TOP

OCR Categories Archives: Module 2: Foundations in Biology

Enzymes

2.1.3 Enzymes

(a) state that enzymes are globular proteins, with a specific tertiary structure, which catalyse metabolic reactions in living organisms

All enzymes are globular proteins with a specific tertiary structure, which catalyse metabolic reactions in all living organisms. This means that they speed up chemical reactions, but are not ‘used-up’ as part of the reaction.

Enzymes are relatively large molecules, consisting of hundreds of amino acids which are responsible for maintaining the specific tertiary structure of the enzyme. Each enzyme has a specific active site shape, maintained by the specific overall tertiary structure. Therefore the tertiary structure must not be changed.

(b) state that enzyme action may be intracellular or extracellular

Extracellular enzyme action occurs outside the cell, which produces the protein. For example, some enzymes in digestive systems are extracellular as they are released from the cells that make them, onto food within the digestive system spaces.

Intracellular enzyme action occurs inside the cell, which produces the enzyme. For example, some enzymes in digestive systems are found in the cytoplasm of cells or attached to cell membranes and the reaction takes place inside the cell.

 

(c) describe, with the aid of diagrams, the mechanism of action of enzyme molecules, with reference to specificity, active site, lock and key hypothesis, induced-fit hypothesis, enzyme-substrate complex, enzyme-product complex and lowering of activation energy.

 

The activation energy is the minimum level of energy required to enable a reaction to take place. Enzymes work by lowering the activation energy of reactions. This means reactions can proceed quickly at temperatures much lower than boiling point as less energy is required for the reaction.

 

(d) describe and explain the effects of pH, temperature, enzyme concentration and substrate concentration on enzyme activity

(e) describe how the effects of pH, temperature, enzyme concentration and substrate concentration on enzyme activity can be investigated experimentally

(f) explain the effects of competitive and non-competitive inhibitors on the rate of enzyme-controlled reactions, with reference to both reversible and non-reversible inhibitors

An enzyme inhibitor is any substance or molecule that slows down the rate of an enzyme-controlled reaction by affecting the enzyme molecule is some way.

Reversible inhibitors are inhibitors that bind to the active site for a short period and then leave. The removal of the inhibitor from the reacting mixture leaves the enzyme molecules unaffected.

 

Irreversible inhibitors are inhibitors that bind permanently to the enzyme molecule. Any enzyme molecules bound by inhibitor molecules are effectively denatured.

 

 

(g) explain the importance of cofactors and coenzymes in enzyme controlled reactions

A cofactor is any substance that must be present to ensure enzyme-controlled reactions can take place at the appropriate rate. Some cofactors are part of the enzymes (prosthetic groups); others affect the enzyme on a temporary basis (coenzymes and inorganic ion cofactors).

(h) state that metabolic poisons may be enzyme inhibitors, and describe the action of one named poison

(i) state that some medicinal drugs work by inhibiting the activity of enzymes

 

 

Continue Reading

Nucleic Acids

Nucleic Acids

  • The monomer units in nucleic acids are called nucleotides.
  • They consist of a pentose sugar (deoxyribose/ribose) a phosphate group and a nitrogenous base that is either a pyrimidine or a purine.
  • These three components are joined in condensation reactions by covalent bonds.

Nucleotide derivatives

ATP and ADP are nucleotide derivatives and are often present in co-enzymes such as NADP – nicotinamide adenine dinucleotide phosphate which is used in photosynthesis.

 

 

 

 

 

DNA structure

  • DNA is made of two polynucleotide strands, antiparallel to each other.
  • The monomers in DNA include deoxyribose sugar, a phosphate group and the bases cytosine, thymine, adenine and guanine.
  • The monomers are bonded by covalent phosphodiester bonds.
  • The bases are bonded with hydrogen bonds in complementary base pairing. These hydrogen bonds are weak but together are stronger as there is a large number of them.
  • It stores genetic information and hereditary material in the sequence of its bases.
  • DNA coils into a double helix shape.
  • DNA is a macromolecule and is very long to store all the information.
  • Purines and pyrimidines always pair together to provide equal sized rungs on the ladder like structure of DNA. A pairs with T, C pairs with G and vice versa.
  • The 5’ end is where the phosphate is attached to the fifth carbon and the 3’ end is where the phosphate is attached to the third carbon.
  • In eukaryotes, DNA is stored in the nucleus and is wound around histone proteins to form chromosomes. Each chromosome is one molecule of DNA. There is also a loop inside mitochondria and chloroplasts.
  • In prokaryotes, DNA is in a loop floating free within the cytoplasm and is not wound around histone proteins. It is therefore naked.

 

DNA Replication

DNA uses semi-conservative replication as both of the original strands are used in the two daughter strands.

DNA is a self-replicating molecule and its replication takes place during interphase in cell division.

The DNA in mitochondria and chloroplasts also replicates each time these organelles divide.

 

  • DNA unwinds (catalysed by gyrase enzyme) and unwinds (catalysed by DNA helicase)
  • Free DNA nucleotides form hydrogen bonds to the exposed bases (using complementary base pairing) this is catalysed by DNA polymerase and occurs in the 5’ – 3’ direction ONLY
  • Discontinuous okazaki fragments are made on the lagging strand of DNA that flows from 3’ – 5’ which are then connected up by DNA ligase
  • The nucleotides join together to form a new molecule of DNA

Mutations may occur in replicating the genetic code. These mutations occur when DNA is not accurately copied and when the wrong nucleotide is inserted into the strand. Some mutations are harmful, such as achondroplasia (a form of dwarfism), Marfan syndrome (a connective tissue disorder), and Huntington disease (a degenerative disease of the nervous system). Some are not, such as red hair.

Mutations can be passed on and inherited from parents or can occur spontaneously.

 

 

Protein synthesis

Transcription

  • In the nucleus, DNA unwinds and unzips

  • Hydrogen bonds between the complementary nucleotides break
  • RNA polymerase catalyses the pairing of free RNA nucleotides to the template strand of the DNA
  • The RNA strand is identical to the other coding strand of DNA
  • The mRNA chain passes out of the nucleus through a nuclear pore
  • Exons are regions of the RNA strand that code for the amino acids of the protein being synthesized whereas introns are segments that do not code for the protein and are not useful
  • Introns are cut out and the exon regions are spliced together to form a long chain of codons
  • The mRNA chain progresses out of the nucleus and over onto the rough endoplasmic reticulum that has the ribosomes on it
  • Ribosomes are made up of two subunits

  • Transfer RNA molecules bring amino acids to the ribosome and pair up their anticodons with the codons in the mRNA molecule.
  • Peptide bonds form between the adjacent amino acids forming the polypeptide
  • ATP is required for translation
  • When the polypeptide has been assembled the RNA chain breaks down to be recycled again
  • The newly synthesized polypeptide is folded into its shape to form the protein

 

 

 

 

 

Continue Reading

Cell Structure #2

Microscopes

Light microscope – Light microscopes shine light through a specimen and then uses focused lenses to magnify it.

Laser scanning microscope – These use laser light to scan an object, point by point, before using the information to assemble an image on the computer. They create very high definition, high contrast images and have depth selectivity (they can focus on structures at different depths in the specimen). They are used for biological research and in the medical progression e.g. to use on a patient with a fungal corneal infection as the fungal filaments within the cornea will be visible on the microscope image. It helps give faster diagnosis so the treatment is given earlier and is therefore more effective.

  1. Nerve Cell

  1. Lung tissue

  1. Plant vascular bundle

  1. E.Coli bacteria

  2. Mitochondria

Magnification

The magnification is how many times bigger an image is compared to the original specimen. Microscopes produce linear magnification. (it’s width and length are magnified by the same amount)

Magnification = Size of Image/Size of Object

Size of Object = Size of image/Magnification

Size of image = Size of Object x Magnification

 

Resolution

Resolution is the microscopes ability to show fine detail and produce clear, sharp images.

An eyepiece graticule is an eye piece that fits on a microscope with a ruler etched into it. The ruler has 100 divisions which are measured in Eye Piece Units or EPU’s. To calibrate the eyepiece graticule a graticule slide is placed under the light microscope with another ruler displaying either 1cm or 1mm in 100 divisions. Using the graticule slide, we can calibrate the lens to work out how long each division on the eyepiece would be after the image is magnified. The image of the ruler is then superimposed over your slide sample so that you can use the scale you have worked out with the graticule slide to measure samples and specimens.

Stage graticules are available in two types

  • (book) 1mm long graticule with 100 divisions. 1mm = 1000μm so each division = 10µm
  • (class) 1cm long graticule with 100 divisions. 1cm = 10000µm so each division = 100µm

 

 

Eukaryotic Cells

  • Robert Hooke 1665 discovered cells
  • Cilia/flagellum – long whip like tail made of microtubules
  • Cell membrane – encloses the cell contents, selective permeability, flexible
  • Cytoplasm – water and nutrients, contains the cytoskeleton and centrosomes which assemble microtubules
  • Endoplasmic reticulum – phospholipid bilayer: Rough – ribosomes and create protein: Smooth – enzymes create lipids cell detox and stores ions such as sodium ions
  • Ribosomes assemble amino acids into poly peptides
  • Nucleus – nucleoplasm inside, stores the cell’s DNA, chromatic holds the DNA, Cell division means the chromatin makes chromosomes Nucleolus makes rRNA combines with proteins which makes ribosomes
  • Golgi apparatus – processes and packaging and sends them out, contains Golgi bodies – these are the Golgi apparatus layers, proteins cut up into smaller hormones and combine proteins with carbs to make various molecules e.g. mucus
  • Lysosomes – cell digestion, enzyme sacks, cell waste >> simple compounds used for building materials
  • Vesicles – phospholipid bilayer, responsible for transporting substances around the body
  • Mitochondria – respiration – makes energy adenosine tri-phosphate, muscle cells need more energy so have more mitochondria, they used to exist as prokaryotes and contain a small amount of DNA

Eukaryotic Animal Cell

Mitochondrion

Mitochondria are double membrane structures enclosing a semi-fluid matrix, in which aerobic respiration (ATP synthesis) occurs, producing the energy the cell needs to move, contract, divide, and produce secretory products. The outer membrane of a mitochondrion is smooth, whereas the inner membrane forms cristae (folds) and is very convoluted. On the cristae, simple sugars such as glucose are combined with oxygen to produce ATP. Both the cristae and the semi-fluid matrix contain the enzymes that allow for aerobic respiration.

Vesicle – Lysosome

Lysosomes assist in intracellular digestion as they contain hydrolytic enzymes that break down bacteria. In a white blood cell, lysosomes are released into the vacuole to kill and digest the bacteria the cell has engulfed. Having to many lysosomes in the cytoplasm can cause necrosis.

Plasma Membrane/Cell Surface Membrane

The plasma membrane is a bilayer of phospholipid molecules with hydrophilic heads and hydrophobic tails, there are protein channels set into the barrier to transport substances into the cell. It’s function is to be a partially permeable membrane that provides protection and physical allows the import and export of chemicals and substances to and from the cell.

Golgi Apparatus

The Golgi apparatus is membrane-bound structure composed of a single membrane that binds a stack of large vesicles in a network, where they can modify and package proteins for transport. The stack of large vesicles

is surrounded by many smaller vesicles that contain the packaged protein macromolecules. The enzymatic/hormonal contents of lysosomes, peroxisomes and secretory vesicles are also packaged in vesicles at the periphery of this organelle. The vesicles can become detached from the Golgi which allows chemicals to be kept isolated from each other in the cytoplasm. These detached vesicles allow for secretion by merging with the plasma membrane of the cells surface.

Peroxisome

These are membrane bound packets of oxidative enzymes responsible for turning hydrogen peroxide into harmless water and oxygen.

Cytoplasm/Cytosol

The cytoplasm is the semi-liquid medium that the animal cell’s organelles are suspended in. It makes up the main body of the cell, contains many dissolved ions and is the site of most chemical reactions within the cell.

Cytoskeleton

The cytoskeleton is composed of microfilaments, microtubules and intermediate filaments and functions for both movement and support in the cell.

Smooth Endoplasmic Reticulum (SER)

The smooth endoplasmic reticulum is a continuation of the outer nuclear membrane. It assists the synthesis and transport of lipids. Unlike the rough endoplasmic reticulum, the smooth ER doesn’t have ribosomes.

Nuclear Pore

Nuclear pores are protein lined channels that regulate the transport of chemicals and substances to and from the nucleus. mRNA moves in and out of these entrances.

Centrioles/Microtubules

Centrioles are the two short cylinders which contain a ring of nine groups of fused microtubules, with three in each group. These migrate to the opposite poles to aid cell division when the spindle begins to develop. Microtubules and centrioles are part of the cytoskeleton.

Secretory Vesicles

Hormones and neurotransmitters and other cell secretions are packaged in the secretory vesicles at the Golgi apparatus. The vesicles are then transported to the cell membrane where they can release the cell secretions outside the cell.

Nucleolus

The nucleolus is where RNA and ribosomes are made within the nucleus. It is made of proteins and unlike many of the cell organelles in an animal cell, is not a membrane bound structure

Vacuole

Vacuoles are membrane bound sacks that aid in intracellular digestion, storing nutrients and waste products and increasing the size of the cell during growth. In animal cells, vacuoles are generally small, unlike in plant cells where they are generally larger.

Rough Endoplasmic Reticulum (RER)

A folded membrane structure and a continuation of the outer nuclear membrane, the rough endoplasmic reticulum is very similar to the smooth. However the RER has ribosomes which synthesize proteins, before they are collected in the RER for transport around the cell.

 

Centrosome/Microtubule Organizing Centre (MTOC)

A centrosome/microtubule organizing centre (MTOC) is the area of the cell that produces microtubules. A complete animal cell centrosome is a pair of centrioles held perpendicular to each other. At cell division, the centrioles replicate and the centrosome divides, resulting in two centrosomes with a pair of centrioles each. They migrate to the cells poles and there microtubules grow into a spindle, responsible for separating replicated chromosomes into the two daughter cells the original animal cell will divide into.

Ribosomes

Ribosomes are the site of protein synthesis. The protein chains are lengthened by transfer RNA adding individual amino acids to the messenger RNA strand that the nucleus has sent to the ribosomes. Ribosomes are structured in two parts, a large subunit and a small subunit. They are full of RNA.

 

Cell Wall

In plants this is made of cellulose and is strong to prevent cells from bursting when turgid. They provide support, maintain the cells shape and allow solutions to pass through. Fungi have cell walls of chitin and not cellulose.

Prokaryotic Cells

Prokaryotic cells are much smaller than eukaryotic and do not contain some of the organelles present in eukaryotes. They do not have centrioles or a nucleus and so divide by binary fission. They also do not have membrane bound organelles (e.g. ER and Golgi). Around their edge they sometimes have a waxy capsule and a cell wall made of peptidoglycan as well as pili and flagella. Instead of a nucleus the cell stores its genetic material in the plasmid and a nucleoid. Its ribosomes are smaller and it contains starch granules as well.

 

 

 

Continue Reading

Cell Membranes

Cell Membranes

(a) outline the roles of membranes within cells and at the surface of cells

 

(b) state that plasma (cell surface) membranes are partially permeable barriers

Plasma membranes are partially permeable meaning they let some molecules through but not others.

(c) describe, with the aid of diagrams, the fluid mosaic model of membrane structure

The phospholipid bilayer is the basic structural component of plasma membranes. It consists of 2 layers of phospholipid molecules. The centre of the bilayer is hydrophobic so the membrane doesn’t allow water-soluble substances (like ions) through it – it acts as a barrier to these dissolved substances

In the fluid mosaic model, phopholipid molecules form a continuous double layer (bilayer). The bilayer is ‘fluid’ because the phospholipids are constantly moving. The fluid mosaic model also contains cholesterol molecules, proteins, glycoproteins and glycolipids.

(d) describe the roles of components of the cell membrane:

(e) outline the effect of changing temperature on membrane structure and permeability

(f) explain the term cell signalling

(g) explain the role of membrane-bound receptors as sites where hormones and drugs can bind

Cell signalling is when cells communicate with one another by signals. In order to detect signals, cells must have on their surface ‘sensors’ capable of receiving signals, these are known as receptors and are often protein molecules or modified protein molecules (e.g. glycoproteins). In multicellular organisms, communication is often mediated by hormones between cells. Hormones are chemical messengers, produced in specific tissues and then released. Any cell with a receptor for the hormone molecule is called a target cell.

Cells communicate with each other using messenger molecules:

  1. One cell releases a messenger molecule (e.g. hormone)
  2. This molecule travels to another cell (e.g. in the blood)
  3. The messenger molecule is detected by the cell because it binds to a receptor on its cell membrane

Receptor proteins have specific shapes – only messenger molecules with a complementary shape can bind to them. Different cells have different types of receptors – they respond to different messenger molecules. A cell that responds to a particular messenger molecule is called a target cell.

Glycoproteins have receptors. They have a role in:

  • cell adhesion – bind cells together in a tissue
  • acting as antigens on the surface of cells. Cells of the immune system have receptors that detect the glycoproteins and can determine whether they are ‘self’ or ‘non self’

Many drugs work by binding to receptors in cell membranes. They either trigger a response in the cell, or block the receptor and prevent it from working e.g. cell damage causes the release of histamine. Histamine binds to receptors on the surface of other cells and causes inflammation. Antihistamines work by blocking histamine receptors on cell surfaces. This prevents histamine from binding to the cell and stops inflammation.

(h) explain what is meant by passive transport (diffusion and facilitated diffusion including the role of membrane proteins), active transport, endocytosis and exocytosis

Substances can move across a membrane through 2 processes: passive and active

Active Transport:

(i) explain what is meant by osmosis, in terms of water potential

Osmosis is the movement of water molecules by diffusion from a region of high water potential to a region of low water potential across a partially permeable membrane

Water potential is a measure of the concentration of water molecules that are ‘free’ to diffuse.

Adding solutes to water means the water molecules cluster around the solute molecules, lowering the concentration of ‘free’ water molecules and therefore lowers the water potential.

(j) recognise and explain the effects of solutions of different water potentials can have upon plant and animal cells

In pure water, water moves into a cell by osmosis down a water potential gradient.

  • Animal Cell – becomes haemolysed (bursts open)
  • Plant Cell – the cell wall prevents bursting. The membrane pushes against the cell wall and the cell becomes turgid

In a very low water potential solution (e.g. concentrated sugar solution), water moves out of a cell by osmosis down a water potential gradient.

  • Animal Cellshrinks and appears wrinkled and the cell becomes crenated
  • Plant Cell – the membrane pulls away from the cell wall and the cell becomes plasmolysed

 

 

Continue Reading

Enzymes #2

Enzymes

Biological Catalysts

Enzymes are biological catalysts that speed up metabolic reactions and remain unchanged at the end of the reaction. The number of reactions that an enzyme can catalyse per second is known as the turnover number

Active site– the indented area on the surface of the enzyme which has a complementary shape to the substrate molecule

Metabolic reactions – chemical reactions inside living cells/organisms

Catalysts can speed up reactions as they can speed up reactions without altering the pH or temperature and instead function at temperatures and pressures that sustain life. They are more specific than chemical catalysts because of their complementary shape to the substrate so rarely produce unwanted by-products.

Enzyme Structure

  • Enzymes are proteins and have protein structure (primary, secondary, tertiary, quaternary) and therefore are coded for by genes
  • Some use cofactors
  • Metabolic disorders are the result of deficient enzymes in metabolic pathways
  • Enzymes also catalyse the formation of an organism’s structural components e.g. collagen in bone and cartilage in blood vessel walls
  • Active site contains about 6 – 10 amino acids and the tertiary structure is essential as the shape of the active site must be complementary to the substrate molecule
  • Active sites are changed by temperature and pH as this alters the bonds that hold together the bonds of the tertiary structure

Intracellular – inside the cell

  • Metabolic pathways contain a series of consecutive reactions each catalysed by a specific enzyme
  • The reactants and intermediates act as substrates and are known as metabolites
  • Catabolic – metabolites broken down, Anabolic – larger metabolites synthesised from smaller ones
  • g. respiration and photosynthesis
  • Catalase breaks down hydrogen peroxide, has four polypeptide chains and a haem group, is the fastest acting enzyme with the highest turnover number known, found in peroxisomes in eukaryotes, white blood cells use it to kill microbes

Extracellular – outside the cell

  • Amylase is produced in salivary glands to digest polysaccharides
  • Trypsin is made in the pancreas and digests proteins in the small intestine

Cofactors

Prosthetic groups – a cofactor that is permanently bound by covalent bonds to an enzyme molecule.

E.g. Zinc ion bound to the active side of carbonic anhydrase

Some cofactors act as co-substrates and some change the distribution of charge on the enzyme’s surface and make temporary bonds to aid the substrate in binding to the enzyme.

Coenzymes – these bind temporarily to the active site of the enzyme with the substrate and are organic non-protein molecules which are chemically changed during the reaction

Lock-and-key hypothesis

Induced-fit hypothesis

Enzymes lower the activation energy for a reaction.

Effect of temperature on enzymes

  • Extra heat energy causes the molecules to vibrate which increases the rate of successful collisions between molecules and increases the force with which they collide
  • Both enzyme and the substrate move faster, therefore the rate of formation of ES complexes increases and the rate of reaction increases.
  • Rate of reaction is at its maximum at optimum temperature
  • Heat also makes molecules vibrate which may break some of the weaker bonds in the tertiary structure of the active site, denaturing it (bonds like the ionic bonds and hydrogen bonds)
  • As the active side changes the substrate will no longer fid
  • As more heat is applied the enzyme active site changes shape completely and irreversible so the reaction cannot proceed at all.

Effect of pH on enzymes

Acidic – 0-6 pH

Neutral – 7 pH

Alkaline – 8-14 pH

Acids are proton (H+) donors

Buffers – Can donate or accept protons, resist changes to pH

Enzymes work at different pH’s as they work in different areas and extra/intracellularly.

Effect of substrate concentration

Initially rate of reaction increases as more enzyme substrate complexes while the substrate concentration is the limiting factor but when the reaction reaches Vmax the limiting factor is the enzyme concentration as all the enzyme active sites are occupied and the maximum turnover rate is reached.

Enzyme synthesis – genes for synthesising particular enzymes can be switched on or off depending on a cells needs

Enzyme degradation – Cells degrade old enzymes to regulate the metabolism in the cell and to ensure abnormal proteins are not accumulated in the cell

The initial rate can be measured by finding the gradient of the tangent of the steepest part of the curve of any given reaction. Initial rates for both A and B can then be compared.

 

 

 

 

End product inhibition – when enzyme catalysed reactions are regulated by the final product molecule acting as an inhibitor for the first enzyme in the sequence. This is an example of negative feedback. In metabolic pathways this is non-competitive and reversible

Poisons

Medicines

 

 

 

 

 

Continue Reading

Biological Membranes #2

Biological Membranes

Plasma membranes are partially permeable as they allow some but not all substances to pass through them.

  • Very small molecules diffuse through the plasma membrane
  • Some substances dissolve in the lipid layer to pass through
  • Larger substances pass through protein channels or are carried by carrier proteins

Roles of the plasma membrane

  • Separates the cell’s contents from the external environment
  • Regulates transport of materials into and out of the cell
  • May contain specific enzymes involved in metabolic pathways
  • Contains antigens so that the immune system can recognise the cell as being self and not attack it
  • May release chemical signals to other cells and contains receptors for cell communication and signalling (hormone bind to membrane bound receptors)
  • May be the site of chemical reactions

Roles of membranes within cells include:

  • The cristae of mitochondria which provides a large surface area for aerobic respiration
  • The thylakoid of chloroplasts which house chlorophyll and are the site of photosynthesis
  • The plasma membrane of the epithelial cells of the small intestine which contain digestive enzymes that breakdown certain sugars

Fluid mosaic model – theory of cell membrane structure with proteins embedded in a sea of phospholipids

  • Channel proteins – allow ions to mass through
  • Carrier proteins – allow specific molecules across the membrane
  • Glycolipid – lipid/phospholipid with a carbohydrate chain
  • Glycoprotein – protein with a carbohydrate chain
  • Others include: Enzymes, antigens & receptor sites for hormones
  • Cholesterol – regulates fluidity and gives mechanical stability and resists the effect of temperature changes on the membrane
  • Glycocalyx – the hydrophilic area just outside the cell consisting of carbohydrate chains attached to both lipids and proteins

 

Neuron cell membranes

  • Protein channels and carriers covering the long axon allow the transport of ions to bring the conduction of electrical impulses along their length
  • They have a myelin sheath of flattened cells around them several times to give more membrane layers and to insulate the electrical impulses

Root hair cell membranes

They have many carrier proteins which transport nitrate ions from the soil into the cell as part of the nitrogen cycle.

 

 

 

Cristae of Mitochondria

These contain many electron carriers made of protein and hydrogen ion channels which are associated with ATP synthesis

White Blood Cell Membranes

These contain protein receptors for detection of antigens on foreign cells and pathogens

Diffusion across membranes

Diffusion – movement of molecules from an area of high concentration of that molecule to an area of low concentration across a partially permeable membrane along a concentration gradient. It is passive and does not involve metabolic energy (ATP)

Facilitated diffusion – the movement of molecules from an area of high concentration of that molecule to an area of low concentration across a partially permeable membrane via protein channels or carriers. This still does not require metabolic energy (ATP)

Passive processes only use the kinetic energy of the molecules, not ATP.

When molecules move down their concentration gradient they are still moving randomly but remain evenly dispersed which is called net diffusion. They have reach equilibrium.

Concentration gradient is maintained by the respiring cells using the O2 in animals and the carbon dioxide diffusing into the palisade cell to be used in chloroplasts for photosynthesis and the constant use of these molecules inside the cell maintains a concentration gradient as there is always a higher concentration in the external environment.

Factors the affect the rate of simple diffusion

  • Temperature – as this increases, kinetic energy increases so rate of diffusion increases
  • Diffusion Distance – the thicker the membrane/diffusion distance, the slower the rate of diffusion
  • Surface area – more diffusion can take place of a larger surface area
  • Size of diffusing molecule – smaller molecules/ions diffuse more quickly
  • Concentration gradient – steeper the gradient the faster the diffusion

Neurons have many ion channels at synapses to aid the electrical conductivity between cells.

Epithelial cell membranes always have chloride ion channels as these play a part in regulating mucus composition.

Osmosis

This is the net passage of water molecules down their water potential gradient, across a partially permeable membrane.

Water potential – measure of the tendency of water molecules to diffuse from one region to another

In a solution the solute is dissolved in the solvent. Water molecules can pass directly through the phospholipid bilayer.

If solute molecules dissociate into charged ions water will be attracted to them, as it is a polar molecule.

 

Water potential

  • Pure water has the highest water potential of 0kPa
  • Solute molecules lower the water potential
  • Water molecules move from a high water potential to a low water potential
  • When water potential is equal on both sides there will be no net movement of osmosis
  • Water with solutes has negative water potential values

Active transport

Active transport – the movement of substances against their concentration gradient across a cell membrane requiring ATP

Endocytosis  – bulk transport of molecules too large to pass through a cell membranes into a cell

Exocytosis – bulk transport of molecules too large to pass through a cell membrane out of a cell

Sodium Potassium pumps

3x Na+ ions are transported in one direction while 2x K+ ions are transported in the opposite direction.

Carrier proteins

ATP allows some carrier proteins to change their conformation to carry the molecule from one side of a gradient to another

Bulk transport

Endocytosis

Pinocytosis – cells ingesting liquids

Phagocytosis – cells ingesting solid matter (e.g. WBC ingesting a bacteria)

Exocytosis

  1. A membrane bound vesicle, containing substance to be secreted, is moved towards the cell surface
  2. The vesicle fuses to the cell membrane
  3. The fused site splits, releasing the contents of the vesicle to the external environment

Factors affecting membranes

Temperature

Increased temperature

  • Molecules have more kinetic energy and therefore move faster
  • Membrane fluidity increases as phospholipids have more kinetic energy
  • Permeability increases
  • The tertiary structure of the proteins may be compromised both on the plasma membrane and the cytoskeleton threads beneath the membrane surface which may impede their functions (e.g. enzymes unable to catalyse reactions when they are denatured)
  • Membrane fluidity may affect the infolding of the membrane during phagocytosis
  • It may also change the ability of the cell to signal other cells by exocytosis
  • The presence of cholesterol acts as a temperature buffer as it provides more stability even through the phospholipids move more fluidly in high temperatures

Decreased temperature

  • Saturated fatty acids become compressed
  • Unsaturated fatty acids maintain fluidity as the kinks in their tails push the other phospholipids away
  • Cholesterol also buffers this as it prevents phospholipid molecules packing in too tightly
  • Molecules have lowered kinetic energy and therefore move slower

Solvents

  • Organic solvents such as acetone and ethanol will damage cell membranes as they dissolve lipids

 

 

 

 

 

Continue Reading

Nucleotides and Nucleic Acids

Nucleotides and Nucleic Acids

(a) state that deoxyribonucleic acid (DNA) is a polynucleotide, usually double stranded made up of nucleotides containing the bases adenine (A), thymine (T), cytosine (C) and guanine (G)

Nucleic acids come in two forms: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

 

(b) state that ribonucleic acid (RNA) is a polynucleotide, usually single stranded, made up of nucleotides containing the bases adenine (A), uracil (U), cytosine (C) and guanine (G)

(c) describe, with the aid of digrams, how hydrogen bonding between complementary base pairs (A to T, G to C) on two antiparallel DNA polynucleotides leads to the formation of a DNA molecule, and how the twisting of DNA produces its ‘double-helix’ shape

The five organic nitrogenous bases are grouped into purines and pyramidines. Pyramidines are smaller than purines.

  • Purines: Adenine (A) and Guanine (G) – Ag (Silver) is PURE metal = PURINES
  • Pyramidines: Thymine (T), Uracil (U) and Cytosine (C)

DNA is found in the nucleus. The molecule is twisted into a double helix in which each of the strands are antiparallel to each other, meaning the strands always run in opposite directions to each other. It has two sugar phosphate backbones attached to one another by complementary bases. These bases pair in the centre of the molecule by means of hydrogen bonds. The chains are always the same distance apart because the bases pair up in a specific way. Where a pyramidine appears on one side, a purine appears on the other.

 

(d) outline, with the aid of diagrams, how DNA replicates semi-conservatively, with reference to the role of DNA polymerase

Replicating DNA:

  1. The double helix unwinds.
  2. Hydrogen bonds between the bases are broken apart to ‘unzip’ the DNA to form two single strands, exposing the bases.
  3. Hydrogen bonds form between free DNA nucleotides and exposed bases through complementary base pairing.
  4. Covalent bonds are formed between the phosphate of one nucleotide and the sugar of the next to seal the backbone using the enzyme DNA polymerase.
  5. Each new DNA molecule consists of one conserved strand plus one newly built strand. This process of DNA replication is described as semi-conservative replication.

(e) state that a gene is a sequence of DNA nucleotides that codes for a polypeptide

A gene is a sequence of DNA nucleotides that codes for a polypeptide (protein)

 

Proteins are made from amino acids. Different proteins have a different number and order of amino acids. Each amino acid is coded for by a sequence of 3 bases in a gene.  It’s the order of nucleotide bases in a gene that determines the order of amino acids in a particular protein. Different sequences of bases code for different amino acids.

 

(f) outline the roles of DNA and RNA in living organisms (the concept of protein synthesis must be considered in outline only)

There are 3 forms of RNA:

 

 

 

 

 

 

Continue Reading

Cell Structure

Cell Structure

(a) state the resolution and magnification that can be achieved by a light microscope, a transmission electron microscope and a scanning electron microscope

Light Microscope – uses a number of lenses to produce an image that can be viewed directly at the eyepiece. Light passes from a bulb under the stage, through a condenser lens and then through the specimen. This beam of light is passed through an objective lens (x4, x10, x40) and then the eyepiece lens (x10).

Overall Magnification = Objective Lens Magnification x Eyepiece Lens Magnification

Transmission Electron Microscope (TEM) – uses electromagnets to focus a beam of electrons, which is transmitted through the specimen. Denser parts of the specimen absorb more electrons, which makes them look darker on the image you end up with creating a contrast.

 

Scanning Electron Microscope (SEM) – an electron beam is scanned across the specimen. The electrons don’t pass through the specimen, they bounce off and are detected at multiple detectors.

(b) explain the difference between magnification and resolution

  • Magnification – the number of times greater an image is than the object itself
  • Resolution – the ability to distinguish two separate points as distinct from each other

 

 

(c) explain the need for staining sample for use in light microscopy and electron microscopy

Material needs to be stained to allow the specimen to be seen under the microscope. Images are produced because some parts of the object absorb more light/electrons than others to create contrast, but sometimes the object being viewed is completely transparent – this makes the whole thing look white because the light rays/electrons pass straight through. This problem is solved by staining the specimen. Different types of stains bind to different specific cell structures:

  • Acetic Orcein stains DNA dark red
  • Genetian Violet stains bacterial cell walls

Some specimens are embedded in wax, to prevent distortion of the structure when being cut.

 

Electron microscopes are stained with heavy metals (like lead) to scatter the electrons and create contrast.

(e) describe and interpret drawings and photographs or eukaryotic cells as seen under an electron microscope

(f) outline the functions of the structures listed in (e)

(g) outline the interrelationship between the organelles involved in the production and secretion of proteins

  1. In the nucleus is the DNA needed to make proteins. The DNA from the nucleus is copied into a molecule called mRNA
  2. The mRNA leaves the nucleus and attaches itself to a ribosome on the rough endoplasmic reticulum
  3. The ribosome reads the instructions and uses the code to make proteins and is folded and processed in the rough endoplasmic reticulum
  4. The proteins are transported to the Golgi apparatus in vesicles where they fuse with it to modify the protein
  5. The protein leaves the Golgi apparatus in vesicles and fuses with the plasma cell membrane to be secreted.

 

(h) explain the importance of the cytoskeleton in providing mechanical strength of cells, aiding transport within cells and enabling cell movement

The cytoskeleton is the network of protein fibres found within cells that gives structure and shape of the cell, aids transport and enables cell movement. Its functions are:

  • to support the cell’s organelles by keeping them in position
  • to strengthen the cell and maintain its shape
  • to transport materials within the cell
  • to make the cells move (flagella and cilia)

Microfilaments (Actin) are proteins which cause movement and move some organelles around inside cells by moving against each other.

 

Microtubules are made of a protein called tubulin and these proteins will move organelles and other cell contents along the fibres using ATP to drive movement.

 

Flagella (Undulopodia) and cilia are both hair-like extensions that stick out from the surface of the cell. There are two microtubules in a central bundle surrounded by nine microtubules arranged in a circle. Flagella is longer than cilia and usually occur in ones or twos in cells. Cilia is less than 10µm long and occur in large numbers. Flagella enables movement of the cell and cilia causes sweeping movements to move substances across the surface of the cells.

(i) compare and contrast, with the aid of diagrams and electron micrographs, the structure of prokaryotic cells and eukaryotic cells

Eukaryotic Cells – (means having a true nucleus) cells contain many organelles some of which are bound by a membrane e.g. animals, plants and fungi

Prokaryotic Cells – (means before nucleus) cells lack membrane organelles such as a nucleus e.g. bacteria. These cells are about to 10,000 times smaller than eukaryotic cells

(j) compare and contrast, with the aid of diagrams and electron micrographs, the structure and ultrastructure of plant cells and animal cells 

 

 

Continue Reading

Cell Division, Cell Diversity and Cellular Organisation

Cell Division, Cell Diversity and Cellular Organisation

(a) state that mitosis occupies only a small percentage of the cell cycle and that the remaining percentage includes the copying and checking of genetic information

(b) describe, with the aid of diagrams and photographs , the main stages of mitosis (behaviour of the chromosomes, nuclear envelope, cell membrane and centrioles)

(c) explain the meaning of the term homologous pair of chromosomes

One chromosome in each pair comes from each parent and theyare the same size and have the same genes, although they could have different versions of those genes (called alleles) – these are homologous pairs

(d) explain the significance of mitosis for growth, repair and asexual reproduction in plants and animals

(e) outline, with the aid of diagrams and photographs, the process of cell division by budding in yeast

  1. A budforms/bulges at the surface of the cell
  2. The cell undergoes interphase – the DNA and organelles are replicated ready for the cell to divide
  3. The cell begins to undergo mitosis
  4. Nuclear division is complete – the budding cell contains a nucleus that has an identicalcopy of the parentcell’sDNA
  5. Finally the budseparates/pinchesoff from the parent cell, producing a new, geneticallyidentical yeast cell (daughter cell)

 

 

(f) state that cells produced as a result of meiosis are not genetically identical (details of meiosis are not required)

Meiosis is a type of cell division that happens in the reproductive organs to produce gametes. Cells that are formed from meiosis have half the number of chromosomes as the parent cell. They are NOT genetically identical because each new cell ends up with a different combination of chromosomes.

 

During cell division by meiosis, homologous chromosomes pair up and one member of each pair goes into each daughter cell. Most eukaryotes have pairs of homologous chromosomes because one is inherited from each parent. They carry the same genes but may carry different alleles of each.

 

 

(g) define the term stem cell

Only SUM cells are stem cells in adult organisms, for example:

  • in bone marrow of human adults
  • in meristems (e.g. root and shoot tips) of plants

 

Stem cells are:

  • able to Specialiseinto any type of cell
  • Undifferentiated
  • capable of Mitosis

 

 

 

 

 

(h) define the term differentiation, with reference to the production of erthrocyes (red blood cells) and neutrophils derived from stem cells in bone marrow, and the production of xylem and phloem sieve tubes from cambium

Differentiation is the process of becoming specialised.

 

In animals, adult stem cells are used to replace damaged cells e.g. to make new skin or blood cells. Plants are always growing, so stem cells are needed to make new shoots and roots throughout their lives. Stem cells in plants can differentiate into various plant tissues including xylem and phloem.

 

Being specialised means being adapted for a specific function. Organisms can be specialised by:

  • having a specific size/shape of cell e.g. root hair cell
  • having a certain number of organelleswithin the cell e.g. sperm cells have a large number of mitochondria for movement and energy
  • having specific contents in the cell e.g. phagocytes have enzymes to break down substances

 

(i) describe and explain, with the aid of diagrams and photographs, how cells of multicellular organisms are specialised for particular functions, with reference to eythrocytes (red blood cells), neutrophils, epithelial cells, sperm cells, palisade cells, root hair cells and guard cells

 

(j) explain the meaning of the terms tissue, organ and organ system

(k) explain, with the aid of diagrams and photographs, how cells are organised into tissues, using squamous and ciliated epithelia, xylem and phloem as examples

(l) discuss the importance of cooperation between cells, tissues, organs and organ systems

Multicellular organisms work efficiently because they have different cells specialised for different functions. It’s advantageous because each different cell type can carry out its specialised function more effectively than an unspecialised cell could. Specialised cells can’t do everything on their own. Each cell type depends on other cells for the functions it can’t carry out. This means the cells, tissues and organs within multicellular organisms must cooperate with each other to keep the organism alive and running.

For example:

  • In plants, a palisade cell is good at photosynthesising, but it’s not good at absorbing water and minerals from the soil, so it depends on root hair cells to do this.
  • In humans, muscle cells need oxygen but depend on erythrocytes (red blood cells) to carry oxygen to them from the lungs.

 

Continue Reading

Biological Molecules

Biological Molecules

Metabolism is the sum total of all the biochemical reactions (anabolic and catabolic) taking place in the cells of an organism.

  • Anabolic Reactions: building smaller molecules into larger ones e.g. muscle growth
  • A condensation reaction is where bonds are formed and water is removed
  • Catabolic Reactions: breaking larger molecules into smaller ones e.g. digestion
  • A hydrolysis reaction is where bonds are broken by the addition of water

Carbon:

Carbon can form so many different molecules because it has a valency of 4 which means it can form 4 single covalent bonds with 4 other atoms

 

  • describe how hydrogen bonding occurs between water molecules, and relate this and other properties of water, to the roles of water in living organisms

 

The shared electrons between the oxygen and hydrogen atoms in water are not shared evenly. The oxygen atom has a greater pull on the shared electrons than the hydrogen atoms so the oxygen atom becomes slightly negatively charged and the hydrogen atom becomes slightly positively charged so that there is an uneven charge distribution across the molecule, making water polar.

 

b) describe, with the aid of diagrams, the structure of an amino acid

 

c) describe, with the aid of diagrams, the formation and breakage of peptide bonds in the synthesis and hydrolysis of dipeptides and polypeptides

The quaternary structure is made up of more than one polypeptide chains joined together.

Haemoglobin is a globular protein made of 4 polypeptide chains (2 alpha chains and 2 beta chains), bonded together. They have a prosthetic group which is the haem group – they have 4 haem groups.

 

Haemoglobin’s function is to carry oxygen from the lungs to the tissues. It binds oxygen in the lungs and releases it in the tissues.

 

(g) explain, with the aid of diagrams, the term quaternary structure, with reference to the structure of haemoglobin

 

 

 

 

 

 

 

 

 

 

Denaturation:

Heating a protein increases the kinetic energy in the molecules. This causes the molecules to vibrate and break the bonds holding the tertiary structure in place as most of the bonds holding the tertiary structure in place are quite weak (not covalent – hydrogen, ionic, hydrophilic or hydrophobic bonds), so they are easily broken.

 

If enough heat is applied, the whole tertiary structure can unravel and the protein will no longer function – this is called denaturation.

 

(h) describe, with the aid of diagrams, the structure of a collagen molecule

Collagen is a fibrous protein which is an important structural component in cell walls as it’s very strong. It can be found in skin, tendons, cartilages, bones and teeth.

 

A collagen molecule is made up of three polypeptide chains wound around each other to form a twisted rope. Hydrogen bonds form between the chains, which gives the structure strength. Covalent bonds, called cross-links, form between other collagen molecules, adds to the strength.

 

Collagen can give strength in the walls of arteries to withstand high pressure as well as the tendons to connect skeletal muscles to bonds. Collagen can form bones, cartilage and connective tissue.

 

 

(i) compare the structure and function of haemoglobin (as an example of a globular protein) and collagen (as an example of a fibrous protein)

Functions of Lipids in Living Organisms:

  • Source of energy – respire to release energy
  • Energy storage – stored as adipose cells
  • Membranes – phospholipid bilayer
  • Insulation – e.g. blubber in whales
  • Protection – e.g. surface of plant protected against drying out
  • Hormones – e.g. steroid hormones

(s) describe how the concentration of glucose in a solution may be determined using colorimetry

The Benedict’s Test reveals the presence of reducing sugars by producing an orange-red precipitate. The more reducing sugar there is present, the more precipitate will be formed, and the more Benedict’s solution (copper sulfate) will be ‘used up’. If the precipitate is filtered out, then the concentration of the remaining solution can be measured. This will tell you how much Benedict’s solution has been used up.

 

Calorimeter:

The calorimeter is a device that shines a beam of light through a sample. A photoelectric cell picks up the light that is passed through the sample and gives a reading on how much light has passed through.

  • Use water to calibrate the colorimeter (for 100% transmission/ 0% absorption)
  • Place the solution in a sample chamber between the light and the photoelectric cell in a cuvette.
  • The more copper sulfate that is used up in Benedict’s Test in a sample, the less light will be blocked out and the more light will be transmitted.
  • Plot these readings on a graph to show light getting though (transmission) against reducing sugar concentration, creating a calibration curve.
  • If there is an unknown sample, use the graph to find the equivalent reducing sugar concentration for the reading on the calorimeter.
  • Colour filters are often used for greater accuracy – in this case, a red filter would be used.

 

The higher the glucose concentration, the higher the transmission and the lower the absorption.

 

 

Continue Reading