hard Flashcards
bases
A,G-Purines. C,T-pyrimidines always bond with each other, a-t is two hydrogen bonds between each other. c-g is always three
mutagenic agents
increase error rate-carcinogenic agents are sub category, cause mutations in genes to do with cell cycle
dna code
-non overlapping-each base triplet is read in sequence, seperate from the triplet before and after it -degenerate-some AA coded for by more than one base triplet -universal-same specific base triplets code for the same AA in all living things
mutations
point mutation-change in one base
missense mutation-base change changes AA-could affect tertiary structure
silent mutation-no change to AA because new triplet codes for same AA-because code is degenerate
nonsense mutation-cuts short the protein-truncated protein-too short- because triplet changes to stop codon-ribosome stops adding AA
indel mutation-frameshift mutation, base is added or deleted
Name organelles in animal and plant cell
animal-plasma (cell surface membrane)
-RER
-nucleolus
-nucleus
-SER
-lysosome
-ribosome
-nuclear envelope
-golgi apparatus
cytoplasm
-mitochondrion
-Plant cell has same but few added extras
-cell wall with plasmodesmata
-vacuole (contains cell sap)
-chloroplasts
organelles
plasma(cell surface) membrane-The membrane found on the surface of animal cells and just inside the cell wall of plant cells and prokaryotic cells. It’s made mainly of lipids and protein.-Regulates the movement of substances into and out of the cell.
It also has receptor molecules on it, which allow it to respond to chemicals like hormones.
cell wall-A rigid structure that surrounds plant cells. It’s made mainly of the carbohydrate cellulose.-supports plant cells
nucleus-A large organelle surrounded by a nuclear envelope (double membrane), which contains many pores. The nucleus contains chromatin (which is made from DNA and proteins) and a structure called the nucleolus.-The nucleus controls the cell’s activities (by controlling the transcription of DNA - see page 40). DNA contains instructions to make proteins
— see page 38. The pores allow substances (e.g. RNA) to move between the nucleus and the cytoplasm. The nucleolus makes ribosomes (see below).
lysosome-A round organelle surrounded by a membrane, with no clear internal structure.-Contains digestive enzymes.
These are kept separate from the cytoplasm by the surrounding membrane, and can be used to digest invading cells or to break down worn out components of the cell.
ribosome-A very small organelle that either floats free in the cytoplasm or is attached to the rough endoplasmic reticulum.
It’s made up of proteins and
RNA (see page 34). It’s not surrounded by a membrane.-The site where proteins are made.
rough endoplasmic reticulum-A system of membranes enclosing a fluid-filled space. The surface is covered with ribosomes.-Folds and processes proteins that have been made at the ribosomes.
smooth endoplasmic reticulum-Similar to rough endoplasmic reticulum, but with no ribosomes.-Synthesises and processes lipids.
vesicle-A small fluid-filled sac in the cytoplasm, surrounded by a membrane.-Transports substances in and out of the cell (via the plasma membrane) and between organelles. Some are formed by the Golgi apparatus or the endoplasmic reticulum, while others are formed at the cell surface.
-golgi apparatus-A group of fluid-filled,
membrane-bound, flattened sacs.
Vesicles are often seen at the edges of the sacs.-It processes and packages new lipids and proteins.
It also makes lysosomes.
mitochondrion-They’re usually oval-shaped.
They have a double membrane
— the inner one is folded to form structures called cristae.
Inside is the matrix, which contains enzymes involved in respiration.-The site of aerobic respiration, where ATP is produced. They’re found in large numbers in cells that are very active and require a lot of energy.
chloroplast-A small, flattened structure found in plant cells. It’s surrounded by a double membrane, and also has membranes inside called thylakoid membranes. These membranes are stacked up in some parts of the chloroplast to form grana. Grana are linked together by lamellae - thin, flat pieces of thylakoid membrane.-The site where photosynthesis takes place. Some parts of photosynthesis happen in the grana, and other parts happen in the stroma (a thick fluid found in chloroplasts).
centriole-Small, hollow cylinders, made of microtubules (tiny protein cylinders). Found in animal cells, but only some plant cells.-Involved with the separation of chromosomes during cell division
cilia-Small, hair-like structures found on the surface membrane of some animal cells. In cross-section, they have an outer membrane and a ring of nine pairs of protein microtubules inside, with two microtubules in the middle. 9+2 formation-The microtubules allow the cilia to move. This movement is used by the cell to move substances along the cell surface.
flagellum-Flagella on eukaryotic cells are like cilia but longer. They stick out from the cell surface and are surrounded by the plasma membrane. Inside they’re like cilia too — two microtubules in the centre and nine pairs around the edge.-The microtubules contract to make the flagellum move.
Flagella are used like outboard motors to propel cells forward (e.g. when a sperm cell swims).
info
ribosomes on RER make proteins that are excreted or attached to cell membrane. Free ribosomes in cytoplasm make proteins that stay in cytoplasm. folded and processed in RER and then transported to Golgi in vesicles
-cytoplasm-has network of protein threads running through it-cytoskeleton
-cytoskeletal protein filaments
-resolution is how well a microscope is able to distinguish between two points that are close together. If a microscope lens can’t separate two objects, then increasing the magnification wont help.
4 main functions cytoskeleton
1)microtubules and microfilaments support the cells organelles, keeping them in position.
2)They also help to strengthen the cell and maintain its shape
3)they’re also responsible for movement of materials within the cell, eg movement of chromosomes when they separate during cell division depends on contraction of microtubules in spindle.
4)Proteins of cytoskeleton can also cause cell to move eg movement of cilia and flagella is caused by cytoskeletal protein filaments that run through them
cytoskeleton is dynamic-constantly changing which allows it to respond to changes in the cell and carry out its functions
prokaryotes vs eukaryotes
prokaryotes-
Extremely small cells (less than 2 um diameter)
DNA is circular
No nucleus — DNA free in cytoplasm
Cell wall made of a polysaccharide, but not cellulose or chitin
Few organelles and no membrane-bound organelles, e.g. no mitochondria
Flagella (when present) made of the protein flagellin, arranged in a helix
Small ribosomes
eukaryotes-
Larger cells (about 10-100 pm diameter)
W
DNA is linear
Nucleus present — DNA is inside nucleus
No cell wall (in animals), cellulose cell wall (in plants) or chitin cell wall (in fungi)
Many organelles - mitochondria and other membrane-bound organelles present
Flagella (when present) made of microtubule proteins arranged in a ‘9 + 2’ formation
Larger ribosomes
Microscopes
1) Light microscopes use light (no surprises there).
2) They have a lower resolution than electron microscopes — they have a maximum resolution of about 0.2 micrometres (um). So they’re usually used to look at whole cells or tissues.
3) The maximum useful magnification of a light microscope is about × 1500.
=
Laser Scanning Confocal Microscopes use laser beams (intense beams of light) to scan a specimen, which is usually tagged with a fluorescent dye.
2)
The laser causes the dye to fluoresce - give off light. This light is then focused through a pinhole onto a detector. The detector is hooked up to a computer, which generates an image. The image can be 3D.
3)
The pinhole means that any out-of-focus light is blocked, so these microscopes produce a much clearer image than a normal light microscope.
4) They can be used to look at objects at different depths in thick specimens.
Electron microscopes use electrons instead of light to form an image.
They have a higher resolution than light microscopes so give more detailed images. There are two kinds of electron microscope:
1) Transmission electron microscope (TEM) - use electromagnets to focus a beam of electrons, which is then transmitted through the specimen.
Denser parts of the specimen absorb more electrons, which makes them look darker on the image you end up with. TEMs are good because they provide high resolution images (so they can be used to look at a range of organelles) but they can only be used on thin specimens.
A TEM image of a mitochondrion is shown above on the right.
Scanning electron microscope (SEM) - scan a beam of electrons across the specimen. This knocks off electrons from the specimen, which are gathered in a cathode ray tube to form an image. The images produced show the surface of the specimen and can be 3D. But they give lower resolution images than TEMs. Here’s an SEM image of a mitochondrion.
magnification figures
light microscope-max resolution 0.2 um, max mag x1500
TEM-max resolution 0.0002, max mag can be more than x1000000(million)
SEM-max resolution-0.002um, max mag usually less than x500,000
carbohydrates
monomers that make up carbohydrates=monosaccharides eg glucose-hexose monosaccharide-its structure makes it soluble so it can be easily transported-chemical bonds contain lots of energy-alpha beta H and OH groups reversed alpha h on top
monosaccharides joined by glycosidic bonds
-when form-h and oh group react releasing molecule of water-condensation
-when water react with glycosidic bond breaking it-hydrolysis
-two a glucose join to form maltose
-glucose and fructose=sucrose
-a/b glucose and galactose=lactose
-lots of a glucose=amylose
polysaccharides
starch-1) Cells get energy from glucose. Plants store excess glucose as starch (when a plant needs more glucose for energy it breaks down starch to release the glucose).
2) Starch is a mixture of two polysaccharides of alpha-glucose - amylose and amylopectin:
• Amylose — a long, unbranched chain of a-glucose. The angles of the glycosidic bonds give it a coiled structure, almost like a cylinder. This makes it compact, so it’s really good for storage because you can fit more in to a small space.
• Amylopectin - a long, branched chain of a-glucose. Its side branches allow the enzymes that break down the molecule to get at the glycosidic bonds easily.
This means that the glucose can be released quickly.
Starch is insoluble in water, so it doesn’t cause water to enter cells by osmosis (see p. 58) which would make them swell. This makes it good for storage.
-glycogen-1) Animal cells get energy from glucose too. But animals store excess glucose as glycogen - another polysaccharide of alpha-glucose.
2)
Its structure is very similar to amylopectin, except that it has loads more side branches coming off it. Loads of branches means that stored glucose can be released quickly, which is important for energy release in animals.
3) It’s also a very compact molecule, so it’s good for storage.
cellulose-1) Cellulose is made of long, unbranched chains of beta-glucose.
2) When beta-glucose molecules bond, they form straight cellulose chains.
3)
The cellulose chains are linked together by hydrogen bonds to form strong fibres called microfibrils. The strong fibres mean cellulose provides structural support for cells (e.g. in plant cell walls).
lipids
triglycerides-In animals and plants, triglycerides are mainly used as energy storage molecules.
Some bacteria (e.g. Mycobacterium tuberculosis) use triglycerides to store both energy and carbon.
Triglycerides are good for storage because:
1) The long hydrocarbon tails of the fatty acids contain lots of chemical energy — a load of energy is released when they’re broken down. Because of these tails, lipids contain about twice as much energy per gram as carbohydrates.
2) They’re insoluble, so they don’t cause water to enter the cells by osmosis (see p. 58) which would make them swell. The triglycerides bundle together as insoluble droplets in cells because the fatty acid tails are hydrophobic (water-repelling) — the tails face inwards, shielding themselves from water with their glycerol heads.
phospholipids-Phospholipids are found in the cell membranes of all eukaryotes and prokaryotes.
They make up what’s known as the phospholipid bilayer (see p. 50).
Cell membranes control what enters and leaves a cell.
1) Phospholipid heads are hydrophilic and their tails are hydrophobic, so they form a double layer with their heads facing out towards the water on either side. —
2)
The centre of the bilayer is hydrophobic, so water-soluble substances can’t easily pass through it — the membrane acts as a barrier to those substances.
cholesterol-Cholesterol is another type of lipid - it has a hydrocarbon ring structure attached to a hydrocarbon tail. The ring structure has a polar hydroxyl (OH) group attached to it.
In eukaryotic cells, cholesterol molecules help strengthen the cell membrane
by interacting with the phospholipid bilayer.
1) Cholesterol has a small size and flattened shape — this allows cholesterol to fit in between the phospholipid molecules in the membrane.
2) They bind to the hydrophobic tails of the phospholipids, causing them to pack more closely together. This helps to make the membrane less fluid and more rigid.
lipids
-triglycerides-type of lipid-macromolecule-relatively large molecular mass-CHO-hydrocarbon tail-one glycerol three fatty acids-ester bond-esterification-saturated fatty acids(no double bonds between C) or unsaturated(at least one double bond)
tertiary structure bonding
• lonic bonds. These are attractions between negatively-charged R groups and positively-charged
R groups on different parts of the molecule.
• Disulfide bonds. Whenever two molecules of the amino acid cysteine come close together, the sulfur atom in one cysteine bonds to the sulfur in the other cysteine, forming a disulfide bond.
• Hydrophobic and hydrophilic interactions. When hydrophobic (water-repelling) R groups are close together in the protein, they tend to clump together. This means that hydrophilic (water-attracting) R groups are more likely to be pushed to the outside, which affects how the protein folds up into its final structure.
• Hydrogen bonds — these weak bonds form between slightly positively-charged hydrogen atoms in some R groups and slightly negatively-charged atoms in other R groups on the polypeptide chain.
ions
1) An ion is an atom (or group of atoms) that has an electric charge.
2) An ion with a positive charge is called a cation.
3) An ion with a negative charge is called an anion.
4) An inorganic ion is one which doesn’t contain carbon (although there are a few exceptions to this rule).
inorganic ions
Calcium-Ca2+-Involved in the transmission of nerve impulses and the release of insulin from the pancreas. Acts as a cofactor for many enzymes (see p. 47), e.g. those involved in blood clotting. Is important for bone formation.
Sodium-Na+-Important for generating nerve impulses, for muscle contraction and for regulating fluid balance in the body.
Potassium-K+-Important for generating nerve impulses, for muscle contraction and for regulating fluid balance in the body. Activates essential enzymes needed for photosynthesis in plant cells.
Hydrogen-H+-Affects the pH of substances (more H* ions than OH- ions in a solution creates an acid). Also important for photosynthesis reactions that occur in the thylakoid membranes inside chloroplasts (see p. 12).
Ammonium-NH4+Absorbed from the soil by plants and is an important source of nitrogen (which is then used to make, e.g. amino acids, nucleic acids).
Nitrate-NO3-Absorbed from the soil by plants and is an important source of nitrogen (which is then used to make, e.g. amino acids, nucleic acids).
Hydrogencarbonate HCO3-Acts as a buffer, which helps to maintain the pH of the blood.
Chloride CL- -Involved in the ‘chloride shift’ which helps to maintain the pH of the blood during gas exchange (see p. 87). Acts as a cofactor for the enzyme amylase (see p. 47). Also involved in some nerve impulses.
Phosphate PO4 3- -Involved in photosynthesis and respiration reactions. Needed for the synthesis of many biological molecules, such as nucleotides (including ATP), phospholipids, and calcium phosphate (which strengthens bones).
Hydroxide OH- -Affects the pH of substances (more OH ions than H* ions in a solution creates an alkali).
benedict’s test sugar
Reducing sugars include all monosaccharides (e.g. glucose) and some disaccharides (e.g. maltose and lactose)
2)
You add Benedict’s reagent (which is blue) to a sample and heat it
Always use an excess of Benedict’s solution -
in a water bath that’s been brought to the boil.
this makes sure that all
The colour of the precipitate blue green → yellow→ orange → brick red
If the test’s positive it will form a coloured precipitate (solid particles suspended in the solution).
4)
The higher the concentration of reducing sugar, the further the colour change goes — you can use this to compare the amount of reducing sugar in different solutions. A more accurate way of doing this is to filter the solution and weigh the precipitate.
non-reducing
1)
If the result of the reducing sugars test is negative, there could still be a non-reducing sugar present.
To test for non-reducing sugars, like sucrose, first you have to break them down into monosaccharides.
2)
You do this by getting a new sample of the test solution, adding dilute hydrochloric acid and carefully heating it in a water bath that’s been brought to the boil. You then neutralise it with sodium hydrogencarbonate. Then just carry out the Benedict’s test as you would for a reducing sugar.
3)
If the test’s positive it will form a coloured precipitate (as for the reducing sugars test). If the test’s negative the solution will stay blue, which means it doesn’t contain any sugar (either reducing or non-reducing).
test strips for glucose
Glucose can also be tested for using test strips coated in a reagent. The strips are dipped in a test solution and change colour if glucose is present. The colour change can be compared to a chart to give an indication of the concentration of glucose present. The strips are useful for testing a person’s urine for glucose, which may indicate they have diabetes.
other tests
Use the lodine Test for Starch
Just add iodine dissolved in potassium iodide solution to the test sample.
• If starch is present, the sample changes from browny-orange to a dark, blue-black colour.
• If there’s no starch, it stays browny-orange.
biuret test for proteins-
There are two stages to this test.
1) The test solution needs to be alkaline, so first you add a few drops of sodium hydroxide solution.
2) Then you add some copper(Il) sulfate solution.
• If protein is present the solution turns purple.
• If there’s no protein, the solution will stay blue.
Use the Emulsion Test for Lipids
Shake the test substance with ethanol for about a minute, then pour the solution into water.
• If lipid is present, the solution will turn milky.
• The more lipid there is, the more noticeable the milky colour will be.
• If there’s no lipid, the solution will stay clear.
colorimeter
1)
You can use Benedict’s reagent and a colorimeter to get a quantitative estimate light detector
of how much glucose (or other reducing sugar) there is in a solution.
2) A colorimeter is a device that measures the strength of a
coloured solution by seeing how much light passes through it.
3) A colorimeter measures absorbance (the amount of light absorbed by the
transmitted light
solution). The more concentrated the colour of the solution, the higher the absorbance is.
4)
It’s easiest to measure the concentration of the blue Benedict’s solution that’s left after the test (the paler the solution, the more glucose there was). So, the higher the glucose concentration, the lower the absorbance of the solution.
Initially you need to make up several glucose solutions of different, known concentrations. You can do this using a serial dilution technique:
This is how you’d make five serial dilutions with a dilution factor of 2, starting with an initial glucose concentration of 40 mM…
1) Line up five test tubes in a rack.
2) Add 10 cm’ of the initial 40 mM glucose solution to the first test tube and 5 cm’ of distilled water to the other four test tubes.
3)
Then, using a pipette, draw 5 cm’ of the solution from the first test tube, add it to the distilled water in the second test tube and mix the solution thoroughly. You now have 10 cm’ of solution that’s half as concentrated as the solution in the first test tube (it’s 20 mM).
4)Repeat this process three more times to create solutions of 10 mM, 5 mM and 2.5 mM.
Once you’ve got your glucose solutions, you need to make a calibration curve. Here’s how:
1) Do a Benedict’s test on each solution (plus a negative control of pure water).
Use the same amount of Benedict’s solution in each case.
Remove any precipitate - either leave for 24 hours (so that the precipitate settles out) or centrifuge them.
3)
Use a colorimeter (with a red filter) to measure the absorbance
1.0
of the Benedict’s solution remaining in each tube.
4)
Use the results to make the calibration curve, showing absorbance against glucose concentration.
Then you can test the unknown solution in the same way as the known concentrations and use the calibration curve to find its concentration.
biosensors
Biosensors Can Detect Chemicals in a Solution
1) A biosensor is a device that uses a biological molecule, such as an enzyme (see page 42) to detect a chemical.
2) The biological molecule produces a signal (e.g. a chemical signal), which is converted to an electrical signal by a transducer (another part of the biosensor).
3) The electrical signal is then processed and can be used to work out other information.
Example: Glucose Biosensors
1) A glucose biosensor is used to determine the concentration of glucose in a solution.
2) It does this using the enzyme glucose oxidase and electrodes.
3) The enzyme catalyses the oxidation of glucose at the electrodes — this creates a charge, which is converted into an electrical signal by the electrodes (the transducer).
4) The electrical signal is then processed to work out the initial glucose concentration.
1) Draw a pencil line near the bottom of a piece of chromatography paper and put a concentrated spot of the mixture of amino acids on it. It’s best to carefully roll the paper into a cylinder with the spot on the outside so it’ll stand up.
Add a small amount of prepared solvent (a mixture of butan-1-ol, glacial ethanoic acid and water is usually used for amino acids) to a beaker and dip the bottom of the paper into it (not the spot).
This should be done in a fume cupboard. Cover with a lid to stop the solvent evaporating.
3)
As the solvent spreads up the paper, the different amino acids (solutes) move with it, but at different rates, so they separate out.
4) When the solvent’s nearly reached the top, take the paper out and mark the solvent front with pencil. Then you can leave the paper to dry out before you analyse it (see below).
5) Amino acids aren’t coloured, which means you won’t be able to see them on the paper. So before you can analyse them, you have to spray the paper with ninhydrin solution to turn the amino acids purple.
This should also be done in a fume cupboard and gloves should be worn. (Note: you can’t use ninhydrin to detect all biological molecules, only proteins and amino acids.)
6)
You can then use R, values to identify the separated molecules:
An R, value is the ratio of the distance travelled by a solute to the distance travelled by the solvent. You can calculate it using this formula:
R value of amino acid =
distance travelled by solute/ distance travelled by solvent
When you’re measuring how far a solute has travelled, you measure from the point of origin to the vertical centre of the spot.
You can work out what was in a mixture by calculating an R, value for each solute and looking each R, value up in a database, or table, of known values.
