Module 2 - OCR A Level Biology

Magnification

The number of times larger an image appears compared to the size of the object

Magnification calculation

Objective lens x eyepiece lens

Image size / actual size

Using stage graticule

1. insert eyepiece graticule into x10 eyepiece

2. place stage graticule on microscope stage and bring into focus using low power objective (total mag=40)

3. align eyepiece graticule and stage graticule. Check value of one eyepiece division at this mag

4. 1mm = 40 eyepiece divisions

5. each eyepiece divison 1000/40 = 25

6. use x10 objective lens on microscope and focus on stage graticule

7. align them both

8. 100 eyepiece divisions now correspond 1mm

9. 1000/100 = 10

Nucleus

Control centre of cell

Stores organisms genome

Transmits genetic information

Nuclear envelope

Separates contents of nucleus from the rest of the cell

Nucleolus

Found inside the nucleus and produces ribosomes

RER

Ribosomes attached

Large surface area

SER

Synthesis cholesterol

Synthesis lipids/phospholipids

Synthesis steroids hormones

Golgi apparatus

Stack membrane bound flattened sacs

Processes and packages proteins

Mitochondria

Site of ATP production during aerobic respiration

Fluid filled matrix

Folded into cristae

Chloroplasts

Site of photosynthesis

Plant cells

Stacks flattened membranes (thylakoids)

Vacuole

Filled with water and solutes

Maintain cell stability

Lysosomes

Engulf old organelles and foreign matter then digest

Formed from Golgi apparatus

Cilia

Beat and move mucus

Ribosomes

Synthesise proteins

Small spherical

Attached to RER

Centrioles

Cell organelle that aids in cell division in animal cells only

Formation cilia

Two bundles microtubules right angle

Cytoskeleton

A network of fibers that holds the cell together, helps the cell to keep its shape, and aids in movement

Cellulose cell wall

The rigid cell wall which surrounds plant cells

How insulin is made

1. mRNA copy of instructions for insulin made in nucleus

2. mRNA leaves nucleus through nuclear pore

3. mRNA attached to a ribosome on RER leads to assemble protein (insulin)

4. insulin molecules pinched off in vesicles travel towards Golgi apparatus

5. vesicles fuse with Golgi apparatus

6. process and package insulin molecules ready for release

7. insulin pinched off in vesicles move towards plasma membrane

8. vesicles fuses

9. exocytosis

Similarities of Prokaryotes and Eukaryotes

Plasma membrane

Cytoplasm

Ribosomes

DNA

RNA

Differences of Prokaryotes and Eukaryotes

Smaller

Less developed cytoskeleton

No nucleus

No membrane bound organelles

Peptidoglycan

Smaller ribosomes

Naked DNA

Flagella

Pili

binary fission

A form of asexual reproduction in which one cell divides to form two identical cells.

covalent bond

A chemical bond that involves sharing a pair of electrons between atoms in a molecule

condensation reaction

Two molecules join with the removal of water

hydrolysis reaction

Two molecules split by addition of water

hydrogen bond

Weak interaction

Slightly negative and slightly positive charge (delta neg/pos)

water as a liquid

provide habitats major component of tissues in living organisms medium for chemical reactions effective transport medium

density of water

more dense as it gets colder up until 4 degrees then due to polarity will become less dense stable environment insulate bodies of water

water as a solvent

positive and negative parts of water attracted to positive and negative parts of solute molecules and ions move around and react transport whilst in water

cohesion and surface tension of water

hydrogen bonding between molecules pulls them together (cohesion) surface of water contracts to resist forces applied (surface tension) xylem pond skaters

high specific heat capacity of water

need a lot of heat energy to increase KE and temperature amount of energy needed to raise 1KG substance by 1 degree stable environment for enzyme controlled reactions aquatic animals

high latent heat capacity of water

helps molecules break away from each other to become a gas large amount of energy needed for evaporation cool things and keep temperature stable

water as a reactant

photosynthesis hydrolysis digestion synthesis large molecules

carbohydrates

carbon, oxygen, hydrogen 1:1:2

use of carbohydrates

energy source energy store structural units

monosaccharides

simplest form carbohydrates source of energy soluble in water insoluble in solutes straight chains or ring

Monosaccharide examples

glucose, fructose, galactose

disaccharide

two monosaccharides joined by a glycosidic bond soluble sweet can hydrolyse

Disaccharide examples

alpha glucose + alpha glucose = maltose

alpha glucose + fructose = sucrose

alpha glucose + beta glucose = lactose

beta glucose + beta glucose = cellulose

polysaccharides

polymers of monosaccharides

homopolysaccharide or heteropolysaccharide

Polysaccharide examples

amylose, amylopectin, glycogen

Amylose

coils into spiral

alpha glucose molecules

1-4 glycosidic bonds

less soluble

unbranched

Amylopectin

coils into spiral shape

alpha glucose molecules

1-4 and 1-6 glycosidic bonds

branched

glycogen

in mammals smaller chains, less tendency to coil 1-4 and 1-6 glycosidic bonds

branched more compacted (easier to snip off)

Cellulose

plant cell walls

long chains

15,000 beta glucose molecules

condensation reaction

1-4 glycosidic bonds

second molecule turned 180 degrees

microfibrils

60-70 cellulose cell walls joined

10-30 nm in diameter

bundle in to macrofribrils embedded in pectins

plant cell wall structure and function

cellulose macrofibrils run in all directions

glycosidic and hydrogen bonds provide high tensile strength

hard to digest

fully permeable

can be reinforced with other substances

bacteria cell wall

peptidoglycan

exoskeleton cell walls

chitin

lipids

group of substances soluble in alcohol rather than water

examples of lipids

triglycerides, phospholipids, steroids

Trigylcerides

glycerol + 3 fatty acids condensation reaction ester bonds

Saturated triglycerides

No double bonds

Tend to be solid at room temp

unsaturated triglycerides

double bonds

liquid at room temp

Phosopholipids

phosphate + two fatty acids condensation reaction

hydrophilic head, hydrophobic tail

micelle phospholipid bilayer (cholesterol)

Cholesterol

steroid alcohol lipid

4 carbon based rings

hydrophobic molecule

regulates fluidity of membrane

amino acids

N-C-C amino group

r group

carboxyl group

dipeptide

Two amino acids bonded together

peptide bond (polypeptide)

primary structure

sequence of amino acids

hydrogen bonds

secondary structure

Either an alpha helix or a beta-pleated sheet

hydrogen bond

tertiary structure

precise shape

supercoiled or spherical

hydrogen bonds, ionic bonds, disulfide bridges

quaternary structure

Results from two or more polypeptide subunits

hydrogen bonds, ionic bonds, disulfide bridges

fibrous proteins

regular, repetitive sequences

amino acids insoluble form fibres

structural function

fibrous proteins examples

collagen (mechanical strength)

keratin (strong eg. hair, nails, horns)

elastin (skin stretch around bones)

globular proteins

spherical shape

hydrophobic R groups turned inwards, hydrophilic R groups turned outwards

soluble

specific shapes

roles as enzymes, hormones, haemoglobin

globular protein examples

haemoglobin

insulin

pepsin (digests protein in stomach)

inorganic ions

cations (Ca, Na , K, H )

anions (NO, HCO, Cl, OH)

Test for Carbohydrates (Starch)

add iodine solution

blue-black

test for carbohydrates (reducing sugars)

benedict's test

place sample of food in boiling tube

add benedicts solution then heat in water baths at 80 degrees for 3 mins

orange-red precipitate

test for carbohydrates (non-reducing sugars)

test sample for reducing sugars

take separate sample and boil in hydrochloric acid to hydrolyse sucrose and fructose

cool solution and use sodium hydrogencarbonate ions to neutralise

test for reducing sugars again

green-yellow-orange-red

testing for lipids

emulsion test

mix sample with ethanol

filter

pour into clean test tube

cloudy white

testing for proteins

Biuret test

lilac

Chromatography

1. wear eye protection

2. draw line in pencil

3. put dot on line to show where to place solution

4. spot mixture onto the pencil dot line using a capillary tube

5. wait for spot to dry before putting another

6. cover beaker with watch glass

7. let apparatus run until solvent has reached point just below top

8. TLC plate lay on white tile till dry

Rf value equation

Distance travelled by substance / distance travelled by solvent

Nucleotide

A building block of DNA, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and a phosphate group

Structure of DNA

polymer of nucleotides

antiparallel (5’ to 3’/3’ to 5’)

adenine, cytosine, thymine, guanine

phosphodiester bond

long

encode genetic information

Purines

Adenine and Guanine

Bases with a double-ring structure

Pyrimidines

Cytosine and Thymine

Bases with a single-ring structure

antiparallel sugar-phosphate backbone

5 end is where phosphate group attached to 5th carbon of deoxyribose (left)

3 end is where phosphate group is attached to 3rd carbon of deoxyribose (right)

very stable

semi-conservative replication

in each new DNA double helix, one strand is from the original molecule, and one strand is new

DNA replication steps

1. helix unwinds

2. helicase enzyme unzips

3. free phosphorylated nucleotides in nucleoplasm bonded to exposed bases

4. dna polymerase catalyses addition new nucleotide bases in 5 and 3 direction to single strands of dna using it as a template

5. leading strand is synthesised continuously and the lagging strand is in fragments

6. later joined by ligase

7. hydrolysis activated nucleotides to release extra phosphate makes phosphodiester bond

RNA

ribose

uracil

single strand

shorter chain

mRNA, tRNA, rRNA

genetic code

universal: all organisms have same

triplet DNA bases code for same amino acids

degenerate: for all amino acids there are more than one base triplet

non-overlapping: read starting at fixed point in groups of three bases

transcription

1. gene unwinds and unzips

2. H bonds between complementary nucleotide bases break

3. RNA polymerase catalyses the formation of temporary H bonds between complementary nucleotides and unpaired bases (A-U)

4. the length RNA complementary to template strand of gene is produced, coding strand

5. mRNA passes out the nucleus through envelope and attaches to ribosome

Translation

1. tRNA brings amino acids and find their place when anticodon binds by temp H bonds to complementary codon on mRNA molecule

2. ribosome moves along length mRNA when two amino acids adjacent peptide bond forms

3. energy in form ATP needed for polypeptide synthesis

4. after assembled mRNA breaks down and can be recycled into new lengths

5. chaperone proteins fold protein into 3D shape

Active site of an enzyme

the region of an enzyme that attaches to a substrate

Intracellular enzymes

work inside the cell where they control cell metabolism (eg respiration)

catabolic: metabolites broken down into smaller

anabolic: synthesise larger molecules

Extracellular enzymes

enzymes that act outside of the cell in which they are produced

amylase, trypsin

prosthetic group

A non-protein, but organic, molecule (such as vitamin) that is covalently bound to an enzyme as part of the active site, e.g. zinc + carbonic anhydrase

Cofactors

Any nonprotein molecule or ion that is required for the proper functioning of an enzyme

Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis

coenzyme

organic cofactor

B12, folic acid, B3, B6, B1

lock and key hypothesis

The idea that enzymes are specifically shaped to fit only one type of substrate

induced fit hypothesis

Theory of enzyme catalysis which states that the partial binding of a substrate to an enzyme alters the structure of the enzyme so that its active site becomes complementary to the structure of the substrate, enabling binding.

Enzymes and temperature

1. gain KE

2. increase collisions

3. ES complexes increase

4. optimum

5. vibration break H bonds

6. breaks tertiary structure

7. denatured

Rate of reaction equation

1 / time taken to reach end point

temperature coefficient (Q10)

a measure of how much the rate of a reaction increases with a 10 °C temperature increase.

enzymes and PH

H bonds hold structures like alpha helix in place as H+ increases the positive charges are attracted to the negative charges so replace the H bonds

work at narrow range PH

buffers

resists changes in PH can donate or accept H+ e.g. haemoglobin

Enzymes and substrate concentration

increased substrate conc leads to increased ROR so substrate conc limiting factor

all enzymes present at max rate so no longer limiting factor

all active sites activated

enzymes and enzyme concentration

enzyme concentration is limiting factor

substrate concentration is limiting factor

fixed conc