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Dr Bhavsar's A level Biology (OCR, A) > OCR A Biology Module 2 Masterdeck > Flashcards

OCR A Biology Module 2 Masterdeck Flashcards

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1
Q
A
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2
Q

State the key aspects of cell theory

A
  1. Both plant and animal tissue is composed of cells
  2. Cells are the basic unit of all life
  3. Cells only develop from existing cells
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3
Q

Describe the role of microscopy in the development of biological understanding

A
  1. Microscopes produce magnified images of biological material
  2. It gives us information about the structure of living organisms
  3. Which can be related to functions at various levels (ultrastructure (organelles), cell structure, tissues, organs, organisms)
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4
Q

List the types of microscopes

A
  1. Light microscope
  2. Transmission electron microscope
  3. Scanning electron microscope
  4. Laser scanning confocal microscope
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5
Q

Describe light microscopy and the images it produces

A
  1. Light passing through samples is passed through objective and eyepiece lenses to produce a magnified image
  2. Natural colours of samples can be observed
  3. Up to 2000x magnification possible
  4. Resolution of 200 nm (organelles apart from nucleus not visible)
  5. Specimens can be living or dead
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6
Q

Describe electron microscopy and the images it produces

A
  1. Electrons are used to illuminate the specimens
  2. In transmission electron microscopy (TEM), electrons passing through the specimen are detected and used to produce the magnified image.
  3. TEM has a resolution of 0.5 nm (more detailed images)
  4. TEM provides detailed but 2-D images
  5. Internal cellular detail such as organelles are visible in TEM
  6. In scanning electron microscopy (SEM), electrons that are reflected off the surface of the sample are detected.
  7. SEM has a resolution of 3-10 nm
  8. SEM provides less detail, but gives 3-D information as well, outer details of organisms should be visible, but not necessarily organelles.
  9. For both TEM and SEM sample preparation is complex and samples always dead
  10. Images produced are black and white (but could be false coloured)
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7
Q

Describe laser scanning confocal microscopy and the images it produces

A
  1. A modified light microscopy technique that used high intensity laser to illuminate the sample, and detects fluorescence emitted from specifically labelled cellular components
  2. Resolution is higher than light microscopy because only fluorescence from a single focal plane is detected
  3. Images are false colour and depend on the fluorescence wavelength of the labels
  4. Samples can be fixed (dead) or living
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8
Q

Describe the preparation of a slide for light microscopy

A
  1. Samples can be: dry mounted (whole samples or thin sections), wet mounted (aquatic organisms), squash slides (tissue squashed to thin it out) or smear slides (liquid biological samples, eg blood)
  2. In all cases samples but be spread thinly to allow light to pass through
  3. Must be covered with a glass coverslip
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9
Q

Describe the purpose of differential stains

A
  1. Biological materials/components usually don’t absorb a lot of light, this means contrast is low, and structures difficult to differentiate
  2. Chemical stains bind to cellular components and increase their visibility/image contrast
  3. Different stains, with different chemical properties, bind to different cellular components
  4. Which allows their structure to observed..
  5. ..And the structures to be identified (and related to function)
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10
Q

State the types of differential stain and what they are used to identify

A
  1. Eosin red is basophilic and will bind to positively charged components (usually in the cytoplasm)
  2. Methylene blue is acidophilic and will bind to negatively charged components such as DNA (identifies nucleus)
  3. Crystal violet is a dye taken up and retained by bacterial cells with thick cell walls, and washed out of bacterial cells with thinner cells walls. This stain helps to identify different types of bacteria.
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11
Q

Explain the need for different subcellular structures within cells

A
  1. Cells carry out a range of different metabolic processes in order to function
  2. The enzymes, substrates and conditions for these processes can be very different
  3. Membranes allow compartmentalisation, separation and concentrations required for these processes to proceed optimally
  4. Membranes and specialised proteins within membranes ensure selective transport of substances into and out of each compartment
  5. Additionally, certain functions of a cell may require very specific and specialised structural arrangements and components, for example for support, transport or motility.
  6. The structure of each organelle is related to its function
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12
Q

List the components of the ultrastructure of eukaryotic cells (key organelles)

A
  1. Nucleus
  2. Nucleolus
  3. Nuclear envelope
  4. Rough endoplasmic reticulum
  5. Smooth endoplasmic reticulum
  6. Golgi apparatus
  7. Ribosomes
  8. Mitochondria
  9. Lysosomes
  10. Chloroplasts
  11. Plasma membrane
  12. Centrioles
  13. Cell wall
  14. Flagella
  15. Cilia
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13
Q

Describe how the structure is related to the function of: Nucleus

A

S: Contains the genomic information of the organism

S: in the form of DNA (chromosomes)

S: Chromosomes consist of DNA associated with histone proteins

F: genes code for proteins, which carry out the metabolic and other functions of the cell

F: nucleus thus control the activities of the cell

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14
Q

Describe how the structure is related to the function of: Nucleolus

A

S: composed of protein and RNA

F: this is where genes for ribosomal protein and ribosomal RNA are transcribed

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15
Q

Describe how the structure is related to the function of: Nuclear envelope

A

S: a double membrane structure (two membrane bilayers)

F: separating the chromosomal DNA from the cytoplasm

F: where it may be damaged / digested by enzymes

S: it contains nuclear pores

F: which selectively allow molecules to move in and out of the nucleus

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16
Q

Describe how the structure is related to the function of: Mitochondria

A

F: carries out link reaction, Kreb’s cycle and oxidative phosphorylation for aerobic ATP generation during respiration.

S: Enveloped (double-membraned) organelle in all eukaryotic cells

S: Outer mitochondrial membrane and inner mitochondrial membrane

S: inner mitochondrial membrane is folded to form cristae to…

F: …increase surface area and components for oxidative phosphorylation

S: Stalked particles on cristae are part of ATP synthase

S: inner mitochondrial membrane contains the matrix

F: which contains enzymes required for link reaction and Kreb’s cycle

S: The matrix also contains circular DNA with some mitochondria-specific genes

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17
Q

Describe how the structure is related to the function of: vesicles

A

S: single membrane surrounding fluidic contents

S: contents depend on which organelle it pinched off from

F: transport of substances from one organelle to another

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18
Q

Describe how the structure is related to the function of: lysosomes

A

S: modified vesicles

S: contain hydrolytic enzymes (proteases, carbohydrases, lipases, nucleases)

F: membrane prevents other cellular components being digested

F: digest old organelles, or pathogens

F: especially important in phagocytes (inflammation, immune response)

F: and programmed cell death, apoptosis

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19
Q

Describe how the structure is related to the function of: cytoskeleton

A

S: certain globular proteins can be polymerised to form fibres in the cell.

S: polymerised actin forms actin fibres (microfilaments)

F: microfilaments are involved in cell movement, cytokinesis

S: polymerised tubulin forms microtubules

F: these are used to transport vesicles across the cell

F: and form spindle fibres during cell division

S: intermediate fibres give mechanical strength to the cell

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20
Q

Describe how the structure is related to the function of: centrioles

A

S: cylindrical structures formed of microtubules

F: a pair of centrioles forms the centrosome involved in the separation of chromosomes/chromatids during cell division

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21
Q

Describe how the structure is related to the function of: Flagella and cilia

A

S: hair-like structures made of proteins

F: cilia are more numerous and have sensory function, or they move fluid away from cells (for example in the lungs)

S: flagella are fewer per cell, and function to propel cells

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22
Q

Describe how the structure is related to the function of:

Rough endoplasmic reticulum

A

S: network of interconnected, flattened membrane sacs called cisternae

S: continuous with the nuclear envelope

S: has ribosomes bound to the surface

F: synthesis of membrane proteins (eg channels) and secreted proteins (eg antibodies)

F: contains enzymes for the synthesis of carbohydrates and modification of proteins

F: transport of synthesised proteins to Golgi apparatus

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23
Q

Describe how the structure is related to the function of:

Smooth endoplasmic reticulum

A

S: network of interconnected, flattened membrane sacs called cisternae

S: continuous with the nuclear envelope

F: contains enzymes for lipid and carbohydrate synthesis

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24
Q

Describe how the structure is related to the function of:

Ribosomes

A

S: free-floating in the cytoplasm or attached to endoplasmic reticulum

S: Not membrane-bound structures: composed of protein and ribosomal RNA

F: Site of protein synthesis

F: bind to mRNA and tRNA

F: join amino acids with peptide bonds in condensation reactions, forming polypeptides

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25
Q

Describe how the structure is related to the function of:

Golgi apparatus

A

S: flattened membrane sacs that are not interconnected, called cisternae

S: cis face faces nucleus, trans face faces plasma membrane

F: receives proteins from RER in transport vesicles (utilising cytoskeleton) which fuse to cis face

F: enzymes modify the proteins as they move through the cisternae

F: vesicles containing modified protein are packaged into vesicles leaving the trans face

F: thus, proteins may be delivered to lysosomes, plasma membrane or secreted

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26
Q

Describe how organelles in the eukaryotic cell are involved in

protein synthesis

A
  1. A gene in one of the chromosomes may be transcribed (by RNA polymerase)
  2. The mRNA formed moves through a nuclear pore to the cytoplasm
  3. It will bind a ribosome on the RER
  4. The ribosome will carry out the translation of the mRNA and a polypeptide will be formed inside the cisternae of the RER
  5. As the polypeptide moves through the cisternae of the RER, it adopts its secondary and tertiary structure, and pinches off the RER in a transport vesicle
  6. The vesicle is transported along cytoskeletal filaments
  7. The vesicle fuses with the cis face of the Golgi apparatus
  8. And within the cisternae of the Golgi apparatus, enzymes modify the protein, for example adding carbohydrate chains
  9. The protein pinches off the trans face of the Golgi apparatus in a vesicle
  10. Moving to fuse with lysosomes or the plasma membrane using the cytoskeleton
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27
Q

Describe how the structure is related to the function of:

cellulose cell wall

A

S: the cell wall surrounds the cell surface membrane

S: made of bundles of cellulose (insoluble, polysaccharide) composed of ẞ-glucose

F: the cellulose is permeable to water so water and solutes can freely move into and out of cells

F: the cell wall is rigid, so provides support to cells and the whole plant

F: the cell wall exerts pressure back on the cytoplasm in turgid cells, preventing them from bursting, this also supports the plant

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28
Q

Describe how the structure is related to the function of:

vacuoles

A

S: membrane sacs in the cytoplasm of plant cells

S: the membrane of the vacuole is called the tonoplast

F: the fluid content of vacuoles maintain pressure on the cell wall (turgor) which ensures proper support of plant tissues

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29
Q

Describe how the structure is related to the function of:

chloroplasts

A

S: enveloped (double-membraned) organelle (outer membrane, inner membrane)

S: The fluid contained in the chloroplast is called the stroma

S: the stroma contains circular DNA containing chloroplast genes and ribosomes

S: within the stroma there are interconnected, flattened sacs called thylakoids, forming stacks of grana, connected by lamellae, this structure has a high surface area

S: starch grains are found in the stroma

F: the thylakoid membranes contain the photosynthetic pigments and photosystems and ATP synthase for the light-dependent stage (the high surface area ensures there is enough of these components, and maximise light absorbance)

F: the stroma contains the coenzymes, enzymes and substrates for the light-independent stage (Calvin cycle).

F: starch grains store fixed carbon in the form of insoluble polysaccharide

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30
Q

Describe the similarities between prokaryotes and eukaryotes

A
  1. Both have genomic information (their genes) contained on molecules of DNA
  2. Both have ribosomes in the cytoplasm
  3. Both have cytoplasms enclosed by a cell-surface membrane
  4. Both prokaryotic and eukaryotic cells (not all) can have flagella
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31
Q

Describe the differences between prokaryotes and eukaryotes

A
  1. Prokaryotes have a single molecule of circular DNA, eukaryotes can have multiple molecules of (linear) DNA
  2. Prokaryotic DNA is contained in the cytoplasm, eukaryotic DNA is contained in the nucleus
  3. Ribosomes in prokaryotes are smaller (70S) than eukaryotic ribosomes (80S)
  4. Eukaryotic organisms such as plants and fungi, and prokaryotes all have cell walls, but these are different in composition. Plant cell walls are composed of cellulose, whereas fungi cell walls are made of the polysaccharide chitin. Bacterial cell walls are made of peptidoglycan (a polymer of amino acids and sugars)
  5. Prokaryotic flagella have a different structure to eukaryotic flagella
  6. Prokaryotes do not have membrane-bound organelles, eukaryotes do
  7. Prokaryotic DNA is not associated with histones, eukaryotic DNA is.
  8. Prokaryotic cells (up to 1µm) are much smaller than eukaryotic cells (10 µm)
  9. Prokaryotic cells have extra DNA called plasmids, only present in eukaryotic mitochondria and chloroplasts
  10. Prokaryotes can only reproduce asexually, eukaryotic reproduction can be asexual and/or sexual
  11. Prokaryotes are always unicellular, eukaryotes can be multicellular
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32
Q

Describe the structure of a water molecule

A
  1. Two Hydrogen atoms joined to a single oxygen atom
  2. By covalent bonds
  3. Oxygen is more electronegative than Hydrogen so each bond is polar
  4. Resulting in oxygen being partially negative
  5. And both Hydrogens being partially positive
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33
Q

Explain how the properties of water are linked to its structure

A
  1. The polar O-H bonds result in the water molecule have a partially negative Oxygen and partially positive Hydrogens
  2. The Oxygen of one water molecule can be attracted to the Hydrogen of a different water molecule, forming a Hydrogen bond
  3. This results in intermolecular attractions between water molecules resulting in cohesiveness of water molecules
  4. Water has an unusually high boiling point, and is a liquid at room temperature (or most of the naturally occuring temperatures on Earth), due to the large amounts of energy that would be needed to break the Hydrogen bonds
  5. The polarity of water molecules also allows them to attract other surfaces, resulting in adhesiveness
  6. The polarity of water means it can interact with other polar or ionic substances and act as a solvent
  7. Due to the formation of Hydrogen bonds in a lattice structure, freezing causes water (ice) to be less dense than liquid water
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34
Q

Describe how the properties of water support life on Earth

A
  1. The cytoplasm of cells is primarily water, which means the substances involved in metabolic reactions (including biological molecules such as sugars, amino acids, proteins) can be stored, and transported because water is a solvent
  2. Water is also the main component of transport media in multicellular organisms. As water is a solvent it can transport many biological molecules. It can be moved around the body because its cohesive properties allow it to be a liquid
  3. The adhesiveness of water allows it to stick to the walls of xylem vessels, and the cohesion allows columns of water to move by capillary action
  4. The high-specific heat capacity of water means it has a stabilising effect on the temperatures of organisms (preventing rapid fluctuations), enabling enzyme-dependent reactions to proceed
  5. Water is also a habitat for organisms, which are protected from dramatic temperature changes
  6. Ice on the surface of large bodies of water has an insulating effect, preventing the whole body from freezing and thus maintaining ecosystems
  7. Some organisms live and feed on the surface of water due to its surface tension (as a result of cohesion of water molecules)
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35
Q

Be able to draw the structure of alpha glucose

A
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36
Q

Be able to draw the structure of beta glucose

A
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37
Q

Be able to draw the structure of ribose

A
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38
Q

Be able to draw the structure of deoxyribose

A
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39
Q

Be able to draw a condensation reaction between two alpha glucose molecules to form maltose

A
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40
Q

Be able to draw a condensation reaction between alpha glucose and fructose to form sucrose

A
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41
Q

Be able to draw a condensation reaction between galactose and beta glucose to form lactose

A
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49
Q

Describe the structure of starch

A
  1. Alpha glucose monomers joined by condensation reaction, and alpha 1-4 glycosidic bonds
  2. (the hydroxyl group on carbon one, undergoes condensation reaction with the hydroxyl group on carbon 4 of another glucose molecule)
  3. To form a polysaccharide
  4. Amylose is coiled and unbranched (only contains 1-4 glycosidic bonds)
  5. Amylopectin is branched, by having 1-4 and 1-6 glycosidic bonds
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50
Q

Relate the structure of starch to its function

A
  1. Function of starch is glucose storage in plants
  2. The glucose is used in respiration to release energy, generate ATP
  3. Starch polysaccharides are insoluble, so they don’t affect the water potential of the cell
  4. Both amylose and amylopectin store a large amount of glucose in a small space (compact)
  5. Amylopectin’s branched structure allows for a higher rate of hydrolysis and glucose mobilisation as well as storage
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51
Q

Describe the structure of glycogen

A
  1. Composed of alpha glucose monomers joined by condensation reaction
  2. Contain alpha 1-4 glycosidic bonds, and 1-6 glycosidic bonds
  3. To form a highly branched polysaccharide
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52
Q

Relate the structure of glycogen to its function

A
  1. The function of glycogen is the storage of glucose in animals
  2. The stored glucose can be mobilised for use in respiration to generate ATP
  3. Glycogen is an insoluble polysaccharide so it doesn’t affect the water potential of the cell
  4. High branch density means that it is a compact store of glucose
  5. High branch density means that glucose can be mobilised more quickly by hydrolysis, and stored more quickly
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53
Q

Describe the structure and function of sterols such as cholesterol

A
  1. Structure contains four carbon rings
  2. And a hydroxyl group
  3. Arranged in a planar structure
  4. The hydroxyl group is polar and hydrophilic
  5. The carbon ring structure is hydrophobic
  6. Cholesterol regulates the fluidity of phospholipids in membranes
  7. Forms the basis of steroid hormones, vitamin D and bile
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54
Q

Draw the generalised structure of an amino acid

A
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55
Q

Describe the structure of cellulose

A
  1. Cellulose is a polysaccharide composed of beta-glucose monomers
  2. Joined by condensation reaction, joining carbon one of one beta glucose molecule to carbon four of the next beta glucose molecule with a beta glycosidic bond
  3. Every other beta glucose molecule is inverted (not rotated)
  4. This produces a linear, unbranched molecule (not coiled)
  5. 1Because they are linear, adjacent molecules can form hydrogen bonds to form bundles of molecules
  6. Forming microfibrils and then macrofibrils
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56
Q

Draw a diagram to show how two amino acids are joined to form a dipeptide (and understanding the reverse of this process is called hydrolysis)

A
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57
Q

Relate the structure of cellulose to its function

A
  1. It is insoluble, so continues to provide support while in contact with water
  2. Beta glycosidic bonds produce linear molecules, which can hydrogen bond to form bundles with a high tensile strength
  3. Cellulose has many polar (hydroxyl) groups, which allow cellulose fibres to be permeable to water, mineral ions, glucose, amino acids and plant hormones
  4. Cellulose molecules can be cross-linked, making them rigid, and withstanding hydrostatic pressure of turgid plant cells
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58
Q

Describe the structure of triglycerides

A
  1. Composed of three fatty acids chains and a molecule of glycerol
  2. The carboxyl group of each fatty acid undergoes condensation reaction with a hydroxyl group on the glycerol molecule
  3. Joining them via ester bonds (esterification)
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59
Q

Describe and discuss saturated and unsaturated triglycerides

A
  1. Fatty acids (gained from the diet) can be saturated or unsaturated
  2. Saturated fatty acids have no carbon-carbon double bonds, and have a straight chain
  3. Unsaturated fatty acids have one or more carbon-carbon double bonds, resulting in kinks in the chain
  4. Kinks in the chain cause lipids to pack less closely, reducing their density
  5. There is evidence to suggest diets high in saturated fats may cause cardiovascular disease.
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60
Q

Describe how the structure, properties and functions of triglycerides are related

A
  1. The fatty chains of lipids are composed of Carbon and Hydrogen, which makes them non-polar and hydrophobic
  2. The many C-H bonds can be broken down in aerobic respiration (Kreb’s cycle), to release energy for the production of ATP
  3. Triglycerides provides thermal insulation (due to low density)
  4. They also provide physical cushioning (protection) of organs (due to low density)
  5. They provide buoyancy to some aquatic animals such as whales (due to low density)
  6. Waterproof coating on animals and plants
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61
Q

Describe the structure of phospholipids

A
  1. Composed of two fatty acids chains, a phosphate group and a molecule of glycerol
  2. The carboxyl group of each fatty acid undergoes condensation reaction with a hydroxyl group on the glycerol molecule
  3. Joining them via ester bonds (esterification)
  4. The phosphate group is joined to the third hydroxyl group
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62
Q

Describe how the structure, properties and functions of phospholipids are related

A
  1. The fatty acid tails are extremely non-polar and hydrophobic
  2. The phosphate head is negatively charged and very hydrophilic
  3. As a result, phospholipids in water form bilayers
  4. Which forms the basis of biological membrane structures and compartmentalisation of organelles and selective permeability
  5. Electrical insulation (for example the Schwann cells which allow faster transmission of nerve impulses)
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65
Q

Describe the structure of an amino acid

A
  1. Four groups attached to a central carbon:
  2. Amine group, Hydrogen, carboxyl group and variable side-chain
  3. There are twenty different amino acid types characterised by a different side chain
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67
Q

Describe the primary structure of proteins

A
  1. Specific amino acids are joined together in condensation reactions, to form peptide bonds.
  2. The order of the amino acids in a polypeptide is the primary structure
  3. The polypeptide has an N terminus (amino group at one end of the chain)
  4. It also has a C terminus (carboxyl group at the other end)
  5. The side chains project outward along the length of the polypeptide
  6. The positions and types of these side chains is determined by the primary structure
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68
Q

Describe the secondary structure of proteins

A
  1. The secondary structure is the initial coiling or folding of the polypeptide chain due to
  2. The partially negative oxygen of one peptide group forms a Hydrogen bond with the partially positive Hydrogen of another peptide group further along the chain
  3. This forms ether alpha helical structures or beta-pleated sheets
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69
Q

Describe the tertiary structure of proteins

A
  1. The three-dimensional folding of the polypeptide as a result of interactions between the side chains
  2. These interactions can be:
  3. Disulphide bonds: covalent bonds between sulphur atoms of different side chains
  4. Ionic bonds: attractions between oppositely charged side chains
  5. Hydrogen bonds: attractions between opposite partially charged atoms such as H, O, and N
  6. Hydrophilic and hydrophobic interactions, which is the effect that the aqueous environment has on the location of hydrophobic side chains (which move away from water) and hydrophilic side chains (which move to the surface of the protein to interact with water)
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70
Q

Describe the quaternary structure of proteins

A
  1. This is the association of more than one polypeptide chains, in order to make a fully functioning protein
  2. The interactions that allow this to happen are the same as in the tertiary structure
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71
Q

Describe the structure of globular proteins

A
  1. Globular proteins are roughly spherical, compact and water soluble
  2. They have a complex tertiary structure
  3. Hydrophobic side chains are in the core of the protein, away from water
  4. Hydrophilic side chains are on the surface, interacting with water
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72
Q

State the functions associated with globular proteins

A
  1. Transport proteins, soluble so can be transported in blood plasma (e.g. haemoglobin)
  2. Enzymes, soluble so can easily interact with soluble substrates (e.g. catalase)
  3. Hormones, soluble so easily transported in various body fluids, plasma, tissue fluid, cytoplasm (e.g insulin)
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73
Q

State what a conjugated (globular) protein is

A
  1. Globular proteins that contain a permanently associated non-protein component called a prosthetic group
  2. Prosthetic groups can be, lipids, carbohydrates, metal ions and vitamin derivatives
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74
Q

Describe the structure of haemoglobin

A
  1. roughly spherical, compact and water soluble
  2. complex tertiary structure
  3. Hydrophobic side chains are in the core of the protein, away from water
  4. Hydrophilic side chains are on the surface, interacting with water
  5. Has four polypeptide chains in its quaternary structure
  6. Two alpha polypeptide and two beta polypeptides
  7. Each polypeptide has a haem prosthetic group contains an iron ion, which bind oxygen molecules
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75
Q

Describe the structure of fibrous proteins

A
  1. Fibrous proteins tend to be long molecules, that are insoluble in watery environments
  2. There is a high proportion of amino acids with hydrophobic side chains (in the primary structure)
  3. There is a high proportion of amino acids with small side chains
  4. In a repeating sequence
  5. With relatively little tertiary folding
  6. To allow these polypeptides to associate more closely in their quaternary structure
  7. To form long fibres with properties such as high rigidity (Keratin), strength and flexibility (collagen), elasticity (elastin)
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76
Q

Write the chemical symbol for and state the role of: calcium ions

A
  1. Ca2+
  2. Synaptic transmission: Diffuse into the synaptic knob and cause exocytosis of synaptic vesicles
  3. Muscle contraction: released from the sarcoplasmic reticulum, binds to troponin, and allows myosin heads to bind actin filaments
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77
Q

Write the chemical symbol for and state the role of: sodium ions

A
  1. Na+
  2. Resting and action potentials/nerve impulses: diffuse into axons resulting in depolarisation
  3. Selective reabsorption and reabsorption of water: co-transported during the selective reabsorption of glucose and amino acids, used to lower the water potential of the medulla (loop of Henle)
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78
Q

Write the chemical symbol for and state the role of: potassium ions

A
  1. K+
  2. Resting and action potentials/nerve impulses: leak out of axons to maintain resting potential, diffuse into axons during repolarisation of axons
  3. Involved in stomatal closing
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79
Q

Write the chemical symbol for and state the role of: hydrogen ions

A
  1. H+
  2. Pumped using energy to establish proton gradients used in chemiosmosis in photosynthesis and respiration
  3. Affects intracellular and extracellular pH
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80
Q

Write the chemical symbol for and state the role of: ammonium ions

A
  1. NH4+
  2. Nitrogen cycle: used by bacteria to produce nitrates
  3. Toxic waste product of amino acid deamination/converted to urea in ornithine cycle
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81
Q

Write the chemical symbol for and state the role of: nitrate ions

A
  1. NO3-
  2. Nitrogen cycle: absorbed by plants and used to make amino acids (and so proteins)
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82
Q

Write the chemical symbol for and state the role of: hydrogencarbonate ions

A
  1. HCO3-
  2. Affects blood pH: detected by chemoreceptors in wall of carotid arteries and aorta (control of heart rate during exercise)
  3. form in which carbon dioxide is transported from body tissues to the heart/lungs
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83
Q

Write the chemical symbol for and state the role of: chloride ions

A
  1. Cl-
  2. Cofactor for the enzyme amylase
  3. Chloride shift: chloride ions diffuse into red blood cells as hydrogen carbonate ions diffuse out (to maintain electrical balance)
  4. Balances the positive charge of sodium and potassium ions
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84
Q

Write the chemical symbol for and state the role of: phosphate ions

A
  1. PO43-
  2. Required for synthesis of phospholipids, nucleotides, ATP
  3. Used to phosphorylate proteins (and change their activity) in the cell as part of hormone-induced cell signalling
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85
Q

Write the chemical symbol for and state the role of: hydroxide ions

A
  1. OH-
  2. Affects cellular and extracellular pH
86
Q

Describe a positive test for the presence of proteins

A
  1. Biuret test
  2. Add Biuret reagent to the test solution
  3. If protein is present the reagent should turn from blue to purple
  4. Suitable controls would be solutions known to contain no protein, or known to contain protein
87
Q

Describe a positive test for the presence of reducing sugars

A
  1. Benedict’s test
  2. Add Benedict’s reagent to the test solution
  3. Heat the mixture to about 70C
  4. If reducing sugar is present, the blue reagent (Cu2+) should change colour due to the presence of brick red Cu+ ions.
  5. According the concentration of reducing sugar, the colour change should be in the order: blue (none), green, yellow, orange, red (high concentration)
  6. Suitable controls would be solutions known to contain no reducing sugar, or known to contain reducing sugar
88
Q

Describe a positive test for the presence of non-reducing sugars

A
  1. Benedict’s test for non-reducing sugar
  2. If Benedict’s test result is negative
  3. Boil in the presence of dilute hydrochloric acid (to hydrolyse the glycosidic bond)
  4. Add sodium hydroxide to neutralise the acid
  5. Repeat Benedict’s test by adding Benedict’s reagent and warming
  6. A positive result at this stage confirms the presence of a non-reducing sugar originally
89
Q

Describe a positive test for the presence of Starch

A
  1. Iodine test
  2. Add some drops of iodine (potassium iodide solution)
  3. If Iodine changes from brown to blue/black, starch is present
90
Q

Describe a positive test for the presence of lipids

A
  1. Emulsion test
  2. The sample is mixed with ethanol (to dissolve any lipids present)
  3. Water is added and then shaken
  4. The ethanol dissolves in the water, and the lipids form an emulsion
  5. Visible as a white (not clear) layer at the top of the tube
91
Q

Describe how colorimeter can be used to carry out quantitative tests for biological molecules

A
  1. Ensure the correct filter is inserted (which has the ‘opposite’ colour the one being detected)
  2. Use water to calibrate the colorimeter (to zero absorbance)
  3. Measure the absorbance of solutions of known concentrations (on which the test has been carried out), to produce a calibration curve
  4. Carry out the test for the biological molecule for the unknown solution
  5. Measure the absorbance and compare to the calibration curve to determine the concentration
92
Q

Explain how Biosensors can be used to make quantitative measurements of biological molecules

A
  1. The sample contains a particular biological molecule
  2. A protein (enzyme or antibody) is immobilised to the transducer (or to test strip)
  3. When a specific interaction takes place between the sample molecule and the protein, the change in shape is produces a signal from the transducer (or colour change in test strip)
  4. The intensity of the signal is proportional to the concentration of the biological molecule
  5. (or in a test strip, the extent of colour change)
93
Q

Describe how thin layer chromatography can be used to separate a mixture of amino acids

A
  1. Draw a horizontal line near the bottom of the chromatography paper or plate
  2. Draw spots to indicate the initial positions of the mixtures
  3. Use a capillary tube to spot the mixture onto the paper/plate
  4. The bottom of the paper/plate is placed in the solvent
  5. The solvent is allowed to move up the paper/plate
  6. Another horizontal line is drawn at this level
  7. The plate/paper is sprayed with ninhydrin to visualise the position of the amino acids
  8. Rf values are calculated by dividing the distance travelled by the amino acid by the distance travelled by the solvent
  9. Due to unique solubility in the solvent different amino acids travel specific distances and therefore have unique Rf values
94
Q

Describe the structure of nucleotides generally

A
  1. Nucleotides are composed of a pentose sugar
  2. Carbon 1 is joined to a nitrogenous base by a glycosidic bond
  3. Carbon 5 is joined to a phosphate group by an ester bond
95
Q

Discuss the nitrogenous bases in RNA and DNA

A
  1. There are five nitrogenous bases, A, T (DNA), C, G and U (in RNA)
  2. Adenine and guanine and purines, which means they have two rings in their structure
  3. Thymine, cytosine and uracil are pyrimidines, which mean they have one ring in their structure
  4. Base pairing occurs by complementary hydrogen bonding (between opposite partially charged groups)
  5. Base pairing always occurs between a purine and a pyrimidine
  6. A=T, C≡G, A=U
98
Q

Describe how polynucleotides can be formed from nucleotides

A
  1. One nucleotide undergoes condensation reaction with another
  2. (catalysed by DNA polymerase or RNA polymerase)
  3. The 5’ phosphate group of the incoming nucleotide..
  4. ..is joined to the 3’ hydroxyl group of the terminal nucleotide..
  5. ..in the 5’ to 3’ direction
  6. Connecting nucleotides with phosphodiester bonds
99
Q

Describe how polynucleotides can be broken down to nucleotides

A
  1. Polynucleotides can be broken down to nucleotides with hydrolysis reactions
  2. Involving the addition of water
  3. Carried out be nuclease enzymes
  4. exonucleases, which remove the terminal nucleotide
  5. Or restriction endonucleases which cut polynucleotides in the ‘middle’
100
Q

Describe the structure of ADP and ATP

A
  1. Modified adenine ribonucleotides
  2. Adenine nitrogenous base, ribose pentose sugar, two (ADP) or three (ATP) phosphate groups
101
Q

Describe the structure of DNA

A
  1. Deoxyribonucleotides are joined in condensation reactions by phosphodiester bonds
  2. Forming polynucleotide DNA strands with ..
  3. (pentose) sugar-phosphate backbones
  4. And outwardly projecting nitrogenous bases
  5. Two DNA strands with complementary sequence of bases will attract each other due to hydrogen bonding between complementary bases (A=T, C≡G)
  6. The two strands are antiparallel (opposing 5’-3’ directions)
  7. In an aqueous environment, the hydrophobic nitrogen bases and the hydrophilic sugar phosphate backbone result in the twisting of the two strands to form a helical structure, the alpha helix
  8. DNA molecules are very long (and cannot leave the nucleus)
102
Q

Describe the structure of RNA

A
  1. Composed of ribonucleotides joined in condensation reactions to form phosphodiester bonds
  2. Forming a single stranded polynucleotide
103
Q

Compare the structure of DNA and RNA

A
  1. They are both composed of nucleotides with a pentose sugar, nitrogenous base and phosphate group
  2. The pentose sugar is DNA is deoxyribose (carbon 2 doesn’t have an -OH group), but the pentose sugar in RNA is ribose (carbon has an -OH group)
  3. The nitrogenous bases in deoxyribonucleotide can be A, C, T and G, but in a ribonucleotide T is replaced with Uracil (U)
  4. DNA and RNA nucleotides are joined by phosphodiester bonds
  5. Both have sugar-phosphate backbones
  6. DNA forms double-stranded molecules, RNA forms single-stranded molecules
  7. DNA molecules are very long and RNA molecules are relatively shorter
104
Q

Describe how DNA can be purified by precipitation

A
  1. Grinding biological material with a mortar and pestle, dissociates cells and breaks down cell wall if present
  2. Detergent is added: this disrupts the phospholipid bilayer of cell membranes (such as cell surface membrane and nuclear envelope)
  3. Add salt: this breaks the attractions between DNA and water
  4. Add protease enzymes: this breaks down the histone proteins associated with DNA by hydrolysis
  5. Add a layer of alcohol to the surface: DNA is insoluble in the alcohol, and so precipitates out, visible as a white solid
105
Q

Describe the process of semi-conservative DNA replication

A
  1. DNA helicase causes the unwinding of the double-helix, and the separation of the two strands unzipping) by breaking the hydrogen bonds between the complementary nitrogenous bases
  2. Free nucleotides in the nucleoplasm align to the newly exposed nitrogenous bases by complementary base pairing (A=T, C≡G)
  3. DNA polymerase moves along the original strand catalysing condensation reactions between the newly aligned nucleotides and joining them with phosphodiester bonds
  4. This occurs in the 3’ to 5’ direction continuously on one strand, and discontinuously on the other strand
  5. When both original strands have a newly synthesised complementary strand, semi-consertive replication has occurred
106
Q

Describe the nature of the genetic code

A
  1. The sequence of bases in DNA is what codes for the production of proteins with specific functions
  2. Triplet code: it is sequences of three consecutive bases that code for specific amino acids. In the gene these three bases are referred to as triplets, while in the mRNA, they are called codons (anticodons in tRNA)
  3. Universal code: the nature of the code is the same in all known living organisms
  4. The code is degenerate: more than one triplet/codon can code for the same amino acid.
  5. The code is specific: each triplet/codon cannot code for more than one amino acid
  6. The code is non-overlapping: triplets/codons are read one after the other, and do not overlap
107
Q

Describe the process of transcription of a gene

A
  1. DNA helicase unwinds and unzips a section of DNA corresponding to a gene
  2. Free ribonucleotides align to the exposed bases on the template strand by complementary base pairing and hydrogen bonding
  3. RNA polymerase moves along the template strand, catalysing condensation reactions to join the aligned ribonucleotides with phosphodiester bonds
  4. At the end of the gene, RNA polymerase stops, detaches, the DNA rewinds, and mRNA separates, leaving via the nuclear pore
108
Q

Describe the process of translation of an mRNA

A
  1. The mRNA binds to a ribosome
  2. The ribosome reads the mRNA codon by codon
  3. tRNA molecules (carrying specific amino acids) bind to their complementary codon on the mRNA via their anticodon
  4. Thus, specific amino acids enter the Ribosome according to the sequence of codons on the mRNA
  5. Two amino acids thus brought together are joined in the ribosome by peptide bonds (condensation reaction)
  6. As the ribosome moves along the mRNA, amino acids are added according to the sequence of codons
  7. This continues until the STOP codon is encountered, at which point the polypeptide separates from the ribosome
109
Q

State what a mutation is and how it can affect the function of a gene

A
  1. Mutations are changes in the sequence of bases in a gene
  2. These can occur during DNA replication (and made more likely by mutagens such as certain types of radiation and chemicals)
  3. If mutations alter the triplets in the gene, the sequence of codons in the mRNA could be altered
  4. If the sequence of codons in changed, the protein produced will have a different primary structure
  5. The positions of amino acid side chains will be different, and the tertiary structure will be changed
  6. If the tertiary structure is different, the function could be different (most likely, reduced)
110
Q

Describe the structure of enzymes

A
  1. Enzymes are globular proteins (be able to describe the structure of a globular protein)
  2. They have a specific tertiary structure that includes a cleft called the active site
  3. Which is complementary in shape and chemical properties to its substrate
  4. Some enzymes require cofactors, coenzymes or prosthetic groups to function
111
Q

Describe the mechanism of enzyme action

A
  1. The enzyme collides with substrate
  2. If there is enough energy, and the orientation of enzyme and substrate are suitable
  3. The substrate will occupy the active site of the enzyme, forming an enzyme-substrate complex
  4. The enzyme is specific because the shape of its active site is complementary to the shape of the substrate (lock and key hypothesis)
  5. The induced-fit hypothesis states that the enzyme changes shape to accommodate the substrate, putting the substrate bonds under strain
  6. Interactions between the substrate and active site cause the bonds within the substrate molecule to weaken.
  7. The activation energy required for the reaction of the substrate(s) is thus lowered, increasing the rate of reaction
  8. The substrate is converted to product in the enzyme (enzyme-product complex), which has a lower affinity for the enzyme and so is released (product formation)
112
Q

Describe the role of catalase, as example of an intracellular enzyme

A
  1. Intracellular enzymes catalyse chemical reactions within the cell (think of all the chemical changes you know about that occur in the cell. Yeah.)
  2. For example, catalase converts the toxic metabolic waste product hydrogen peroxide into harmless water and oxygen
  3. 2H2O2 →(catalase)→ 2H2O + O2
  4. Intracellular enzymes rely on their substrates being available in the cell and colliding with them
  5. In many cases, the product of one enzyme is the substrate of another, which sets up a metabolic pathway
113
Q

Describe the role of amylase as an extracellular enzyme

A
  1. Amylase is a hydrolytic enzyme
  2. (the amylase gene is expressed in cells in the salivary glands and the pancreatic acinar cells, module 5)
  3. Amylase gene is switched on, transcribed, translated, modified, packaged and released via exocytosis
  4. When mixed with food, amylase breaks down starch into the disaccharide maltose
  5. Which is hydrolysed again by maltase into glucose
  6. Which is small enough to be absorbed into the bloodstream at the small intestine
  7. This ensures dietary glucose is available to the body cells for respiration, and the liver to store as glycogen
114
Q

Describe the role of trypsin as an extracellular enzyme

A
  1. Trypsin is a hydrolytic enzyme
  2. The trypsin gene is expressed in pancreatic acinar cells, module 5
  3. Trypsin gene is switched on, transcribed, translated, modified, packaged and released via exocytosis
  4. Trypsin is released in the pancreatic juice as the precursor enzyme, trypsinogen, an inactive form, to ensure it is only active once in the small intestine
  5. In the small intestine, the enzyme endopeptidase converts trypsinogen into active trypsin
  6. Which hydrolyses polypeptides into shorter peptides
  7. Other proteases hydrolyse peptides into amino acids, which can then be absorbed into the bloodstream
115
Q

Explain the effect of temperature on enzyme activity

A
  1. At low temperatures the kinetic energy of enzymes and substrates is lower
  2. The collide less frequently and with less energy
  3. The rate of enzyme-substrate complex (ESC) formation (and thus product formation) is lower
  4. As temperature increases, the kinetic energy of substrates and enzymes increases
  5. There is a higher rate of collisions, ESC formation and product formation
  6. At higher temperatures (above optimum) the available kinetic energy causes weak interactions in the enzyme’s tertiary structure to break
  7. Changing the shape of the active site so it is no longer complementary to the substrate
  8. Rate of ESC formation becomes lower, and so does product formation
116
Q

Explain what the temperature coefficient (Q10) tells us about an enzyme

A
  1. Enzymatic activity increases as temperature increases until the optimum temperature
  2. Different enzymes have different tertiary structures
  3. So differ in their sensitivity to changing temperature
  4. The temperature coefficient compares the enzyme activity (rate) at two temperatures separated by 10℃
  5. The greater this value, the more sensitive the enzyme is to temperature
117
Q

Explain the effect of pH on enzyme activity

A
  1. The tertiary structure of the enzyme is important in ensuring that the active site is complementary to the substrate.
  2. At the optimum pH, the concentration of hydrogen ions and hydroxide ions ensures the correct active site shape
  3. So that the rate ESC formation, and so product formation is highest
  4. Away from the optimum pH, the concentration of positively charged hydrogen ions (low pH), or negatively hydroxide ions (high pH), will disrupt hydrogen and ionic bonding
  5. Resulting in changes to the tertiary structure and alteration of the active site, so that it is no longer complementary to the active site
  6. This reduces the rate of ESC, and so, product formation
118
Q

Explain the effect of substrate concentration on enzyme activity

A
  1. At low substrate concentrations, the chances of successful collision between enzyme and substrate is relatively lower, and so the rate of ESC, and product formation, is low
  2. As substrate concentration increases, the rate of ESC and product formation increases (as the substrate concentration is the limiting factor)
  3. As substrate concentration becomes saturating, the enzyme reaches a maximum rate of activity, active sites are constantly occupied by substrate, and the rate of product formation can not increase further (reaches a maximum)
  4. Substrate concentration is no longer the limiting factor
119
Q

Explain the effect of enzyme concentration on enzyme activity

A
  1. At low enzyme concentrations, enzyme concentration is the limiting factor
  2. As enzyme concentration increases, the chance of successful collisions, ESC formation and product formation increase
  3. The more enzyme active sites available, the higher the capacity for ESC formation.
120
Q

Describe an investigation of a factor that affects enzyme activity

A
  1. Set up a range of different (factor that you are investigating). For example, range of substrate concentrations (investigating substrate concentration), or range of pH buffers (investigating effect of pH)
  2. Mix substrate and enzyme keeping all other factors constant across the experiment.
  3. Measure the product formed or substrate disappearance (by colour change, gas produced etc.) at regular timed intervals for five minutes
  4. Repeat this for the rest of the range of the independent variable
  5. Plot the results on a graph (product formed or substrate used vs time)
  6. For each of the range of conditions determine the initial rate by drawing a tangent at time zero
  7. To see the effect of ‘the factor’ on enzyme activity, plot the range of the independent variable vs the initial rate
121
Q

Discuss the role of cofactors, giving examples

A
  1. Some enzymes require a non-protein component in order to function (catalyse reactions)
  2. Cofactors are non-protein, inorganic ions or molecules, that associate with enzymes to activate them
  3. Cofactors are not permanently associated with the enzyme.
  4. Mineral ion cofactors are obtained from the diet (forexample Cl- ions are cofactors for the enzyme amylase)
122
Q

Discuss the role of coenzymes, giving examples

A
  1. Coenzymes are non-protein, but organic and not permanently attached to the enzyme, but are required for the enzyme to carry out a reaction.
  2. For example the coenzymes NAD (respiration) and NADP (photosynthesis), are used to transfer hydrogen atoms in reactions carried out by a number of different enzymes
  3. Many coenzymes are synthesised from vitamins obtained in the diet: NAD and NADP are synthesised from vitamin B12, coenzyme A from vitamin B5
123
Q

Discuss the role of prosthetic groups, giving examples

A
  1. Prosthetic groups are non-protein (organic or inorganic) permanently associated molecules or ions which are required for the proper tertiary structure of the enzyme.
  2. Example of prosthetic group is Zn2+ ions for carbonic anhydrase
124
Q

Describe the role of precursor enzymes in metabolism

A
  1. Some enzymes are synthesised as precursor enzymes (apoenzymes) which are inactive
  2. These are inactive until bound by the cofactor/coenzyme..
  3. ..or an inhibitory portion is cleaved off by a protease..
  4. ..or very specific pH or temperatures are encountered
  5. This is a way to ensure enzymes are only active when and where required
125
Q

Describe and explain the effect of a competitive inhibitor on enzyme activity

A
  1. Competitive inhibitor has a shape similar to the substrate
  2. It binds to the active site, reducing the rate of formation of the ESC
  3. This reduces the enzyme activity (rate of reaction)
  4. Increasing the concentration of the substrate makes ESC more likely to form
  5. The effect of the inhibitor can thus be reduced by increasing the substrate concentration
  6. At an infinitely high substrate concentration the effect of the inhibitor is negligible, and a maximum enzyme activity can still be reached (at a higher substrate concentration)
  7. Metabolic pathways are often regulated by negative feedback using end-products to inhibit earlier steps in the pathway, as products usually have similar shapes to enzyme substrates.
126
Q

Describe the effects of a non-competitive inhibitor

A
  1. Non-competitive inhibitor binds to the enzyme at a location away from the active site
  2. A location called the allosteric site
  3. Binding causes a change to the shape of the tertiary structure
  4. This makes the active site no longer complementary to the substrate
  5. This reduces the rate of ESC formation, and thus the rate of reaction
  6. This reduces the number of available active sites
  7. Increasing the substrate concentration does not reduce the impact of the non-competitive inhibitor, and so the maximum enzyme activity is reduced
  8. Many therapeutic drug molecules work by acting as competitive inhibitors of physiological enzymes
127
Q

Discuss reversible and non-reversible inhibition

A
  1. Inhibitors may bind permanently to the enzyme in which case their effect will be irreversible.
  2. If the inhibitor binds the enzyme temporarily, then its effects will be reversible
  3. It important to remember that competitive and noncompetitive inhibition is not exactly the same as reversible and non-reversible
  4. But in competitive inhibition, where the effects of the inhibitor can be reduced, that shows reversible inhibition
  5. And often, non-competitive inhibitors bind permanently to enzymes, so their effects are non-reversible.
  6. Many toxic and poisonous substances are extremely potent in small amounts because they act irreversibly.
128
Q

State the functions of cell membranes

A
  1. Partially permeable barriers between cells and their environment, organelles and the cytoplasm and even within organelles: compartmentalisation
  2. Sites of chemical reactions
  3. Site of cell communication (cell signalling)
  4. Cell-cell communication/recognition
  5. Cell-cell adhesion
129
Q

Describe the fluid-mosaic model of membrane structure

A
  1. The main component of membranes is the phospholipid bilayer
  2. Formed due to the hydrophilic heads interacting with aqueous environments on both sides
  3. And the hydrophobic fatty acid tails facing inward, away from (repelling) the water
  4. Proteins are embedded in the phospholipid bilayer with signalling, adhesion or transport functions
  5. Cholesterol molecules float amongst the phospholipids, regulating its fluidity
  6. Some proteins and lipids are glycosylated
  7. The structure is described as fluid, because the phospholipids and proteins can freely move within the plane of the membrane
  8. The structure is described as a mosaic due to the variety of proteins embedded in it
130
Q

Describe the structure and functions of intrinsic proteins

A
  1. Membrane proteins are globular proteins
  2. the parts that are embedded within the membrane have hydrophobic R groups on the outside (unlike water soluble proteins)
  3. Intrinsic proteins span the membrane
  4. usually function as channel proteins for the facilitated diffusion of small molecules and mineral ions
  5. Channel proteins have hydrophilic R groups at their core providing a hydrophilic environment for their diffusion
  6. Intrinsic proteins can also act as carrier proteins, which change shape to transport ions and molecules across the membrane
  7. Depending on the particular protein they can carry out facilitated diffusion or active transport
131
Q

Describe the structure and functions of glycoproteins

A
  1. Glycoproteins are globular proteins
  2. Modified (in the Golgi apparatus) with added carbohydrate chains that face the tissue fluid
  3. These can be extrinsic proteins, which do not span the entire membrane
  4. But are usually intrinsic proteins with functions other than transport
  5. The carbohydrate chains are adhesive and cells of tissues to stick to each other
  6. Glycoproteins also function in transmitting extracellular signals to the cell interior (cell signalling) by acting as receptors for neurotransmitters and peptide hormones
  7. Their shape must be complementary to the molecules they bind
  8. Therefore they are also targets for toxins and medicinal drugs that manipulate cell signalling to alter physiological responses
132
Q

Describe the structure and functions of glycolipids

A
  1. Glycolipids are lipids modified with carbohydrate chains added which face the exterior of the cell
  2. Glycolipids are synthesised in the Golgi apparatus
  3. The functions of glycolipids are mainly to do with cell-cell communication, adhesion and self/non-self recognition
133
Q

Describe the structure and function of cholesterol

A
  1. Cholesterol is a lipid
  2. Composed of four carbon-based rings (planar, hydrophobic)
  3. And a hydroxyl group (polar)
  4. Cholesterol functions to interact with phospholipids, ensuring the bilayer fluidity (movement of the phospholipids) does not get too high or too low: regulating membrane fluidity
  5. If the fluidity is too high, too many gaps may increase permeability too much and cells may leak their contents
  6. If the fluidity is too low, close packing of phospholipids may reduce the permeability of membranes to the diffusion of things like water, oxygen and carbon carbon dioxide
  7. So yeah, cholesterol: important
134
Q

Give examples of membranes as sites of chemical reaction:

A
  1. Think of examples where the enzymes that catalyse a reaction are associated or embedded within the membrane
  2. Do not confuse this with electron transport chains (these are not enzymatic reactions)
  3. For example, ATP synthase, in the inner mitochondrial membrane (and the thylakoid membrane of the chloroplast), converting ADP and phosphate to ATP
  4. For example, Photosystem II, in the thylakoid membrane acts as enzyme to carry out the photolysis of water
  5. For example NADP reductase (thylakoid membrane) reduces NADP in the light-dependent stage
  6. For example, when peptide hormones bind their receptor, adenylate cyclase, an enzyme in the cell surface membrane is activated, which converts ATP to cyclic AMP, the second messenger
135
Q

Explain how temperature affects the structure and function of membranes

A
  1. Temperature affects kinetic energy of phospholipids and proteins, which in turn affects membrane structure and then function
  2. As temperature increases, the kinetic energy of phospholipids increases
  3. This increases the fluidity of the membrane and opens more gaps in the bilayer
  4. This increases the permeability if the membrane (it is less able to act as a barrier)
  5. Increasing temperature causes the tertiary structure of channel and carrier proteins to change (denaturing them) so they may not be able to function.
  6. Permeability to certain substances (transported by proteins) may therefore decrease as temperature rises
136
Q

Explain how lipid solvents could affect the structure and function of membranes

A
  1. Lipid solvents are able to interact with the fatty acid tails of phospholipids
  2. And enter into the phospholipid bilayer
  3. Increasing the fluidity of the membrane
  4. Increasing permeability
  5. And seriously affecting cell function (dependent on controlling movement across membranes)
  6. Or possibly resulting in tissue damage, if cells leak cytoplasmic contents and damage other cells of the tissue
  7. High concentrations of alcohol are therefore toxic
137
Q

Describe an investigation into the effect of a factor on membrane structure

A
  1. Set up a range of boiling tubes with a known volume of water with either a range of different alcohol concentrations or temperatures (waterbaths)
  2. cut beetroot into equal size/surface area pieces using a cork borer
  3. place one piece into each of the boiling tubes
  4. for a the same length of time
  5. extract the water from each tube, and measure absorbance using a colorimeter
  6. keep other factors the same such as surface area of beetroot, temp (if changing alcohol), volumes of water, concentrations
  7. repeat each temp/alcohol concentration
  8. increasing absorbance shows more red pigment diffused out of the cells, shows more membrane permeability and a more membrane damage
138
Q

Describe how molecules move across membranes by simple diffusion

A
  1. As the membrane interior is hydrophobic, it is a barrier to polar and charged molecules/ions.
  2. The close packing of the phospholipids means large molecules also cannot pass through
  3. Biological membranes are freely permeable to small, non-polar molecules, such as oxygen and carbon dioxide
  4. They move across membranes down concentration gradients
  5. (from high to low concentrations) due to their kinetic energy
  6. The rate of diffusion is affected by temperature (which affects the kinetic energy of particles), and the size of the concentration gradient
  7. The rate of diffusion will also be increased by the surface area of the membrane.
  8. (remember that although shorter diffusion distances can also increase the rate of diffusion, membranes are all the same width, so they are not considered a factor in this context)
139
Q

Describe an investigation into the rate of diffusion

A
  1. Agar prepared with the indicator phenolpthalein (pink) is cut into blocks of different dimensions (to vary diffusion distance and surface area)
  2. Agar blocks are placed in mild acid solution
  3. For a specific length of time, and the distance that has become clear measured
  4. OR the time taken for the entire cube to become clear is measured
  5. Distance or volume is divided by time to determine the rate of diffusion
140
Q

Describe how molecules move across membranes by osmosis

A
  1. Water is a polar molecule and cannot freely move across biological membranes
  2. Water requires channel proteins called aquaporins
  3. Water movement is driven by the concentration of solutes
  4. The higher the concentration of substances dissolved in water, the lower the water potential
  5. Water (net) moves from regions of high water potential (less solute) to regions of low water potential (more solute)
  6. Or..down a water potential gradient
141
Q

Describe the effect of different external water potentials on animal cells (for example red blood cells)

A
  1. When the water potential outside the cell is higher than inside, water will enter cells by osmosis, causing them to swell and burst due to the increased hydrostatic pressure (cytolysis)
  2. When water potential outside the cell is the same as inside the cell, water is entering and leaving the cell at equal rates - there is no change in shape
  3. When the water potential outside the cell is lower than inside the cell, water leaves the cell by osmosis, reducing cell volume, and causing crenation
  4. Animals have homeostatic mechanisms that maintain the water potential of fluids such as tissue fluid and plasma, that prevent cytolysis and crenation
142
Q

Describe the effect of different external water potentials on plant cells

A
  1. Remember that plants do not have homeostatic mechanisms to regulate water potential outside of cells. Cell structure in plants is primarily ensured by the cellulose cell wall
  2. When water potential outside of plant cells is higher than inside, water enters by osmosis, increases the hydrostatic pressure, and the cell membrane exerts turgor pressure against the cell wall. Thus the cell wall prevents further entry of water and the cell is described as turgid
  3. When the water potential outside the plant cell is the same as inside, the rate of water movement in both directions is the same and there is no change in shape. There is no pressure exerted against the cell wall, cells are not turgid.
  4. When the water potential outside the plant cell is lower than inside the cell, water leaves the cell by osmosis, and the cell surface membrane comes away from the cell wall.
143
Q

Describe how to investigate movement across a partially membrane in model cells

A
  1. Use dialysis tubing to simulate the partially permeable membrane of a cell.
  2. The tubing is permeable to water and mineral ions and glucose but not starch
  3. Fill dialysis tubing with a solution containing starch and glucose
  4. The external solution can be varied with different water potentials, and solutes compositions, or temperature
  5. The movement of substances can be monitored by measuring changes in the ‘cell’ volume or mass, or testing the solutions for the presence of biological molecules
144
Q

Describe how molecules move across membranes by facilitated diffusion

A
  1. Charged, polar and relatively large molecules cannot freely move across phospholipid bilayers
  2. Intrinsic proteins such as channel proteins or carrier proteins
  3. Provide a hydrophilic route for their movement (channel proteins)
  4. Or bind them and change shape, moving them across the membrane (carrier proteins)
  5. In a direction dependent on the concentration/electrical gradient
  6. At a rate dependent on the size of the gradient, number of protein molecules available and the rate at which they can work
145
Q

Describe how molecules move across membranes by active transport

A

Some carrier proteins use the energy of ATP hydrolysis to change shape

And move molecules or ions from one side of the membrane to the other

In a direction determined by the protein, and independent of the concentration/electrical gradient

Active transport is usually works to create gradients, by moving substances UP their gradients

(often, it is these gradients that allow (other) substances to move passively by diffusion)

146
Q

Summarise the ways in which bulk transport occurs across cell membranes

A
  1. Relatively large volumes of liquid, or large solid particulates such bacteria enter cells by endocytosis
  2. Liquids enter by pinocytosis
  3. Solids enter by phagocytosis
  4. Substances produced by cells are secreted by exocytosis
147
Q

Describe how exocytosis occurs

A
  1. Material to released, for example, a peptide hormone, or antibodies
  2. Are modified and packaged into vesicles by the Golgi apparatus
  3. These vesicles move to the cell membrane along the cytoskeleton
  4. The phospholipid bilayer of the vesicle then fuses with that of the cell surface membrane
  5. This step requires proteins and ATP (therefore: active)
  6. Once fused, the contents of the vesicle diffuse away from the cell, into the tissue fluid, and possibly into the blood plasma
148
Q

Describe how endocytosis occurs

A
  1. The material to be transported nears the cell surface membrane (or the membrane is extended towards it)
  2. The membrane begins to invaginate around the material in a process requiring proteins and ATP
  3. The invaginated portion of the membrane then pinches off, forming a vesicle that contains external contents (liquid or solid)
  4. In phagocytosis, lysosomes then fuse with the vesicle, to digest the internalised contents using hydrolytic enzymes
149
Q

Identify the functions of cell division by mitosis

A
  1. mitosis (nuclear duplication and separation) and the resulting cell division, or cytokinesis (separation of organelles and cytoplasm) has a number of functions:
  2. They produce genetically identical cells required for the growth of the multicellular organism
  3. As old and damaged cells undergo cell death, cell division by mitosis allows repair and maintenance of tissues (identical cells with identical functions)
  4. In asexually reproducing organisms, mitosis is also a means by which offspring genetically identical to the parent organism can be produced
150
Q

Summarise the key stages of the cell cycle

A
  1. The cycle cycle has two main phases, interphase and mitotic phase
  2. Interphase consists of G1 (first growth phase), S phase and G2 (second growth phase)
  3. Mitotic phase consists of mitosis (nuclear division), and then cytokinesis (cytoplasmic division)
  4. Once cytokinesis has occurred, cells enter interphase, G1 again
  5. Cells that have exited the cell cycle are in G0
151
Q

Describe the events taking place during G1 of interphase

A
  1. Proteins and lipids required for the formation of organelles are synthesised (gene expression, the Endoplasmic reticula and the Golgi apparatus are highly involved in this)
  2. Mitochondria and chloroplasts undergo fission (much like prokaryotic cell division) and increase in number
  3. The cell size increases as its contents increase
  4. There is still only one copy of all the original chromosomes
152
Q

Describe the events of S phase of interphase

A
153
Q

Describe the events of G2 of interphase

A
154
Q

State what G0 is and describe its purpose

A
155
Q

Describe how checkpoints control the progression of the cell cycle

A
156
Q

Describe the key events occurring in the cell before mitosis begins

A
157
Q

Name the stages of mitosis

A
158
Q

Detail the key events that occur during prophase

A
  1. DNA condenses to form chromosomes (these are visible in a microscope when stained)
  2. The nucleolus disappears (as synthesis of ribosomes stops)
  3. The nuclear membrane breaks down (so that spindle fibres can attach to chromosomes)
  4. Centrioles move to opposite poles of the cell
  5. Spindle fibres emanating from centrioles attach to the centromeres of chromosomes
159
Q

Detail the key events that occur during metaphase

A
  1. Spindle fibres from opposite poles are attached to each chromosome
  2. Spindle fibres from opposite poles of the cell begin to shorten, pulling on the chromosomes
  3. This results in chromosomes aligning across the cell equator
  4. This is called the metaphase plate
160
Q

Detail the events that occur during anaphase

A
  1. The pulling of the spindle fibres at the centromeres continues until the sister chromatids are separated from each other
  2. The sister chromatids are pulled towards each of the spindle poles
161
Q

Detail the events that occur during telophase

A
  1. Chromatids reach the poles of the cells and are now called chromosomes (again)
  2. The nuclear envelope reforms
  3. Chromosomes decondense
  4. Nucleolus reforms
162
Q

Describe cytokinesis in animal and plant cells

A
  1. In animal cells, the actin cytoskeleton (microfilaments) causes the membrane at the cell equator to pull inwards
  2. A cleavage furrow is formed
  3. When the cleavage furrow around the cell meets in the middle the cytoplasms of the two cells are separated
  4. In plant cells, golgi vesicles fuse at the metaphase plate
  5. Forming the new cell membrane boundaries of the daughter cells
  6. Cellulose is released to form new cell wall
163
Q

State the key features of meiosis as well as its role in organisms

A
  1. Meiosis produces haploid cells (one of each type of chromosome) from diploid cells (two of each type of chromosome)
  2. The haploid cells produced are called gametes
  3. Gametes from male and female organisms fuse to produce the zygote during fertilisation
  4. Meiosis introduces genetic variation in the gametes through independent assortment and crossing over
164
Q

List the key events that occur during the two stages of meiosis

A
  1. Each of the chromosomes in a diploid cell is duplicated by the process of DNA replication
  2. The duplicated DNA joins at centromeres to form chromosomes with identical sister chromatids
  3. In meiosis I, homologous pairs of chromosomes are separated into two daughter cells
  4. In meiosis II, the identical sister chromatids are separated into two daughter cells
  5. This results the production of cells that have only one of each chromosome
165
Q

Describe the events of prophase 1

A
  1. Chromosomes condense
  2. Nuclear envelope breaks down
  3. Nucleolus disappears
  4. Spindle forms
  5. Duplicated homologous chromosomes form bivalents
  6. Crossing over (formation of chiasmata) can occur at this stage
166
Q

Describe the events of Metaphase 1

A
  1. Homologous pairs of chromosomes (bivalents) align on the cell equator due to spindle fibres
  2. The arrangement of maternal and paternal chromosomes occurs by chance and results in independent assortment
167
Q

Describe the events of Anaphase 1

A
  1. Spindle fibres shorten
  2. Non-sister homologous chromosomes are separated
  3. pulled to opposite poles of the cell
168
Q

Describe the events of Telophase 1

A
  1. Chromosomes reach the poles of the cell
  2. Chromosomes decondense
  3. The nuclear membrane reforms
169
Q

Describe the events of cytokinesis

A
  1. Actin cytoskeleton is involved in pulling the cell membrane inwards at the equator
  2. The cleavage furrows become narrower until two daughter cells are formed
170
Q

Describe the events of Prophase 2

A
  1. Chromosomes condense
  2. Each chromosome consists of two sister chromatids
  3. Spindle forms
  4. Nuclear membrane breaks down
171
Q

Describe the events of Metaphase 2

A
  1. Individual chromosomes (sister chromatids)
  2. align on the equator due to the action of attached spindle fibres
  3. centromes are attached to spindle fibres
172
Q

Describe the events of Anaphase 2

A
  1. Sister chromatids are pulled apart by the spindle fibres
  2. sister chromatids move towards opposite poles of the cell
173
Q

Describe the events of Telophase 2

A
  1. Chromatids arrive at the poles of the cell
  2. Begin to decondense
  3. Nuclear membrane reforms
  4. Nucleolus reappears
174
Q

Explain how independent assortment increases genetic variation in gametes

A
  1. During metaphase 1 of meiosis bivalents (duplicated homologous chromosome pairs) align on the cell equator independently of other chromosomal pairs
  2. The allocation of maternal and paternal chromosomes is affected by this arrangement
  3. In different cells undergoing meiosis, the arrangement of the bivalents can be different
  4. Resulting in a number of different types of gametes possible, each with a different combination of maternal and paternal chromosomes
  5. (even though one cell undergoing meiosis could produce only four genetically different gametes, remember that other combinations are possible in other cells also undergoing meiosis)
  6. The number of genetically different gametes possible is related to the number of chromosome pairs (n): 2n
175
Q

Explain how crossing over increases genetic variation in gametes

A
  1. During prophase 1, the chromosomes of non-sister homologous chromosomes (same genes, but possible different alleles) can intertwine and swap over sections
  2. This causes sister chromatids to no longer be identical and generates new allele combinations within chromosomes
  3. Which produce gametes with new allele combinations when chromosomes are separated during anaphase 2
176
Q

Describe the role of specialised cells in multicellular organisms

A
  1. Many organisms are multicellular
  2. But the cells of these organisms are not identical in structure and function
  3. Groups of cells differentiate (expressing different genes) to become specialised
  4. So that they can perform specific functions better
  5. These groups of specialised cells form tissues that perform a specific function
  6. And tissues may work together form an organ with a particular function
  7. A number of organs may work together for a collective purpose in an organ system
  8. Such adaptations all work to give organisms a better chance of survival and reproduction
177
Q

Describe the specialisations of the following cell types in animals: erythrocytes (red blood cells)

A
  1. Flattened, biconcave shape increases surface area to volume ratio to exchange gases by diffusion
  2. No nucleus, ER or mitochondria: maximises space available to store haemoglobin
  3. Contain haemoglobin which is used to transport oxygen, and to some extent, carbon dioxide
  4. Cells are flexible, which allows them to squeeze through narrow capillaries, minimising distances for the diffusion of gases (maximising rate of diffusion)
178
Q

Describe the specialisations of the following cell types in animals: neutrophils (phagocyte)

A
  1. Multilobed nucleus to help cells migrate through small gaps to sites of infection/damage
  2. Cytoplasm contains many lysosomes, each filled with hydrolytic enzymes which can break down pathogens
179
Q

Describe the specialisations of the following cell types in animals: sperm cells

A
  1. Flagellum allows sperm to move towards an egg to fertilise it
  2. Numerous mitochondria are contained in the mid section to provide energy for flagellar movement
  3. The acrosome in the sperm head is a modified lysosome, containing hydrolytic enzymes needed to penetrate the substances surrounding the egg
  4. There is very little cytoplasm contained in the sperm, which helps sperms cells to encounter less resistance/be more streamlined
180
Q

Describe the specialisations of the following cell types in plants: Palisade cells

A
  1. Numerous chloroplasts to maximise absorbance of light for photosynthesis
  2. Cells have a regular box-like shape, minimising gaps and maximising the number of cells in the tissue (making light absorbance more efficient)
  3. Thin cell walls to maximise the rate of diffusion into/out of cells
  4. Large vacuole allows turgor pressure to maintain the cell shape
  5. Chloroplasts can be repositioned in the cytoplasm to maximise light absorbance
181
Q

Describe the specialisations of the following cell types in plants: Root hair cells

A
  1. Have long thin extensions called root hairs, which increase the surface area of the cell (increasing the rate of osmosis and diffusion)
182
Q

Describe the specialisations of the following cell types in plants: Guard cells (forming stomata)

A
  1. Their shape allows the formation of a pore through which carbon dioxide can enter the leaf for photosynthesis
  2. Water loss causes guard cells to change shape, closing the stomatal pore, reducing further water loss
  3. This is possible because the cell wall is thicker on the inner side of the pores than the outside
183
Q

Describe the specialisations of the following animal tissues: squamous epithelium (alveoli)

A
  1. Cells form a continuous layer to be effective barriers
  2. Cells have flat shape to reduce diffusion distance
  3. Layers are one cell thick to minimise diffusion distance
  4. For example the alveoli of the lungs
184
Q

Describe the specialisations of the following animal tissues: ciliated epithelium (lung airways)

A
  1. Cells form a continuous layer to form effective barriers
  2. Some cells are further specialised to produce mucus (goblet cells), which traps inhaled pathogens
  3. Most cells are ciliated: these hair-like structures move mucus out of the airways
  4. For example in the trachea and bronchioles
185
Q

Describe the specialisations of the following animal tissues: cartilage (e.g. trachea/bronchioles)

A
  1. Connective tissue
  2. Chondrocyte cells embedded in lots of extracellular matrix
  3. Extracellular matrix is made of fibrous proteins such collagen and elastin
  4. Cartilage is firm and flexible
  5. For example outer ear, nose and at the end of bones
186
Q

Describe the specialisations of the following animal tissues: muscle (e.g. smooth muscle of airways)

A
  1. Muscle cells (and so muscle tissue) is contractile
  2. The cytoskeleton of muscle cells is specialised to form a contractile structure made of the proteins actin and myosin called a myofibril
  3. Connective tissue exists between muscle cells
187
Q

Describe the specialisations of the following plant tissues: Epidermis

A
  1. A layer of cells one cell thick (to reduce diffusion distances) covering the surface of plants
  2. Has a waxy cuticle to reduce water loss
  3. Contains stomata to allow and control movement of water and gases contained in air (carbon dioxide and oxygen)
188
Q

Describe the specialisations of the following plant tissues: Xylem

A
  1. Functions to transport water and mineral ions and support the plant
  2. Composed of elongated, dead cells joined end-to-end to form tubes (to allow movement of water)
  3. The walls of the cells are strengthened with waterproof lignin (support function)
  4. The walls of cells have pits, that allow water to move into and out of xylem vessels
189
Q

Describe the specialisations of the following plant tissues: Phloem

A
  1. Functions to transport organic molecules (for example sucrose)
  2. Usually from leaves towards stem and roots
  3. Living cells, joined end-to-end
  4. Sieve tubes have no organelles which aids movement of substances
  5. Perforated sieve plates allow fluid to move from one cell to the next
  6. Companion cells carry out functions for the sieve tube elements
  7. Companion cells have many mitochondria which provide energy for active transport of substances
190
Q

Summarise the role of stem cells in organisms

A
  1. Stem cells are unspecialised, undifferentiated cells which have unlimited proliferative potential (they can divide many times, have not exited the cell cycle into G0)
  2. They can divide by mitosis, and undergo the process of differentiation
  3. To become specialised cells, with particular structures and function
  4. But once specialised, they cannot divide again, or revert back to being stem cells, they have exited the cell cycle into G0
  5. Stem cells can divide to produce more stem cells
  6. They are a way to generate, regenerate or repair tissues within the organism
  7. Lack of stem cells is associated with ageing
  8. Overproduction of stem cells is associated with cancer
191
Q

Discuss (with examples) the different types of stem cell potency

A
192
Q

Use blood cells to exemplify the role of stem cells in animals

A
  1. There are various types of specialised (differentiated) cells in the blood.
  2. These include red blood cells (oxygen/carbon dioxide transport), neutrophils and macrophages (phagocytes, inflammation) and lymphocytes (immune response)
  3. They have a limited and varied functioning lifespan in the body, for example red blood cells last for about 120 days, neutrophils for 6 hours and lymphocytes up to a few years
  4. Haematopoietic stem cells in the bone marrow undergo division and differentiation to regenerate these different types of cells to maintain their number (and function) in the body
  5. Stem cell populations must also be maintained so that this process can continue for the lifespan of the organism
193
Q

Use vascular tissue (xylem and phloem) to exemplify the role of stem cells in plants

A
  1. Xylem and phloem have similar but distinct functions
  2. Xylem transports water and mineral ions, phloem transports organic molecules (amino acids, sucrose)
  3. They have different structures in order to perform these different functions
  4. Between the two tissues lies the cambium, which is made up of meristem tissue (stem cells)
  5. These stem cells can divide and differentiate into the cells that form xylem and those that form phloem
  6. As the plant grows, new vascular tissue must be produced, for example in the shoots and root tips.
194
Q

State the sources of human stem cells

A
  1. Embryonic stem cells
  2. That are totipotent can be acquired from embryos to the 16 cell stage
  3. After that point, cells from the embryo are pluripotent
  4. These can be acquired from embryos/fetus after the 16 cell stage until birth
  5. Adult stem cells (tissue stem cells)
  6. Are multipotent
  7. And can be acquired from particular parts of the body (for example hematopoietic stem cells from bone marrow. Stems cells can also be acquired from skin and blood vessels)
195
Q

Suggest how stem cells can be used to repair damaged or degenerated tissue

A
  1. Stem cells can be isolated
  2. They can be placed into the affected tissue
  3. Stem cells are exposed to chemical signals from neighbouring cells
  4. Which causes them to differentiate into the affected cell type
  5. The presence of new cells may restore the function of the affected area/tissue
196
Q

Give examples of the use of stem cells in medicine

A
  1. Repair damaged heart tissue (cardiac muscle cells)
  2. Treat type I diabetes, regenerate insulin-producing cells in the pancreas, removing the need for insulin injections
  3. Treat Parkinson’s disease, regenerate dopamine-producing cells in the brain
  4. Treat Alzheimer’s disease, regenerate brain cells destroyed by build-up of abnormal proteins
  5. Treating macular degeneration: loss of vision is caused by the degeneration of cells in the retina.
  6. Reversing birth defects
  7. Restoring spinal cord function after injury
  8. Source of plant-based medicines: plant stem cells can be cultured and used as an unlimited source of possible plant-based medicinal substances
197
Q

Give examples of the use of stem cells in medical research

A
  1. Stems cells are an unlimited source (due to their proliferative potential) of human cells.
  2. These cells can be cultured in vitro
  3. And used for experimentation
  4. for example, to test the effect of drugs, before clinical trials
  5. Or model human tissues and organs reducing the need for animal experimentation

Dr Bhavsar's A level Biology (OCR, A) (20 decks)

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