OCR Biology A-Level Module 2

Light microscope - simple

Poor resolution due to the long wavelength of light

Living samples can be examined and a colour image is obtained

Transmission electron microscopes - simple

High magnification and resolution

Electrons pass through the specimen to create an image

Scanning Electron microscope - simple

High magnification and resolution

Electrons bounce off the surface of the specimen to create an image

Laser scanning Confocal Microscopes - simple

High resolution and 3D imaging

Uses laser light to produce an image

Resolution

The minimum distance between two objects in which they can still be viewed as separate

Optical microscope - resolution

Determined by the wavelength of light

Electron microscope - Determined by the wavelength

Determined by the wavelength of the beam of electrons

Magnification

How many times larger the image is compared to the object.

The 4 types of slide preparations for light microscopes

Dry mount

Wet mount

Squash slide

Smear slide

Dry mounts

When thin slices or whole specimens are viewed, with just the coverslip placed on top. E.g. plant tissue or hair

Wet mounts

When water is added to the specimens before lowering the coverslip a mounted needle to prevent air bubbles from forming. Aquatic organisms could be viewed this way

Squash slides

Wet mounts which you push down on the coverslip to squash the sample to ensure you have a thin layer to enable light to pass through. This is used when creating a rot tip squash sample to view the chromosomes in mitosis.

Smear slides

Created by placing a drop of the sample at one end of the slid and using the edge of another slide (held at an angle) to smear the sample across the first slide to create a smooth, thin, even coated sample. A cover slip is placed on top after smearing. This is used when examining blood cells in a blood sample

Eye piece Graticule

Used to measure the size of objects you are viewing under the microscope. Each time you change the objective lens and the magnification you have to calibrate the eyepiece.

How to calibrate the eye piece graticule

-Line up the stage micrometer and eyepiece graticule whilst looking through the eyepiece

Count how many divisions on the eyepiece graticule fit into one division on the micrometer scale

Each division on the micrometer in 10 um so this can be used to calculate what one division on the eyepiece graticule that is at that current magnification.

Magnification calculation

Size of the image/ size of the real objects

Differential staining

Involves many chemical stains being used to stain different parts of a cell in different colours.

Crystal violet and methylene blue staining

Positively charged, and therefore are attracted to and stain negatively charged materials

Nigrosin and Congo red staining

Negatively charged and therefore cannot enter the cells as cytosol repels them. This creates a stained background and the unstained cells then stand out.

Electron microscopes - explained

A beam of electrons has a very short wavelength - a high-resolution. Small organelles and internal structures can be visualised. Image is created using an electromagnet to focus the beam of negatively charged electron. Electrons are absorbed by air = EM must be in a vacuum Therefore only non-living specimens ca be examined. The image is also black and white as the samples must be stained

Transmission Electron Microscope - explained

Extremely thin specimens are stained and placed in a vacuum. Electron gun produces a beam of electrons that passes through the specimen. Some parts of the specimen absorb the electrons and make them appear darker. The image is 2D and shows detailed images of the internal structures of cells.

Scanning Electron microscope - explanation

Specimen does not need to be thin, as the electron are not transmitting through. Electrons are beamed onto the surface and the electrons are scattered in different ways depending on the contours. This produces a 3D image of the surface of the specimen

Nucleus structure

Nuclear Envelope- Double membrane (protects from damage in the cytoplasm)

Nuclear pore (allows molecules to move into and out of the nucleus)

Nucleoplasm- granular, jelly-like material

Chromosomes - protein-bound, linear DNA

Nucleolus

Nucleolus

Smaller where inside when nucleus which is responsible for producing ribosomes. It is composed of proteins and RNA.

Nucleus function

Site of DNA replication and transcription (making mRNA)

Contains the DNA for each cell

Site of ribosome synthesis

Flagella structure and function

Whip like structure

- For mobility and sometimes as a sensory organelle for chemical stimuli

Cilia structure and function

Hairlike projections out of cells

- Can be mobile of stationary

-Mobile cilia help move substances in a sweeping motion

- Stationary cilia are important in sensory organs such as the nose

Mitochondria

- Site of final stages of cellular respiration

- Site of ATP production

- Contains the DNA to code for enzymes needed in respiration

Inner membrane highly folded to form cristae and it has a fluid interior (matrix). Contains loop of mitochondrial DNA to produces enzymes and reproduce themselves.

Vesicles

Membranous sac that have storage and transport roles. They consist of a single membrane with fluid inside. Vesicles are used to transport materials inside the cell.

Lysosomes

Specialised vesicles that contain hydrolytic enzymes. Break down waste material in cells. Break down pathogens ingested by phagocytic cells. Play an important role in programmed cell death.

- Bags of digestive enzymes - can contain 50 different enzymes

Cytoskeleton

A network of fibre found within the cytoplasm all over a cell. Consisted of microfilaments, microtubules and intermediate fibres.

-Provides mechanical strength and helps maintain shape and stability of a cell.

- Microfilaments are responsible for cell movement and cell contraction during cytokinesis (contractile fibres formed from actin)

- Microtubules are responsible for creating a scaffold like structure that determines the shape of the cell and acts as a track for movement of organelles.

- Intermediate fibres provide mechanical strength to cells and help maintain their integrity

Centrioles

Composed of microtubules. Occurs in pairs to form a centrosome

- Involved in the production of spindle fibres and organisation of chromosomes in cell division.

Smooth endoplasmic reticulum

Responsible for lipid and carbohydrate synthesis and storage

Rough endoplasmic reticulum

Has ribosomes bound to the surface and is responsible for the synthesis and transport of proteins

Ribosomes

Can be free-floating in the cytoplasm of attached to endoplasmic reticulum, they are not surrounded by a membrane. Made of 2 sub-units of protein and rRNA

80s - Large ribosomes found in eukaryotic cells

70s - smaller ribosome found in prokaryotic cells, mitochondria and chloroplasts.

- Site of protein synthesis

Golgi apparatus

Compact structure formed of cisternae and doesn't contain ribosomes. It has a role in modifying proteins and packaging them into vesicles. Those may be secretory vesicles or lysosomes.

Protein production

- Polypeptide chains synthesised on the ribosomes bound to the endoplasmic reticulum

- They then pass into its cisternae and are packaged into transport vesicles.

- Transport vesicles containing the new proteins move towards the Golgi apparatus via the cytoskeleton

- In the Golgi apparatus the proteins are modified and packaged into secretory vesicles.

- The SV carry the proteins to the cell surface membrane where it fuses and releases the proteins by exocytosis.

Cellulose cell wall

They are freely permeable so substances can pass into and out of the cell.

It gives the plant its shape, the contents of the cell press against the wall making it rigid. It also acts as a defence mechanism protecting the contents of the cell against pathogens.

Vacuoles

Membrane lined sacs in the cytoplasm containing cell sap. The membrane is called the tonoplast, it is selectively permeable.

Chloroplasts

double-membrane organelle that captures light energy and converts it to chemical energy through photosynthesis. The fluid enclosed in the chloroplast is the stroma. They also have an internal network of thykaloids stacked together (granum). The grana are joined by membranes called lamellae. The grana contain chrolophyll pigments, where light dependent reactions occur.

Prokaryotic vs eukaryotic cells

prokaryotes:

- Much smaller

- No membrane bound organelles

- Smaller ribosomes

- DNA not contained in a nucleus

- Cell wall of peptidoglycan

They may also contain:

Plasmids, a capsule around the cell, flagella

Calcium ions (Ca 2+)

Involved in muscle contraction and nerve impulse transmission

Sodium ions (Na+)

Involved in co-transport, reabsorption of water in the kidney, regulating water potential and nerves impulse transmission

Potassium ions (K+)

Involved in stomatal opening and nerve impulse transmission

Hydrogen ions (H+)

Involved in chemiosmosis, regulating PH and translocation

Ammonium ions (NH4 +)

Involved in nitrogen cycle where by bacteria convert ammonium ions into nitrate ions.

Nitrate (NO3 -)

Mineral ion absorbed by plants to provide a source of nitrogen to make amino acids

Hydrogencarbonate (HCO3 -)

Involved in the transport of carbon dioxide in the blood

Chloride (Cl- )

Involved in the transport of carbon dioxide in the blood

Phosphate (PO4 3-)

Involved in the formation of phospholipids for cell membranes, nucleic acid and ATP formation.

Hydroxide (OH-)

Involved in the catalyst of reactions and regulating pH

Elements in lipids

carbon, hydrogen and oxygen

Elements in proteins

Carbon, hydrogen, oxygen, nitrogen and sulfur

Elements in nucleic acids

Carbon, hydrogen, oxygen, nitrogen and phosphorus

Water - polarity

Polar due to unevenly distributed charge

Water - hydrogen bonds

They form between the oxygen and hydrogen atom as the positive and negative regions interact with eachother. Individual hydrogen bonds are weak but collectively provide strength.

Water as a solvent

Polar (hydrophilic) or charged molecules dissolve readily in water due to the fact water is polar. The slight positive charge on the hydrogen atoms will attract any negative

Condensation reaction

Too alpha glucose molecules interact and water is removed forming a glycosidic bond

A glucose + a glucose (alpha)

Maltose + water

Alpha glucose + galactose

Lactose and water

Beta glucose + fructose

Sucrose + water

Starch - amylose

Formed by alpha glucose molecules joined by 1-4 glycosidic bonds. The long chain twists to form a helix which is stabilised by hydrogen bonding - which makes it more compact and much less soluble than glucose.

Starch - amylopectin

Make by 1-4 glycosidic bonds by all so 1-6 glycosidic bonds meaning it is branched approximately every 25 glucose subunits.

Glycogen

Forms more branches than amylopectin, more compact ad less space is needed for it to be stored. Branching also means there are free ends where glucose can be added or removed.

Why are glycogen and amylopectin ideally suited for their functions

They are insoluble, branched and compact.

Hydrolysis reaction

The breaking of the glycosidic bonds by the addition of water. Hj

Cellulose

Make of beta glucose forming 1-4 glycosidic bonds, forms straight, long chains. Chains held in parallel by many hydrogen bonds to form fibrils. Macrofibrils combine to form a cellulose fibre, used for structure strength for cell wall.

Test for starch

- Add iodine solution

Positive result: solution turns from orange to black

Tests for reducing sugars

- Add Benedicts solution and heat for 5 minutes at 80*C

Positive result: solution turns from blue to brick red due to the reduction of Cu2+ ions

Test for non-reducing sugars

After a negative Benedicts result:

- Add HCl and boil - acid hydrolysis

- cool the solution then add an alkali (NaOH) to neutralise

- Add Benedicts and heat for 5 minutes at 80*c

Positive result - solution turns from blue to brick red due

Reagent strips

Can be used to test for the presence of non-reducing sugars, most commonly glucose. The advantage is that with the use of a colour coded chart the concentration of the sugar can be determined.

Test for proteins

- Add Biuret Solution

Positive result: Solution turns from blue to purple

Test for Lipids

- Dissolve in ethanol

- Pour the sample onto distilled water

Positive result: white emulsion forms

Structure of Triglycerides

One glycerol combined with 3 fatty acids, joined by an ester bond formed by the removal of H2O in esterification.

Saturated Triglyceride

No double bonds present

Unsaturated Triglyceride

Double bonds between some of the carbon atoms, this causes the molecule to kink or bend and therefore can't pack closely together, so they are liquids at room temperature.

Structure of phospholipids

Charged phosphate head and 2 non-polar long chains hydrocarbons. The heads are hydrophilic and the tails are hydrophobic

Properties of Trigylcerides

1) Can transfer energy, due to the are energy storing C-H bonds

2) Act as a metabolic water source because they can release water if they are oxidised.

3) Do not effect water potential and osmosis

4) Low in mass, a lot can be stored without increasing the mass and preventing movement

Cholesterol

A steroid alcohol with both hydrophobic and hydrophilic regions. It is embedded into cell membranes to impact fluidity.

High temp - reduce fluidity

Low temp - increase fluidity

Roles of lipids

- Hormones production

- electrical insulation

- waterproofing

- cushioning to protect vital organs such as the heart and kidneys

- buoyancy

The three groups that make up a protein

Amine group, r-group, carboxyl group

Primary structure

The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain.

Secondary structure

The sequence of amino acids causes part if a protein molecule to bend into an alpha helix or beta pleated sheets. Hydrogen bonds hold the secondary structure

Tertiary structure

The secondary structure is bent and folded to form a precise 3D shape. Held in place by:

- Hydrophilic and hydrophobic interactions (weak)

- Hydrogen bonds (weak)

- Ionic bonds (stronger bonds between R groups)

- Disulfide bonds (strong covalent which fins between 2 R groups containing sulphur)

Quarternary structure

The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.

Fibrous proteins

Polypeptide chains form long twisted strands linked together

Stable unreactive structure

From hydrogen binds with adjacent chains

Insoluble in water

Strength gives structural function

E.g collagen and keratin

Globular proteins

Polypeptide chains roll up into a spherical shape

Relatively unstable structure

Have hydrophilic R groups on the outside and hydrophobic groups on the inside

Soluble

Metabolic functions

E.g all enzymes, antibodies, some hormones

Collagen

Fibrous- form part of skin, tendons, cartilage, ligaments, bone and connective tissue. Quarternary structure - 3 polypeptide chains wound around like a rope.

Keratin

Fibrous- used to form skin, hair and nails which all protect the body.

It is important it is insoluble so these structures are not broken down by water in the environment.

Elastin

Fibrous- Males up elastic fibres around alveoli and blood vessels. Allows structures to stretch and recoil to their original shape and size.

Haemoglobin

Globular- Responsible for transport of oxygen. 2 alpha chains an 2 beta chains bind to one molecule of oxygen due to it prosthetic heam group.

Pepsin

Globular enzyme - found in he stomach. Able to digest other proteins using its specific all shaped active site.

Insulin

Globular- produced by he beta cells in the pancreas to lower blood glucose concentrations. Specific 3D shape is complementary to the receptors on the cell surfaces of its target cells (liver and muscle)

Colorimeter

- Set the filter in the colorimeter

- calibrate to zero using distilled water

- Insert samples from you biochemical test

- Measure the percentage transmission of light

- Draw a calibration curve using the results from know concentrations of solution

Biosensors

- A single strand of DNA or proteins which are complementary it the test sample is immobilised. When the sample is added it will bind to the immobilised protein.

- This binding causes a change in a transducer and as a result an electronic current is released.

- The current is processed to determine the concentration of the sample present.

TLC

A concentrated sample of the biological molecule is placed 1cm away from the end of the stationary phase. The stationary phase is them places in a blanked with less than 1cm depth of the mobile phase (solvent). As the solvent moves up the stationary phase, it has an affinity for the biological molecules and dissolves them, carrying them up the stationary phase.

RF value

Distance moved by the solute / distance moved by the solvent

More soluble molecules will be carried the furthest

Nucleotides are made up of... and are joined by

A pentose sugar, a phosphate (PO4 2-) group, a nitrogenous base.

Joined by phosphodiester bonds

Purine

2 carbon ring structures (adenine and guanine)

Pyramidine

1 carbon ring structure (cytosine, thymine and uracil)