture of ribosomes
- small, made up of 2 sub-units of protein and rRNA
- 80s- large, found in eukaryotic cells
- 70s- smaller, found in prokaryotic cells, mitochondria and chloroplasts
34
function of ribosomes
- site of protein synthesis
35
structure of chloroplasts
- surrounded by a double membrane
- contains thylakoids (folded membranes embredded with pigment)
- fluid filled stroma contains enzymes for photosynthesis
- found in plants
36
function of chloroplasts
- site of photosynthesis
37
structure of cell wall
- in plants and fungi cells
- plants- made of microfibrils of cellulose polymer
- fungi- made of chitin, a nitrogen-containing polysaccharide
38
function of cell wall
- provide structural strength to the cell
39
structure of plasma membrane
- found in all cells
- phospholipid bilayer- molecules embed within and attached on the outside (proteins, carbohydrates, cholesterol)
40
function of plasma membrane
- controls the entracne and exit of molecules
41
production and secretion of proteins
1. polypeptide chains are synthesised on the RER (ribosomes on outside)
2. these polypeptide chains move to the cisternae in the RER and are packaged into vesicles to be sent to the Golgi apparatus via the cytoskeleton
3. in the Golgi apparatus, the proteins are modified and packaged into vesicles
4. the secretory vesicles carry the proteins to the cell surface membreane, where it fuses and releases the protein by exocytosis
42
prokaryotic vs eukaryotic cells
- prokaryotic much smaller
- prokaryotic have no membrane bound-organelles
- prokaryotic have smaller ribosomes- 70s
- DNA in prokaryotic cell not contained within nucleus
- prokaryotic cells have cell wall made of peptidoglycan
- some prokaryotic cells contain plasmids, capsule around cell and a flagella
43
plasmids
- small loops of DNA which only carry a few genes
- occur in varying numbers
44
capsule
- slimy layer made of protein
- prevents bacteria from desiccating (drying out) and protects bacteria against host's immune system
45
biological molecules
- all contain carbon
- carbohydrates- C, H, O
- lipids- C, H, O
- proteins- C, H, O, N, S
- nucleic acids- C, H, O, N, P
46
examples of cations
- calcium ions (Ca^2+)- involved in muscle contraction and nerve impulse transmission
- sodium ions (NA+)- involved in co-transport, reabsorption of water in the kidney, regulating water potential and nerves impulse transmission
- potassium ions (K+)- involved in stomatal opening and nerve impulse transmission
- hydrogen ions (H+)- involved in chemiosmosis, regulating pH and translocation
- ammonium ions (NH4+)- involved in nitrogen cycle, where by bacteria convert ammonium ions into nitrate ions
47
examples of anions
- nitrate (NO3-)- mineral ion absorbed by plants to provide a source of nitrogen to make amino acids
- hydrogencarbonate (HCO3-)- involved in the transport of carbon dioxide in the blood
- chloride (Cl-)- involved in the transport of carbon doxide in the blood as they are part of the chloride shift to balance positive charges
- phosphate (PO4^3-)- involved in the formation of phospholipids for cell membranes, nucleic acid and ATP formation
- hydroxide (OH-)- involved in the catalysis of reactions and regulating pH
48
water
- polar due to unevenly distributed charge
- hydrogen bonds form between oxygen and hydrogen atom as positive and negative regions interact with each other
- individual hyrdogen bonds are weak but collectively provide strength
49
# properties of water
water as a solvent
- polar (hydrophillic), or charged molecules dissolve readily in water due to the fact water is polar
- the slight positive charge on hydrogen atoms will attract any negative solutes and the slight negative charge on oxygen atoms of water will attract any positive ions in solutes
- non-polar (hydrophobic) molecules cannot dissolve in water and are repelled by water
- the cytosol in eukaryotic and prokaryotic cells is mainly water, so this ensures many solutes can dissolve within the cell and then be easily transported
50
# properties of water
water as a transport medium
- polar substances dissolve and are easily transported in water around animals and plants, either in the blood of animals or xylem of plants, to cells they are needed in inside of the organism
- due to cohesion, when water moves up the xylem in plants due to transpiration it is as a continuous column of water
51
cohesion
water molecules 'sticking' together by hyrdogen bonds
52
# properties of water
water as a coolant
- water has a high specfic heat capacity (lots of energy is required to raise temperature of water) due to energy required to break the hydrogen bonds between water molecules
- internal temperatures of plants and animals should remain relatively constant- ensures enzymes effective
- large latent heat of vaporisation (a lot of energy is required to convert water in its liquid state to a gaseous state) due energy required to break the hydrogen bonds between water molecules to turn it into a gas
53
# properties of water
water as a habitat
- water buffers temperature means it provides a stable environment, in terms of temperature, for aquatic organisms
- cohesion provides surface tenstion to water- enables small invertebrates to move and live on surface, providing them a habitat away from predators within water
- ice is less dense than liquid water due to hydrogen bonds so ice floats on top of water, providing surface habitat for animals and insulating the water below keeping it a liquid for aquatic organisms
54
monomer
smaller units which can create larger molecules (polymers)
55
polymer
made from lots of monomers bonded together
56
examples of monomers & polymers
- glucose --> starch, cellulose, glycogen
- amino acid --> protein
- nucleotide --> DNA and RNA
57
examples of monosaccharides
- glucose
- ribose
- fructose
58
examples of disaccharides
- sucrose
- maltose
- lactose
59
examples of polysaccharides
- starch
- cellulose
- glycogen
60
disaccharides
- made of 2 monosaccharides
- joined together by a glycosidic bond
- formed via a condensation reaction
- e.g. aglucose + aglucose --> maltose + water
- e.g. aglucose + galactose --> lactose + water
- e.g. bglucose +fructose --> sucrose + water
61
condensation reaction
joining two moleucles together by removing a water molecule
62
hydrolysis reaction
splitting apart molecules through the addition of a water molecule
63
polysaccharide
created by condensation reactions between many glucose monomers
64
starch
- alpha glucose
- 1-4 glycosidic bonds in amylose
- 1-4 and 1-6 glycosidic bonds in amylopectin
- store of glucose
- found in plant cells, e.g. chloroplast
- made of 2 polymers: amylose- unbranched helix and amylopectin- branched molecule
65
cellulose
- beta glucose
- 1-4 glycosidic bonds
- stucture strenght for cell wall
- found in plants in cell wall
- polymer forms long, straight chains which are held in parallel by many hydrogen bonds to form fibrils
- macrofibrils combine to form a cellulose fibre
66
glycogen
- alpha glucose
- 1-4 and 1-6 glycosidic bonds
- store of glucose
- found in animals- mainly in muscle and liver cells
- a highly branched molecule
67
lipids
- macromolecules- not polymers
- non-polar
- insoluble in water
- dissolve in organic solvents, such as ethanol
- hydrophobic
- made up of 2 molecules, fatty acids and glycerol
68
structure triglycerides
- glycerol and 3 fatty acids
- formed via condensation between one molecule of glycerol and 3 molecules of fatty acid
- forms 3 ester bonds
69
properties of triglycerides
- can transfer energy due to the large ratio of energy-storing carbon-hydrogen bonds compared to the number of carbon atoms, a lot of energy can be transferred when it is broken down
- due to high ratio of hydrogen to oxygen atoms they can act as a metabolic water source because they can release water if they are oxidised- essential for animals in the desert
- as lipids are large, hydrophobic molecules they are insoluble in water- won't affect water potential and osmosis
- lipids are relatively low in mass so can be stored in an animal without it increasing the mass and preventing movement
70
phospholipids
- glycerol, 2 fatty acids and a phosphate group
- 2 fatty acids bond to glycerol via 2 condensation reactions, resulting in 2 ester bonds
71
properties of phospholipids
- hydrophilic 'head' of a phospholipid can attract water as it is charged
- due to phosphate being charged, it repels other fats
- fatty acid chain is not charged- known as hydrophobic 'tail' and it repels water, but will mix with fats
- have 2 differently charged regions, so they are polar
- in water they are positioned so that the heads are exposed to water and the tails are not
- this forms a phospholipid bilayer membrane structure which makes up the plasma membrane around cells
72
saturated fatty acids
hydrocarbon chain has only single bonds between carbons
73
unsaturated fatty acids
hydrcarbon chain consists of at least one double bond between carbons
74
cholesterol
- a sterol
- sterols have 4 carbon rings and a hydroxyl group at one end and they have both hydrophobic and hydrophillic regions
- cholesterol is embredded within cell membranes to impact fluidity
- they help reduce the fluidity of membranes at high temperatures and increase fluidity at low temperatures
75
protein
made up of one or more large polymers, creating a macromolecule
contains an amino group, a carboxyl group and an R group (variable group)
76
4 levels of structure in a protein
- primary
- secondary
- tertiary
- quaternary
77
primary structure of a protein
the order/sequence of the amino acids in the polypeptide chain
78
secondary structure of a protein
* the sequence of amino acids causes parts of a protein molecule to beind into alpha helix shapes of fold into beta pleated sheets
* hydrogen bonds hold the secondary structure
79
tertiary structure of a protein
* the secondary structure is bent and folded to form a precise 3D shape
* help in place by: hydrophobic and hydrophillic interactions (weak), hydrogen bonds (weak), ionic bonds (stronger), disulfide bonds (strong)
* ionic and disulfide bonds form between the R groups of different amino acids
* disulfide bonds only sometimes occur, as there must be a sulfur in the R groups for this bond to occur
80
quaternary structure of a protein
- a protein made up of more than one polypeptide chain
- e.g. haemoglobin- made of 4 polypeptide chains, has prosthetic group containing iron --> described as a conjugated protein
81
fibrous proteins
- long rope-like shape
- polypeptide chains form long twisted strands linked together
- stable (unreactive) structure
- form hydrogen bonds with adjacent chains
- insoluble in water
- stength gives structural function
- e.g. collagen in bone and keratin in hair
82
# examples of fibrous proteins
collagen
* forms part of skin, tendons, cartilage, ligaments, bone, and connective tissue in the bronchi, broncioles and tranchea
* its quaternary structure contains 3 polypeptide chains, wound around each other like a rope
* the chains are held by hydrogen and covalent crosslinks between the molecules
* the crosslinks are staggered for strength and chains lie close each other due to 35% of its a acids being glycine (the smallest)
* flexible but not stetchy
83
# examples of fibrous proteins
keratin
* used to form skin, nails and hair, which all protect the body
* insoluble so structures not broken down by water in the environment
84
# examples of fibrous proteins
elastin
* makes up elastic fibres around alveoli and blood vessels (arteries, arterioles, venules and veins)
* allows these structures to stretch and recoil to their original shape and size
85
globular proteins
- spherical shape
- polypeptide chains 'roll up' into a spherical shape
- relatively unstable structure
- have hydrophobic R groups on the inside and hydrophillic R groups on the outside
- soluble
- metabolic functions
- e.g. all enzymes, antibodies, some hormones (e.g. insulin), haemoglobin
86
# examples of globular proteins
haemoglobin
* responsible for transport of oxygen
* 4 polypeptide chains (2 alpha and 2 beta) each bind to one molecule of oxygen due to its prothetic haem group
87
# examples of globular proteins
enzymes
* e.g. pepsin found in the stomach
* protease enzyme, able to digest other proteins using its specifically shaped active site which is complementary to its substrate
88
# examples of globular proteins
insulin
* hormone produced by the beta cells in the pancreas to lower blood glucose concentration
* specific 3D shape is complementary to the receptors on the cell surface membranes of its target cells (liver and muscle cells)
89
test for starch
1. add iodine solution
2. positive test observation= solution turns from orange to blue-black
90
test for reducing sugars
1. add Benedict's solution and heat for 5 mins at 80ºC
2. positive test observation= solution turns from blue to green, yellow, orange or brick red (the more red the higher the concentration of reducing sugar)
- reagent test strips can also be used to test for presence and concentration
91
test for non-reducing sugars
1. following a negative Benedict's test result- solution remains blue
2. add hydrochloric acid and boil (acid hydrolysis)
3. cool the solution then add an alkali (sodium hydroxide) to neutralise
4. add Benedict's solution and heat for 5 mins at 80ºC
5. positive test observation= solutions turns from blue to green, yellow, orange or brick red (the more red the higher the concentration)
92
test for proteins
1. add biuret solution
2. positive test observation= solution turns from blue to purple
93
test for lipids- emulsion test
1. dissolve sample in ethanol
2. pour sample on top of distilled water
3. positive test observation= white emulsion forms
94
colorimeter method
1. set filter in colorimeter
2. calibrate to zero using distilled water
3. insert samples from your biochemical test (e.g. different concentrations of glucose with Benedict's solution, and filter to remove precipitates)
4. measure the percentage transmission of light
5. draw a calibration curve using the results from known concentrations of glucose
95
biosensors
1. a single strand of DNA or protein, which are complementary to the test samepl, is immobilised. When the sample is added, it will bind to the immobilised DNA/protein
2. this binding causes a change in a transduce and as a result, an electronic current is released
3. this current is processed to determine the concentration of the sample present
96
chromatography
- practical investigations into the separation of proteins, carbohydrates, vitamins or nucleic acids can be conducted using thin-layer chromatography (TLC) or paper chromatography
- there is a stationary phase (paper) and a mobile phase (solvent)
- concentrated sample is placed 1cm from end of paper which is then placed in a beaker with less than 1cm depth of solvent. As solvent moves up paper, it has an affinity for the biological molecules and dissolves them, carrying them up the paper
97
retention factor value
- molecules that are most soluble will be carried furthest
Rf= distance moved by solute/distance moved by solvent
98
nucleotides
the monomers from which nucleic acids, like DNA and RNA are formed
99
2 nitrogenous bases
* purines- 2 carbon ring structures (adenine & guanine)
* pyrimidines- 1 carbon ring structure (cytosine, thymine & uracil)
100
complementary bases
thymine (uracil in RNA) -- adenine
guanine -- cytosine
101
condensation reactions of DNA and RNA nucleotides
- forms phosphodiester bonds between the nucleotide monomers, to create the polymer
- polymer is called a polynucleotide
- phosphodiester bond is a strong covalent bond that forms between the pentose sugar and phosphae of different nucleotides
102
ATP
- contains 3 phosphate ions that play a significant role in energy transfer
- essential for metabolism
- immediate source of energy
- composed of adenine, ribose and 3 phosphate groups
- made during respiration via condensation reaction using enzyme ATP synthase
- ATP is hydrolysed using enzyme ATP hydrolase
- breaking one of bonds between phosphate groups releases a small amount of energy
- the inorganic phosphate released can bond onto completely different compounds to make them more reaction (phosphorylation)
103
DNA
* deoxyribonucleic acid codes for the sequence of amino acids in the primary structure of a protein, which determines the final 3D structure and function of a protein
* polymer forms a double helix made of 2 antiparallel strands joined togtehr by hydrogen bonds between the bases on the 2 different strands
* stable structure due to sugar-phosphate backbone (covalent bonds) and double helix
* double-stranded so replication can occur using both strands as a template
* weak hyrdogen bonds between the bases for easy separation of the 2 strands in a double helix during replication
* a large molecule that carries a lot of information
* complementary base pairing allows identical copies to be made
104
DNA precipitation
1. homogenise the cell with a detergent. This will break open the cells and cell membranes to release their contents
2. filter to remove large debris
3. add salt to break hydrogen bonds between the DNA and water molecules
4. add protease to digest the proteins associated with the DNA
5. add ice-cold ethanol to precipitate out the DNA from the solution. The DNA appears as white strands
105
3 types of RNA
- mRNA (messenger)
- tRNA (transfer)
- rRNA (ribosomal)
106
rRNA
makes up bulk of ribosomes
107
mRNA
* copy of one gene from DNA
* created in nucleus and it leaves via the nuclear pore to carry the copy of the genetic code of one gene to a ribosome in the cytoplasm
* much shorter than DNA
* short-lived
* single-stranded and every 3 bases (codon) in the sequence code for 1 specific amino acid
108
tRNA
- found in the cytoplasm
- single-stranded but folded to create a cloverleaf shape held in place by hydrogen bonds
- brings a specific amino acid to the ribosome
- this is determined by 3 bases found on the tRNA (anticodon) which are complementary to the 3 bases on mRNA (codon)
109
semi-conservative DNA replication
* one strand is conserved and one new strand is created
* copying errors can occur randomly and spontaneously, resulting in a change to the DNA base sequence, known as a mutation
* replication occurs in S-phase in interphase of the cell cycle
* when describing the DNA double helix, the top and bottom of each strand are described as either the 3' end or the 5' end
* enzyme that catalyses DNA replication is complementary in shape to the 3' end- can only attach to DNA at this location
110
stages of DNA replication
1. DNA helicase breaks the hydrogen bonds between the complementary bases of the 2 DNA polymers causes the double helix to unwind and the 2 strands to separate
2. both strands act as templates for DNA replication
3. free-floating DNA nucleotides align opposite their complementary base on the template strand of DNA. Hydrogen bonds will form between the base pairs
4. DNA polymerase joins adjacent DNA nucleotides together, forming a phosphodiester bond between these nucleotides to create a new polymer chain of DNA
111
3 features of the genetic code
* degenerate- amino acids are coded for by more than one triple of bases
* universal- the same triplet of bases codes for the same amino acid in all organisms
* non-overlapping- each base in a gene is only part of one triplet of bases that codes for one amino acid. Each codon, or triplet of bases, is read as a discrete unit
112
2 stages of protein synthesis
1. transcription- where the DNA sequence for one gene is copied into mRNA
2. translation- where the mRNA joins with a ribosome (made of protein and rRNA), and a corresponding tRNA molecule brings the specific amino acid the codon codes for
113
introns
sequences of bases in a gene that do not code for amino acids and therefore polypeptide chains. These get removed, spliced, out of mRNA molecules after transcription
114
exons
sequences of bases in a gene that code for sequence of amino acids
115
start and stop codons
* at the start of every gene, there is a start codon, which enables the ribosome to attach
* at the end of every gene, there are 3 bases that do not code for an amino acid and this is called the stop codon- this stop codon causes the ribosome to detach and therefore ends translation
116
transcription
- DNA helicase breaks the hydrogen bonds between the bases in the 2 strands of DNA
- this causes the DNA helix to unwind and one strand acts as a template
- free mRNA nucleotides align opposite exposed complementary DNA bases
- the enzyme RNA polymerase joins together the adjacent RNA nucleotides, forming phosphodiester bonds, to create a new mRNA polymer chain
- once one gene is copied, the mRNA is modified and then leaves the nucleus through the nuclear envelope pores
117
translation
- once the modified mRNA has left the nucleus it attaches to the small subunit of the ribosome at the start codon
- the tRNA molecule with the complementary anticodon to the start codon aligns opposite the mRNA, held in place by the ribosome. The ribosome can hold 2 tRNA molecules at a time
- the 2 amino acids that have been delivered by the tRNA molecule are joined together via a peptide bond which is catalysed by an enzyme using ATP
- the ribosome will move along the mRNA molecule to the next codon and another complementary tRNA will attach to the next codon on the mRNA
- this continues until the ribosome reaches the stop codon at the end of the mRNA molecule causing the ribosome to detach and ends translation
- the polypeptide chain is now created and will enter the Golgi body for folding and modification
118
enzymes
- biological catalysts made of globular proteins
- active site is specific and unique in shape due to the specific folding and bonding in the tertiary structure of the protein
- due to this specific shape active site, enzymes can only attach to substrates that are complementary in shape
- enzymes catalyse intracellular and extracellular reactions, e.g catalase is an intracellular enzyme inside liver cells that breaks down hydrogen peroxide into oxygen and water. Trypsin is an extracellular enzyme, in the small intestines, that hydrolyses proteins
119
activation energy
the minimum amount of energy needed for a reaction to take place
120
lock and key model hypothesis
- suggest the enzyme is like a lock and the substrate is like a key that fits into it due to the enzyme's specific tertiary structure
- enzyme active site is a fixed shape and due to random collision the substrate can collide and attach to the enzyme, forming an enzyme-substrate complex and the charged groups within the active site are thought to distort the substrate and therefore lower the activation energy
121
induced fit hypothesis
- suggests that the enzyme is like a glove and the substrate is like your hand
- the enzyme active site is induced, or slightly changes shape, to mould around the substrate. When the enzyme-substrate complex occurs it puts strain on the bonds and therefore lowers the activation energy
122
4 factors affecting enzymes
- temperature
- pH
- enzyme concentration
- substrate concentration
123
# factors affecting enzymes
temperature
- if temp too low, insufficient kinetic energy for successful collisions
- as temp increases, frequency of successful collions increases
- if temperature too high enzymes denature, active site changes shape and enzyme-complexes cannot form
- high temperatures causes bonds to break and the tertiary structure alters, causng a change in the shape of the active site
124
Q10 temperature coefficient
* a measure of the rate of change of an enzyme-controlled reaction as a result of increasing the temperature by 10ºC
Q10= R2/R1
R1: rate of reaction at temp of XºC
R2: rate of reaction at temp of (X+10)ºC
125
# factors affecting enzymes
pH
- too high or too low will interfere with charges in amino acids in active site
- causes (ionic/hydrogen) bonds to break
- alters tertiary structure and chnages shap of active site and enzyme denatures
- enzymes have different optimal pH values that they work at
126
# factors affecting enzymes
enzyme concentration
- at low enzyme concentrations, there will be a lower rate of reaction
- increasing the enzyme concentration will increase the rate of reaction as enzyme-substrate complexes will be more likely to form
- at high enzyme concentrations, unless unlimited substrate is added, the rate of reaction plateaus as there will be insufficient substrate to bind with the large number of enzymes
127
# factors affecting enzymes
substrate concentration
- if there is a low concentration of substrate, the reaction will be lower as there will be fewer collisions between the enzyme and substrate
- increasing substrate concentration will increase rate of reaction
- at high substrate concentrations rate of reaction will plateau as all enzyme active sites are in use (enzymes are saturated)
128
competitive inhibitors
- similar shape to the substrate and complementary in shape to the active site. Therefore they bind to the active site
- this prevents the substrate from binding and enzyme-inhibitor complexes form instead of enzyme-substrate complexes and the rate of reaction is lower
- most competitive inhibitors are reversible (can be removed)
- if a high enough concentration of substrate is added, the substrate can knock out the inhibitor and therefore the rate of reaction will increase
129
non-competitive inhibitors
- bind to the enzyme away from the active site called the allosteric site
- this causes the active site to change shape, and therefore the substrate can no longer bind, regardless of how much substrate is added
- enzyme-substrate complexes form less frequently and the rate of reaction is much lower
130
end-product inhibition
- the products of some reactions are reversible inhibitors for the enzymes involved in controlling the reaction
- this enables the reactions to be controlled
- if there is a lot of product present, it will inhibit the enzymes and cause the reaction to slow or stop
- this prevents resources from being wasted
131
coenzymes and cofactors
- some reactions require atoms to be carried from one reaction to the next in multi-step pathway reactions
- some enzymes also required a non-protein molecule to bind to the active site to make it complementary to the substrate
- these molecules are cofactors and coenzymes
- the difference is coenzymes are organic molecules and cofactors are ignorganic molecules
132
prosthetic groups
- a type of cofactor
- permanently attached to the enzyme by covalent or non-covalent forces
133
precursor activation
- enzymes often occur in an inactive form and reauire activation by a cofactor
- this prevents enzymes from causing damage within cells and ensures they are only used when they are needed
- an enzyme is activated by the binding of a cofactor, as this causes a change in the tertiary structure so that the active site becomes complementary in shape to its substrate
- the precursor protein (the inactive enzyme) is known as the apoenzyme. When it is activated by the binding of the cofactor it is known as the haloenzyme
134
biological membranes
- all cells and organelle membranes are composed of a phospholipid bilayer
- plasma membranes provide a partially permeable membrane, are the site of chemical reactions and have a role in cell communication
135
fluid-mosaic model
- phospholipids align as bilayer due to hydrophillic heads being attracted to water and hydrophobic tails being repelled by water
- proteins within the cell surface membrane can be extrinsic and intrinsic
- extrinsic proteins provide mechanical support, or they make glycoproteins and glycolipids, function is cell recognition
- intrinsic proteins are protein carriers or channel proteins involved in transport of molecules across the membrane
- protein channels form tubes that fill with water to enable water-soluble ions to diffuse, whereas the carrier proteins will bind with other ions and larger molecules, such as glucose and amino acids, and change shape to transport them to the other side of the membrane
- cholesterol is present in some membranes and this restricts the lateral movement of other molecules in the membrane. This is useful as it makes the membrane less fluid at high temperatures and prevents water and dissolved ions from leaking out of the cell
136
# factors affecting membrane structure and permeability
temperature
- high temperatures increase the kinetic energy of the phospholipids so that they move even more
- this increases the fluidity of the membrane, increasing the permeability and the structure can start to break
- this makes it easier for particles to cross the membrane
- high temperatures also denature carrier and channel proteins in the membrane
137
# factors affecting membrane structure and permeability
solvents
- organic solvents, like alcohol, dissolve the phospholipid bilayer in membranes
- this damage causes the fluidity of the membrane to increase and become more permeable
138
simple diffusion
- the net movement of molecules from an area of higher concentration to an area of lower concentration until equilibrium is reached
- does not require ATP
- for molecules to diffuse across the membrane they must be lipid soluble and small
139
facilitated diffusion
- a passive process, down the concentration gradient, through proteins
- the movement of ions and polar molecules, which cannot simply diffuse, can be transported across membranes by facilitated diffusion using protein channels and carrier proteins
140
osmosis
the movement of water from an area of higher water potential to an area of lower water potential (more negative) across a partially permeable membrane
141
types of solution
* isotonic- water potential of solution is same in solution and cell within solution
* hypotonic- water potential of solution is more positive (closer to 0) than cell - causes cell to swell
* hypertonic- water potential of solution is more negative than cell - causes cell to shrink
142
active transport
- the movement of molecules and ions from an area of lower concentration to an area of higher concentration (against concentration gradient) using ATP and carrier proteins
- selective, only certain molecules can bind to receptor site on carrier proteins. ATP will bind to the protein on the inside of the membrane and is hydrolysed into ADP and Pi
- this causes the protein to change shape and open towards the inside of the membrane
- this causes the molecule to be released on the other side of the membrane
- the Pi molecule is then released from the protein, and this results in the protein reverting to its original shape
143
endocytosis
- a type of active transport, the bulk transport of molecules into a cell
- cell surface membrane bends inwards around the molecule surrounding it to form a vesicle
- the vesicle pinches off and moves within the cytoplasm
- endocytosis can be classed as either phagocytosis when it is a solid particle being taken in, or pinocytosis when it is a liquid being taken in
- this requires energy from ATP for the cell to engulf and change shape around the material
144
exocytosis
- bulk transport of molecules out of a cell
- vesicles move toward the cell-surface membrane, fuse with the membrane and the content of the vesicle is released outside of the cell
- this process requires energy because ATP is needed to move the vesicle along the cytoskeleton
145
cell division
- eukaryotic cells enter the cell cycle and divide by mitosis or meiosis
- prokaryotic cells replicate by binary fission
- viruses do not undergo cell division as they are non-living
146
3 stages of cell cycle
- interphase (G1, S, G2)
- nuclear division (mitosis or meiosis)
- cytokinesis
147
interphase G1
- protein synthesis occurs to make proteins involved in synthesising organelles
- organelles replicate
- there is a checkpoint at the end of G1
- cell is checked that it is the correct size and that there is no damaged DNA
- if a cell doesn't pass these checks replication will not continue and apoptosis may occur
148
interphase S
- DNA is replicated
149
interphase G2
- cell continues to grow, energy stores increase and the newly replicated DNA is checked for copying errors (DNA damage) at another checkpoint
- if the DNA is damaged, the cell will attempt to repair the DNA
150
mitosis
- creates 2 genetically identical diploid cells and is used fro growth, tissue repair and asexual reproduction in plants, animals and fungi
151
4 stages of mitosis
- prophase
- metaphase
- anaphase
- telophase
152
prophase
- chromosomes condense and become visible
- in animal cells, the centrioles separate and move to opposite poles of the cell
- the centrioles create spindle fibres which are released from both poles to create a spindle apparatus- these will attach to the centromere and chromatids on the chromosome in later stages
- plants have a spindle apparatus but lack centrioles
153
metaphase
- the chromosomes align along the equator of the cell
- the spindle fibres are released from the centrioles and attach to the centromere and chromatids
- the spindle assembly checkpoint occurs in this stage- a check to ensure every chromosome has attached to a spindle fibre before mitosis can proceed into anaphase
154
anaphase
- the spindle fibres start to shorten and move towards the centrioles and pull the centromere and chromatids they are bound to towards the opposite poles
- this causes the centromere to divide into 2 and and the individual chromatids are pulled to each opposite pole
- this stage requires energy in the form of ATP which is provided by respiration in the mitochondria
155
telophase
- the chromosomes are now each pole of the cell and become longer and thinner again
- the spindle fibres disintegrate, and the nuclear membrane reforms
156
cytokinesis
- the cytoplasm splits in 2 genetically identical cells
- in animals, a cleavage furrow forms in the middle of the cell and the cytoskeleton causes the cell surface membrane to draw inwards until the cell split in 2
- in plants, the cell surface membrane splits into 2 new cells due to the fusing of vesicles from the Gogli apparatus. The cell wall forms new sections around the cell surface membrane to completer the division into 2 cells
157
observing mitosis practical
- thin slice of root tip is placed on microscope slide and broken down with a needle
- a stain is added to make the chromosomes visible and the cover slip is pushed down- to squash the tip to achieve a single layer of cells so light can pass through
158
mitotic index calculation
mitotic index= number of cells in mitosis/total number of cells x100
159
meiosis
- 2 nuclear divisions in this process which result in 4, genetically different haploid daughter cells
- the 2 rounds of division are referred to as meiosis I or meiosis II
- both stages included prophase, metaphase, anaphase, telophase and cytokinesis
160
haploid (n)
one copy of each chromosome
161
diploid (2n)
two copies of each chromosome
162
crossing over (meiosis)
- during prophase I the homologous chromosomes pair to form bivalents
- crossing over genetic material can occur between the non-sister chromatids of bivalents
- breaks can occur in the genetic material where the chromatids cross over and parts of the chromatids are exchanged between the homologous pairs
- this results in new combinations of alleles in the resulting gamete
163
independent assortment (meiosis)
- during metaphase I the homologous pairs of chromosomes line up opposite each other on either side of the equator
- it is random on which side of the equator the paternal and maternal chromosome of each pair aligns
- in metaphase II, the sister chromatids within one chromosome line up at the equator, their orientation on each side of the equator introduces another chance for increased genetic variation
164
organisation of multicellular organisms
cells --> tissue --> organ --> organ system --> entire organism
165
# specialised cells
erythorocytes (RBC)
- biconcave shape to increase surface area for diffusion and to increase cell flexibility for it to fit through narrow capillaries
- no nucleus so there is more space to hold haemoglobin to increase transport of oxygen
166
# specialised cells
neutrophils (WBC)
- lobed nucleus and granular cytoplasm
- flexible to enable them to surround pathogens and engulf them
- contain lysosomes filled with the hyrdolytic enzyme, lysozyme
- made from stem cells in bone marrow
167
# specialised cells
sperm cells
- flagellum contains many mitochondria to release energy for locomotion to enable sperm cell to move towards egg cell
- acrosome in head of cell contains digestive enzymes to digest wall of egg cell so sperm can penetrate and fertilise egg cell
168
# specialised cells
palisade cells
- located in mesophyll tissue layer of leaves
- rectangular, tightly packed cells that contain many chloroplasts to absorb and maximise light energy for photosynthesis
- have thin cell walls to reduce diffusion distance of carbon dioxide
169
# specialised cells
guard cells
- pair of cells have flexible walls, more so on one side, which results in cells bending when turgid to open stomata and closing when flaccid- helps control water loss by transpiration
170
# specialised cells
root hair cells
- on surface of roots
- have long projections to increase surface area for osmosis of water and active transport of mineral ions
- have thin cell wall to reduce diffusion distance
171
# specialised tissues
squamos epithelia
- usually only single layer of flat squamos cells is in contact with basement membrane of epithelium
- provides short diffusion distance, e.g. these form linings of lungs
172
# specialised tissues
ciliated epithelia
- made of ciliated epithelial cells
- have hair-like projections that sway to move substances, such as mucus, out of lungs or an egg in the oviduct
- goblet cells are also located within epithelium and these cells release mucus to trap molecules, such as trapping dust in the trachea
173
# specialised tissues
cartilage
- connective tissue that is firm and flexible, located in outer ear, nose and end of bones
- provides structural support and prevents bones from rubbing together which would damage them
- made up of elastin and collagen fibres and chondrocyte cells within an extracellular matrix
174
# specialised tissues
muscle
- composed of tissues that can contract and relax to create movement
- skeletal muscles cause skeleton to move and are made up of myofibrils containing proteins actin and myosin
- smooth muscle is located within organs and cardiac muscle is within the heart
- muscles have multiple fibres connecting with connective tissues in between
175
# specialised tissues
xylem
- cells that make up part of vascular bundle in plants responsible for transporting water and mineral ions
- tissue is made up of elongated, hollow dead cells, with lignin in walls to strengthen and waterproof the walls
- xylem tissues are made from stem cells in meristem
176
# specialised tissues
phloem
- cells that make up part of vascular bundle responsible for transporting organic substances made in photosynthesis
- made of sieve tube element cells, which have perforated end walls and are lacking most organelles to make transport of sugars easier, and companion cells, which contain organelles to provide resources for the sieve tube elements
- phloem sieve tubes are made from stem cells in meristem
177
stem cells
undifferentiated cells that can self-renew (continually divide) and become specialised
178
4 types of stem cells
- totipotent
- pluripotent
- multipotent
- unipotent
179
totipotent stem cells
- can divide and produce any type of body cell
- during devlopment, they translate only part of their DNA, resulting in cell specialisation
- occur only for a limited time in early mammalian embryos
180
pluripotent stem cells
- found in embryos and can become almost any type of cell (except placenta)
- they are used in research with prospect of using them to treat human disorders
- issues as sometimes treatment doesn't work, or stem cells continually divide to create tumours
- ethics- debate whether it is right to make therapeutic clone of yourself to make an embryo to get stem cells to cure disease, then destroy embryo
181
multipotent and unipotent stem cells
- found in mature mammals and can divide to form a limited number of different cell types
- multipotent, e.g. bone marrow, can differentiate into limited number of cells
- unipotent can only differentiate into one type of cell
182
potential uses of stem cells
- repairing damaged tissues
- treatement of neurological conditions, e.g. Alzheimer's and Parkinson's
- research into developmental biology
