VCE Biology Unit 3/4

Plasma Membrane

Barrier of a cell and controls everything that comes in and out

Aquaporins allow water to travel through

Semi-permeable

Composed of phospholipids

Stabilised by glycoproteins and glycolipids

Cholesterol in the Plasma Membrane

Provides fluidity and rigidity of the phospholipid molecules and prevents them from packing too close together

Prevents solidification at lower temperatures

Effect of Temperature on the Plasma Membrane

Higher temperature causes fluidity of the membrane as phospholipids are less tightly packed

Integral Proteins

Permanent part of the plasma membrane

Have both hydrophilic and hydrophobic regions

Peripheral Proteins

Not embedded in the bilayer

Acts as receptors and recognition sites

Can be attached to either phospholipid molecules or other integral proteins

Transport Proteins

Two types: channel and carrier, they allow some substances typically ions to move through the plasma membrane

Receptor Proteins

Hormones and other substances bind to these - affects cells activities. (Insulin and adrenaline)

Glycoproteins

Acts as markers 'antigens', enables immune system to distinguish self from non- self

Passive Transport

Movement of substances ALONG the concentration gradient

Passive Transport: Diffusion

The net movement of particles from a region of high concentration to a region of low concentration until equilibrium is met (occurs in both gases and liquids)

Passive Transport: Osmosis

The net movement of free water molecules through a semi-permeable membrane from a region with low solute concentration to a region with a high solute concentration until equilibrium is met

Movement is dependent on the solute concentration inside and outside the cell

Osmosis: Hypotonic

Net movement of water molecules INTO the cell

High solute concentration INSIDE the cell so water moves inwards

Hypotonic Environments

Cells swell because of net gain of water across the membrane which can eventually cause the cell to burst if not regulated

Osmosis: Hypertonic

Net movement of water molecules OUT of the cell

High solute concentration OUTSIDE the cell so water moves outwards

Hypertonic Environments

Cells shrink because of net loss of water across the membrane and because of the loss of natural shape the cell is deemed 'crenate'

Hypertonic: Plasmolysis

When a plant cell is hypertonic, water moves out of the cell causing the membrane to pull away from the walls, the wall is intact however the membrane appears to have shrunk inwards

Osmosis: Isotonic

Equal amount of water molecules INSIDE and OUTSIDE the cell

Water molecules move in and out at a regulated level

Isotonic Environments

Cells maintain their normal shape and there is NO NET MOVEMENT of water

Facilitated Diffusion

Assisted diffusion using transport proteins

Faster than simple diffusion

Channel proteins

Tubes that are lined with water and ions (water soluble particles) can diffuse through at a rapid rate

Has a receptor to recognise certain substances and allow them in

Function like a barrier and create a pathway through the phospholipid bilayer (ions can travel through)

Carrier proteins

Works like a revolving door allowing molecules to bind through them and then changing their conformation to release them inside the cell

Function like a revolving door by taking one molecule in and binding it to itself before pushing it through into the cell

Factors that Affect the Rate of Diffusion

Concentration: There will be a higher rate of diffusion when there is a greater difference in concentration between two regions

Temperature: The higher the temperature, the quicker the rate of diffusion is

Heat provides energy which causes particles to collide more frequently

Surface Area: The larger the surface area the faster the diffusion

Diffusion Distance: Faster over shorter distances

Active Transport

ENERGY REQUIRED

Movement of substances AGAINST the concentration gradient

Moves molecules that have a high affinity to water (hydrophilic)

Bulk Transport: Endocytosis - INTO THE CELL

ENERGY REQUIRED

The cell membrane will fold and form a dent that engulfs particles outside of the cell and 'spits' them out inside the cell

Phagocytosis - engulfing solid material

Pinocytosis - engulfing fluid material

Bulk Transport: Exocytosis - OUT OF THE CELL

ENERGY REQUIRED

A vesicle within the cell transports waste from inside the cell to outside the cell

Fusion of vesicle membrane and cell membrane

Prokaryotes

Unicellular

No membrane bound organelles

Cytoplasm contains the genetic information

Circular DNA chromosome

The plasma membrane is surrounded by a cell wall e.g. bacteria

Eukaryotes

Has a nucleus in which DNA is located

Has membrane bound organelles

Examples of this cell type are plants, animals, fungi and protists

Linear DNA that is surrounded by protein and is called

Nucleus

Contains genetic information for synthesis of proteins

Nuclear membrane is partially permeable and transcription occurs here

Golgi Apparatus

Found in the cytoplasm and is linked with ER

Composed of stacked flat membranous sacs called cisternae

Packaging and modification of proteins into vesicles for exiting the cell

Ribosomes

Made up of proteins and ribosomal RNA

Free floating in the cytosol or connected to RER

Free floating ribosomes produce proteins for use within the cell

Connected to RER ribosomes produce proteins which are transported around or out of the cell

Lysosomes

NOT FOUND IN PLANTS

Vesicles that contain digestive intracellular enzymes for breaking down substances (waste and foreign material) composed of fats, proteins, polysaccharides and nucleic acids

Required in apoptosis (programmed cell death)

Rough Endoplasmic Reticulum

Membrane bound and covered in ribosomes

Used in the synthesis, folding and modification of proteins

Transportation of proteins throughout the cell

Mitochondria

Controls cellular respiration

Contains mtDNA and is folded to increase surface area

Found in higher concentrations in areas which require high amounts of energy to function e.g. muscles and kidneys

Flagella

Mobility of a cell e.g. sperm cell has tail that wiggles

High concentration of mitochondria

Chromosomes

Chromatin, genetic material when it is not undergoing division

Chromosomes are how genetic material (DNA) is stored for division

Chloroplasts

FOUND IN PLANTS

6CO2 + 6H2O ------> C6H12O6 + 6O2

Located in cytoplasm of cells

This area has the most direct contact with the sun

Contains chlorophyll

Smooth Endoplasmic Reticulum

Production of lipids (oils, phospholipids and steroids)

Membrane bound

Involved in the removal of drugs and poisons

Cell Wall

FOUND IN PLANTS

Protects the cell and maintains its shape

Ensures there is no excess of water in the plants

Vacuoles

High concentration of liquid

Storage of fluid and secretions

The majority of a plant cell is made up of the vacuole

Centrioles

Forms the spindle fibre in cell division

Composed of microtubules and located in cytoskeleton

Found in plants and occasionally animals

Cytoplasm

Gel like substance that MANY molecules (organelles) are suspended within

Area between the nuclear membrane and the cell membrane

Cilia

'mosh pit' small hairs carry the substances along the surface of cells

Located along the respiratory tract

High concentration of mitochondria

Cytosol

Gel like substance that organelles are suspended in

Just the liquid substance minus the organelles involvement

Area between the nuclear membrane and the cell membrane

Carbohydrates

CHO

Monosaccharide

- Glucose and fructose

Disaccharides

- Sucrose, maltose and lactose

Polysaccharides

- Glycogen - energy storage in animal cells

- Cellulose - plant cell wall

- Starch - energy storage in plant cells

- Chitin - fungi cell wall

Lipids

CHO

Glycerol and Fatty acids

Phospholipids and triglycerides

Phospholipid is the only lipid that has phosphorus

Proteins

CHON

Amino Acid

Amino acids (monomer) - bond between two amino acids is known as peptide bond

Polypeptide chains (polymer)

Functions include

- Catalyse (speed up reactions)

- Regulation of hormones

- Immunity and self-labels for cells are made by proteins

Nucleic Acids

Nucleotide (monomer) and Nucleic acid (polymer

Genetic information

Deoxyribose sugar

Phosphate group

Nitrogenous base

Synthesis of Proteins

Amino acids are joined together by peptide bonds to create polymers. This is known as a condensation polymerisation reaction.

Polypeptide chains form the primary structure of a protein

Folded in our rough endoplasmic reticulum and modified in our Golgi apparatus which is how it starts to develop into a fully functional protein

Protein: Condensation

Amino acids are joined together to form peptide or polypeptide chains

Water is RELEASED

Protein: Hydrolysis

Polypeptide chains are broken down into smaller peptide chains or simple amino acids (monomer)

Water is REQUIRED

Protein Motility

Allows movement of cells and their organelles

E.g. tubulin forms microtubules to move flagella, cilia, chromosomes and organelles

Protein Structural

Support, strength and protection

E.g. collagen for body tissues, fibroin for spider webs and keratin for hair and nails

Protein Enzymes

Used to speed up biochemical reactions (catalyse)

E.g. DNA polymerase is an enzyme that creates DNA polymers by attaching together nucleotide after nucleotide

Protein Transport

Carry molecules from various locations

E.g. Haemoglobin carries oxygen to body cells

Protein Cell Surface Receptors

Labels cells as targets for certain hormones, viruses, growth or transmission of nerve impulse

E.g. MHC (Major histocompatibility Complex) allows the immune system to recognise self so the body does not destroy its own cells

Protein Hormones

Signals cells - stimulation or inhibition, telling them to either start or stop

E.g. insulin travels in the blood and binds to cell receptors to trigger an uptake in glucose

Proteome

The complete set of proteins produced by a cell

Used in medical diagnosis, monoclonal antibodies and designed drugs

Genome

The complete set of genes within a cell

Primary Structure

Linear sequence of amino acids joined together by polypeptide bonds

Chemical interaction of each individual amino acid with other amino acid creates protein shape

Secondary Structure

The protein is becoming more specific

Alpha - helix coil - looks like a spiral

Beta - pleated sheet - looks like a zigzag

Created by hydrogen bonding between CO and NH groups of the polypeptide backbone

Tertiary Structure

At this stage, the protein becomes functional

Disulphide bonding occurring between two cysteine amino acids forming the strongest links

One chain folded together to create conformation

Quaternary Structure

Two or more chains makes up the shape

Functional at this stage

Protein Structure

Protein Structure

Structure and shape (conformation) is determined by the "R" group. A variable group that can be many potential things.

The "r" groups react with each other (want to be near each other) this creates conformation.

Tolerance range is impacted by the type of organism

Denature can be define as the loss of protein shape resulting in it becoming unspecific and unable to function

The 3D structure is lost as the disulphide bridges are broken

Factors that Affect Proteins: Temperature

High heat cause the bonds to break

Low heat slows down the reaction - DO NOT DENATURE

Optimum temperature in humans is 37 degrees

Factors that Affect Proteins: pH

Protein can be denatured going forward or backwards - getting more acidic or basic

Due to R groups the bonds are broken causing a loss in shape and inability to function

Factors that Affect Proteins: Cofactors

Cofactors are like cushions on dining chairs.

Hard wooden seats (active site) are uncomfortable for bottoms to sit on so a cushion (cofactor) lines the seat to provide comfort.

Nucleotides

Consist of a five carbon deoxyribose sugar, nitrogenous base and phosphate group

Nitrogenous Bases

Adenine, Thymine, Guanine, Cytosine (DNA)

Adenine, Uracil, Guanine, Cytosine (RNA)

A and T (U) are complimentary and G and C are complimentary

DNA

Found in the nucleus and made of repeating units of nucleotides

3 DNA bases = Triplet (DNA sequence is read in sets of three to code for amino acids)

A gene is a section of DNA that can be translated to from a polypeptide

DNA Structure

Antiparallel - each strand runs in opposite directions with the 3' end matching with the 5' end of the other strand

Double stranded and connected with hydrogen bond

Free nucleotides link together to form strands through a condensation polymerisation reaction (nucleotide = nucleotide = dinucleotide), (strong covalent bonds = phosphodiester bonds)

RNA

Ribonucleic Acid

Single stranded and much shorter than DNA

Combines with ribosomes to form proteins and is synthesized in the nucleolus

mRNA

Messenger Ribonucleic Acid

Codon - 3 mRNA bases

Created in the nucleus via the process of transcription

Exits the nucleus and is read by the ribosomes to produce proteins, this process is known as translation

Carries DNA message from inside the nucleus to outside the nucleus

tRNA

Transfer Ribonucleic Acid

Anti-Codon - 3 tRNA bases

Transfers amino acids from the cytoplasm to the ribosome

As amino acids join, the polypeptide structure grows

rRNA

Ribosomal Ribonucleic Acid

Associates with a set of proteins to form ribosomes

Genes: Start codon

DNA = TAC

mRNA = AUG

Met = Start

Genes: Stop codon

A stop triplet codes for a release factor which signals the polypeptide chain to be released from the ribosome

UAA, UAG and UGA = Stop codon

Genes: Promoter Region

An upstream binding region for the enzyme RNA polymerase to begin the encoding process (Transcription starts here)

Can be referred to as the 'TATA' box and tells the free floating nucleotides to bind with the DNA strand that is to be transcribed

Genes: Introns

Non-coding regions of DNA

Spliced out by spliceosomes of the primary RNA transcript to form the mRNA molecule

Genes: Exons

Coding regions of DNA

Segments of exons are joined together after introns are removed

Degeneracy

More than one codon can code for the same amino acid

This ensures that a single change in base may not necessarily lead to change in the amino acids produced

Universal = the same four bases in all organisms

Transcription

- RNA polymerase binds to DNA strand and unzips DNA by breaking hydrogen bonds between nucleotides

- RNA polymerase adds complimentary free floating RNA nucleotides are added to the template strand of DNA to form pre-mRNA.

- Pre-mRNA undergoes RNA processing in which non coding segments known as introns are removed through splicing and coding segments known as exons are re-joined

- The strand is then further modified by the addition of a methylated cap on the 5' prime end and a poly-A-tail on the 3'end

- Mature mRNA exits the nucleus through a nuclear pore

Translation

- Ribosomes attaches to methylated cap on the 5' end of an mRNA strand

- Anticodons on a tRNA molecule temporarily bind to codons on an mRNA strand, bringing and releasing specific amino acids

- The ribosomes continues to read the mRNA strand till a stop codon is reached a release factor releases the strand

- A polypeptide chain has now been formed

Lac Operon

FOUND IN E.COLI

INDUCIBLE (able to be turned on and off

Operator (binding site for repressor protein)

Promotor (binding site for RNA polymerase)

Structural genes involved in breakdown of Lactose (Lac Z, Lac Y and Lac A)

1. Lactose molecules bind with repressor protein causing it to change shape and separate from the operator on the DNA strand

2. This allows RNA polymerase to separate the DNA strand for translation

3. After translation, an enzyme is released which breaks down lactose into the useable forms of glucose and galactose

4. Following the breakdown of all lactose, the repressor protein returns to its normal shape and fits back into the operator on the DNA strand resulting in the cease of enzyme production

Enzymes

- Type of biological catalyst - increases the reaction rate by lowering the activation energy, ensures that a higher fraction of collisions between reactant molecules would be above the activation energy, and therefore more reactants would react per unit of time

- Made of protein

- Act by binding to reactants - known as substrates, to form an enzyme-substrate complex

- Enzymes weaken the bonds in the substrates, making the reaction easier to occur and subsequently products are formed and released from the enzyme

- Enzymes only catalyse specific metabolic reactions because they can only bind compounds that have a complementary shape to their active site

- Enzymes have a specific 3D (functional) conformation and are substrate specific

- The functionality of a protein is lost when its conformation is altered

Active Site

Specific physical site on enzyme that binds to complementary substrate

Lock and Key model

States that:

Enzyme and substrates interact with a perfect complimentary shape

Fitting together like a 'lock and key'

Induced Fit Model

States that:

The active site is flexible and has the ability to mould around the shape of the substrate therefore achieving a tighter fit

Catabolic

Reactions in which larger molecules are broken down into smaller substances

The release of energy is refereed to as an exergonic (energy exits) reaction

Anabolic

Reactions in which smaller substances make larger molecules

The input of energy is referred to as an endergonic reaction

Factors that Affect Enzyme Activity: Temperature

High - The activity of an enzyme in high temperature environment decreases

This is because excessively high temperatures break hydrogen bonds in the secondary and tertiary structures changing the shape of the protein, specifically the active site

The change in shape of the active site means that it can no longer bind to complementary structure hence its function is lost

This process is known as denaturation

Factors that Affect Enzyme Activity: pH

Proteins denature if the pH gets higher or lower

pH depends on the organism and the location within the organism

Factors that Affect Enzyme Activity: Enzyme concentration

Increasing enzyme concentration: assume there are large amounts of substrate. If there is limited amount of substrate then it will reach a saturation point.

Plateau = substrate concentration

Continuos diagonal line = enzyme concentration

Factors that Affect Enzyme Activity: Substrate concentration

Increasing substrate concentration: the enzyme can only do so much as eventually all the active sites are full so it will plateau out

Enzymes Regulate Biochemical Pathways

Biochemical pathways are a sequence of reactions, each reaction in the sequence is catalysed by a specific enzyme, this means that the product of one reaction in the sequence becomes the substrate of the next reaction

Pathways can be linear, branched or cyclic

Irreversible inhibition of Enzymes

Strong covalent bonds between inhibitor and enzymes therefore binding is irreversible

The inhibitor blocks the active site PERMENANTLY and will no longer be able to catalyse reactions

Reversible inhibition of Enzymes

Weak hydrogen bonds formed between inhibitor and the enzyme

When a large amount of substrate is present the inhibitor is pushed out

Feedback inhibition of Enzymes

A regulatory process that works with a biochemical pathway (NOT PERMEMANT)

Substrate is made into product. Once there are enough products made, the product becomes an inhibitor, which changes the shape of the enzyme causing it to stop turning substrate into product. Once the product supply starts to deteriorate

Competitive Inhibition (Links with reversible inhibition)

Competitive inhibitors compete with substrate to bind to an active site. The competitive inhibitors sit inside the active site and block substrates from binding to it. This can be overcome by increasing substrate concentration

Non-competitive Inhibition (Links with irreversible inhibition)

Non-competitive inhibitors bind to an allosteric site (not the active site) thus changing the shape of the enzyme and causing irreversible inhibition (can no longer function)

Coenzymes

Organic cofactors, which bind to enzymes and alter the rate of chemical reaction

Cofactors

Non protein part that binds to enzymes, anything that can be taken from the periodic table (non-organic) e.g. metallic ions such as iron, calcium, copper and zinc

Cycling of Coenzymes

ATP, NADH, FADH2 and NADPH can store and transport p+, e- and chemical groups from one reaction another (energy is transferred)

Unloaded form coenzyme

Free to accept a proton, electron or chemical group

Loaded form coenzyme

Will donate a proton, electron or chemical group

Photosynthesis

The action of transforming energy from the sun into chemical energy

Occurs in plant, algae and phytoplankton

Produces:

Energy for use by the autotroph and for use later in the food chain

Oxygen formed may be used for aerobic cellular respiration by the plant

Absorption of light energy into chlorophyll (light dependant stage) chlorophyll is a pigment responsible for capturing light

Synthesise glucose from carbon dioxide and water (light independent stage)