Biology Revision Notes Custom Part 1

8/9/2019 Biology Revision Notes Custom Part 1

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Biology Revision Notes Custom (Part 1 of part one)

Cell Types

•

Cells are structural and functional units

• Small cells: bigger surface area per volume→ allows exchange of more nutrients/waste

• Large cells: smaller surface area per volume→ problems to transport waste out of cell

• More nutrients→ more waste

Table 1-10-1: Differences between prokaryotic and eukaryotic cells

Feature Prokaryotic (bacteria) Eukaryotic (plant/animal/fungi)

Size Small cells - 5µm Large cells - 50µm

Capsule (protection) Present Absent

Cell wall Present (peptidoglycan)

In fungi (chitin)

In plants (cellulose)

NOT in animals

Plasma membrane Present Present

Cytoplasm

- Chloroplast

- Lysosomes

- Golgi Apparatus

- Endoplasmic Reticulum

- Mitochondria

- Ribosomes

Absent

Absent

Absent

Absent

Absent

Small ribosomes, always

free in the cytoplasm

Only in plant cells

Present

Present

Present

Present

Larger ribosomes free in cytoplasm

and attached to rough ER

Nucleus- Nuclear envelope

- Nucleoli

- Chromosomes (DNA)

Absent\ Absent

\ Absent

Single and circular

Present\ Present

\ Present

Many and linear

Centriole (for mitosis) Absent Only in animal cells

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Cell Ultra-Structure

Cell wall (plant cells only)

• Made up of cellulose fibres which provide strength

• Cell does not burst if surrounding solutions become dilute

Nucleus (5µm)

• Contains chromosomes (genes made of DNA which control cell activities)

•

Separated from the cytoplasm by a nuclear envelope

• The envelope is made of a double membrane containing small holes

• These small holes are called nuclear pores (100nm)

• Nuclear pores allow the transport of proteins into the nucleus

Rough Endoplasmic Reticulum (rough ER)

• Have ribosomes attached to the cytosolic side of their membrane

•

Found in cells that are making proteins for export (enzymes, hormones, structural proteins,

antibodies)

• Thus, involved in protein synthesis

• Modifies proteins by the addition of carbohydrates, removal of signal sequences

• Phospholipid synthesis and assembly of polypeptides

Smooth Endoplasmic Reticulum (smooth ER)

•

Have no ribosomes attached and often appear more tubular than the rough ER

• Necessary for steroid synthesis, metabolism and detoxification, lipid synthesis

• Numerous in the liver

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Ribosomes (20-30nm)

• Small organelles often attached to the ER but also found in the cytoplasm

•

Large (protein) and small (rRNA) subunits form the functional ribosomeo Subunits bind with mRNA in the cytoplasm

o This starts translation of mRNA for protein synthesis (assembly of amino acids into

proteins)

• Free ribosomes make proteins used in the cytoplasm. Responsible for proteins that

o go into solution in cytoplasm or

o form important cytoplasmic, structural elements

• Ribosomal ribonucleic acid (rRNA) are made in nucleus of cell

Golgi apparatus

• Stack of flattened sacs surrounded by membrane

• Receives protein-filled vesicles from the rough ER (fuse with Golgi membrane)

• Uses enzymes to modify these proteins (e.g. add a sugar chain, making glycoprotein)

• Adds directions for destination of protein package - vesicles that leave Golgi apparatus move to

different locations in cell or proceed to plasma membrane for secretion

•

Involved in processing, packaging, and secretion

• Other vesicles that leave Golgi apparatus are lysosomes

Vacuole and vesicles

• Membranous sacs of liquid which store substances - vacuoles are storage areas

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Lysosomes (0.05 to 0.5 micron)

• Performs intracellular digestion - more numerous in cells performing phagocytosis

• Limiting membrane keeps digestive enzymes separate from the cytoplasm

• Lysosomal enzymes digest particles

o They function optimally at pH 5 and are mostly inactive at cytosolic pH

o Lysosomal enzymes are synthesized on rough ER

o Transferred to the Golgi apparatus for modification and packaging

• Primary lysosomes are small concentrated sacs of enzymes (no digestion process)

o Primary lysosomes fuse with a phagocytic vacuole

o Become secondary lysosomes

o Digestion begins

o Nutrients diffuse through lysosomal membrane into the cytosol

Mitochondria (1µm in diameter and 7µm in length)

• Mostly protein, but also contains some lipid, DNA and RNA

• Power house of the cell

o Energy is stored in high energy phosphate bonds of ATP

o Mitochondria convert energy from the breakdown of glucose into adenosine

triphosphate (ATP)

o Responsible for aerobic respiration

• Metabolic activity of a cell is related to the number of cristae (larger surface area) and mitochondria

• Cells with a high metabolic activity (e.g. heart muscle) have many well developed mitochondria

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Chloroplast (4-6µm in diameter and 1-5µm in length)

• Only in photosynthesising cells (plants)

•

Light energy, CO2, and H2O are converted to produce carbohydrates and O2• Inner membrane has folds, called lamellae (where chlorophyll is found), which surround a fluid,

called stroma

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Cell division

• Occurs in the nucleus of eukaryotic cells by mitosis and meiosis

o Replacement of the entire lining of your small intestine

o Liver cells only divide for repairing

o Nerve cells do not divide

Chromosomes

•

Long and thin for replication and decoding

• Become short and fat prior mitosis→ easier to separate due to compact form

Meiosis (reduction division)

• During the production of sex cells (gametes) in animals

• In spore formation which precedes gamete production in plants

• Haploid gametes (sperm ovum) - sexual reproduction

•

DNA in a cell replicates only once, but cell divides twice

The Cell Cycle

• Interphase

o G1: Protein synthesis and growth (10 hours)

Preparation for DNA replication (e.g. growths of mitochondria)

Differentiation, only selected genes are used to perform different functions in

each cell

o S: DNA Replication (9 hours)

o G2: short gap before mitosis, organelles and proteins for mitosis are made (4 hours)

• G0: Resting phase (nerve cells)

• M-phase

o Mitotic division of the nucleus (Prophase, Metaphase, Anaphase, Telophase)

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o Cytokinesis (division of the cytoplasm)

Interphase

• Phase with highest metabolism (mitochondria have a high activity)

• Muscles never complete the whole cycle

Mitosis

• Process of producing 2 diploid daughter cells with the same DNA by copying their chromosomes

(clones)

• Chromosomes can be grouped into homologous pairs

• Mitosis occurs in

o Growth

o Repair

o Replacement of cells with limiting life span (red blood, skin cells)

o Asexual replacement

• Controlled process, cancers result from uncontrolled mitosis of abnormal cells

• Division of the nucleus (karyokinesis) and the cytoplasm (cytokinesis) are two processes of mitosis

•

Division of cytoplasm after nucleus. Delayed if cells have more than one nucleus (muscle)• Active process that requires ATP

Prophase

• Chromosomes become shorter and thicker by coiling themselves (condensation)

• This prevents tangling with other chromosomes

• Nuclear envelope disappears/breaks down

• Protein fibres (spindle microtubules) form

• Centrioles are moving toward opposite poles forming the spindle apparatus of microtubule

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Metaphase

• Centrioles at opposite poles

• Chromosomes line up on the equator of the spindle

• Centromeres (kinetochores) attach to spindle fibres

• Kinetochores consist of microtubules and "motor" proteins which utilise ATP to pull on the spindle

Anaphase

• Spindle fibres pull copies of chromatids to spindle poles to separate them

• Mitochondria around spindle provide energy for movement

Telophase

• Chromatid at the pole

• Sets of chromosomes form new nuclei

• Chromosomes become long and thin, uncoil!

• Nuclear envelopes form around the nucleus

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Enzymes

• All enzymes are globular proteins and round in shape

• They have the suffix "-ase"

• Intracellular enzymes are found inside the cell

• Extracellular enzymes act outside the cell (e.g. digestive enzymes)

• Enzymes are catalysts→ speed up chemical reactions

o Reduce activation energy required to start a reaction between molecules

o Substrates (reactants) are converted into products

o Reaction may not take place in absence of enzymes (each enzyme has a specific catalytic

action)

o Enzymes catalyse a reaction at max. rate at an optimum state

• Induced fit theory

o Enzyme's shape changes when substrate binds to active site

o Amino acids are moulded into a precise form to perform catalytic reaction effectively

o Enzyme wraps around substrate to distort it

o Forms an enzyme-substrate complex→ fast reaction

o E + S→ ES→ P + E

• Enzyme is not used up in the reaction (unlike substrates)

Changes in pH

• Affect attraction between substrate and enzyme and therefore efficiency of conversion process

• Ionic bonds can break and change shape / enzyme is denatured

• Charges on amino acids can change, ES complex cannot form

• Optimum pH

o pH 7 for intracellular enzymes

o Acidic range (pH 1-6) in the stomach for digestive enzymes (pepsin)

o Alkaline range (pH 8-14) in oral cavities (amylase)

• pH measures the conc. of H+ ions - higher conc. will give a lower pH

Enzyme Conc. is proportional to rate of reaction, provided other conditions are constant. Straight line

Substrate Conc. is proportional to rate of reaction until there are more substrates than enzymes present.Curve becomes constant.

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Increased Temperature

• Increases speed of molecular movement→ chances of molecular collisions→ more ES complexes

• At 0-42 °C rate of reaction is proportional to temp

• Enzymes have optimum temp. for their action (varies between different enzymes)

• Above ≈42°C, enzyme is denatured due to heavy vibration that break -H bonds

o Shape is changed / active site can't be used anymore

Decreased Temperature

• Enzymes become less and less active, due to reductions in speed of molecular movement

• Below freezing point

o

Inactivated, not denatured

o Regain their function when returning to normal temperature

• Thermophilic: heat-loving

• Hyperthermophilic: organisms are not able to grow below +70°C

• Psychrophiles: cold-loving

Inhibitors

•

Slow down rate of reaction of enzyme when necessary (e.g. when temp is too high)• Molecule present in highest conc. is most likely to form an ES-complex

• Competitive Inhibitors

o Compete with substrate for active site

o Shape similar to substrates / prevents access when bonded

o Can slow down a metabolic pathway

• [EXAMPLE] Methanol Poisoning

o Methanol CH3OH is a competitive inhibitor

o

CH3OH can bind to dehydrogenase whose true substrate is C2H5OH

o A person who has accidentally swallowed methanol is treated by being given large doses

of C2H5OH

o C2H5OH competes with CH3OH for the active site

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• Non-competitive Inhibitors

o Chemical does not have to resemble the substrate

o Binds to enzyme other than at active site

o This changes the enzyme's active site and prevents access to it

• Irreversible Inhibition

o Chemical permanently binds to the enzyme or massively denatures the enzyme

o Nerve gas permanently blocks pathways involved in nerve message transmission, resulting

in death

o Penicillin, the first of "wonder drug" antibiotics, permanently blocks pathways certain

bacteria use to assemble their cell wall component (peptidoglycan)

End-product inhibition

• Metabolic reactions are multi-stepped, each controlled by a single enzyme

• End-products accumulate within the cell and stop the reaction when sufficient product is made

• This is achieved by non-competitive inhibition by the end-product

• The enzyme early in the reaction pathway is inhibited by the end-product

The metabolic pathway contains a series of individual chemical reactions that combine to perform one or

more important functions. The product of one reaction in a pathway serves as the substrate for thefollowing reaction.

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Genes, DNA, RNA

• Nucleic acids carry the genetic code that determines the order of amino acids in proteins

• Genetic material stores information, can be replicated, and undergoes mutations

• Differs from proteins as it has phosphorus and NO sulphur

DNA Deoxyribonucleic Acid

• Nucleotides are smaller units of long chains of nucleic acids. Each nucleotide has

o A pentose sugar (deoxyribose in DNA, ribose in RNA)

o A phosphate group

o An organic base which fall into 2 groups,

Purines (double rings of C and N - bigger)

Adenine or Guanine

Pyrimidines (single ring of C and N - smaller)

Thymine or Cytosine

Base pairing by weak hydrogen bonds

Adenine-Thymine 2 H- bonds

Cytosine-Guanine 3 H- bonds

• Chains are directional according to the attachment between sugars and phosphate group

•

They are antiparallel which is essential for gene coding and replication

• DNA molecule has 2 separate chains of nucleotides hold together by base pairing / DNA normally

twist into a helix (coil) / forms a double helix

Ribonucleic Acid (RNA)

• Ribose instead of deoxyribose

• Single chain (shorter than DNA - lower molecular mass)

•

Base difference: Uracil instead of Thymine. Adenine, Guanine and Cytosine are the same

o Ribosomal RNA (rRNA)

Located in the cytoplasm - ER

Reads mRNA code and assembles amino acids in their correct sequence to make a

functional protein (translation)

o Messenger RNA (mRNA)

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Commutes between nucleus and cytoplasm

Copies the code for a single protein from DNA (transcription)

Carries the code to ribosomes in the cytoplasm

o Transfer RNA (tRNA)

In the cytoplasm

Transfer amino acids from the cytoplasm to the ribosomes

The Genetic Code

• DNA codes for assembly of amino acids / forms a polypeptide chain (proteins - enzymes)

• The code is read in a sequence of three bases called

o Triplets on DNA e.g. CAC TCA

o

Codons on mRNA e.g. GUG AGU

o Anticodons on tRNA e.g. CAC UCA

o (must be complementary to the codon of mRNA)

• Each triplet codes for one amino acid / single amino acid may have up to 6 different triplets for it

due to the redundancy of the code / code is degenerate. Some amino acids are coded by more

than one codon

• Same triplet code will give the same amino acid in virtually all organisms, universal code

• We have 64 possible combinations of the 4 bases in triplets, 43

• No base of one triplet contributes to part of the code next to it, non-overlapping

• Few triplets code for START and STOP sequences for polypeptide chain formation

• eg START AUG and STOP UAA UAG UGA

DNA Replication (Semi-Conservative Replication)

• Happens during Interphase 'S'

• Separate the strands, a little at a time to form a replication fork

•

Events:

o Unwinding / Enzyme DNA helicase separates 2 strands of DNA by breaking hydrogen

bonds

o Semi-conservative replication / each strand acts as a template for the formation of a new

strand

o Free DNA molecules join up to exposed bases by complementary base pairing

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Adenine with Thymine (A=T 2 -H bonding)

Cytosine with Guanine (CΞG 3 -H bonding)

o For the new 5' to 3' strand the enzyme DNA polymerase catalyses the joining of the

separate nucleotides

o "All in one go"→ completed new strand

o For the 3' to 5' strand DNA polymerase produces short sections of strand but these

sections have to be joined by DNA ligase to make the completed new strand. Specific base

pairing ensures that two identical copies of the original DNA have been formed

Transcription: DNA to mRNA

• DNA in nucleus unzips - bonds break

•

Single template strand of DNA used for mRNA (triplet on DNA = codon for amino acid on mRNA)

• Enzyme RNA polymerase joins nucleotides together

• Free RNA nucleotides are assembled according to the DNA triplets (A-U / C-G / T-A)

• mRNA bases are equivalent to the non-template DNA strand

• Start and stop codons are included

• Introns (Non-coding) and exons (coding) DNA sequences are present in the primary mRNA

transcript. Introns are removed before the mRNA is translated so that exons are only present in the

mature mRNA transcript

[EXAM] Total number of bases in the DNA sense strand and total number of bases in the mRNA aredifferent

• mRNA moves into cytoplasm and becomes associated with ribosomes

Translation: mRNA to Protein via tRNA

• Translation is the synthesis of a polypeptide chain from amino acids by using codon sequences on

mRNA

• tRNA with anticodon carries amino acid to mRNA associated with ribosome

• "Anticodon - codon" complementary base pairing occurs

• Peptide chain is transferred from resident tRNA to incoming tRNA

• tRNA departs and will soon pick up another amino acid

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Requirement for Translation

• Pool of amino acids / building blocks from which the polypeptides are constructed

• ATP and enzymes are needed

•

Complementary bases are hydrogen-bonded to one another

• Structure involved in translation

• Messenger RNA (mRNA)

Carries the code from the DNA that will be translated into an amino acid sequence

• Transfer RNA (tRNA)

Transfer amino acids to their correct position on mRNA strand

•

Ribosomes

Provide the environment for tRNA attachment and amino acid linkage

DNA and Inheritance

• Reactions in cells is referred to as cell metabolism

• A sequence of chemical reactions is called a metabolic pathway

• Different forms of the same gene are alleles

•

A gene is the length of DNA that carries the code for a protein (enzyme)

o Enzyme effect the cell's metabolism

o Visible changes are described with the phenotype

• The phenotype is influenced by the metabolic pathway

• Therefore

o DNA controls enzyme production

o Enzymes control metabolic pathways

o Metabolic pathways influence the phenotype of an organism

Gene Mutations

• Deletion, reading frame shifts

• Substitution, one base replaced by another

• Duplication, repetition of part of the sequence

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• Addition, Addition extra base

• Change in one or more nucleotide bases in the DNA

• Change in the genotype (may be inherited)

Cystic Fibrosis - Defective Gene

• Mutation causes the deletion of 3 bases in DNA. One amino acid (phenylalanine) is not coded for in

the Cystic Fibrosis Transmembrane Regulator CFTR protein

• Faulty CFTR protein cannot control the opening of chloride channels in the cell membrane

• Results in production of thick sticky mucus, especially in lungs, pancreas and liver

• Organs cannot function normally and infection rate increases

Phenylketonuria (PKU) - Defective Gene

• Gene mutation in DNA coding for the enzyme phenylalanine hydroxylase

• Phenylalanine hydroxylase not produced

• Amino acid phenylalanine cannot be converted to the amino acid tyrosine

• Tyrosine is necessary to produce the pigment melanin

• Phenylalanine collects in the blood and causes retardation in young children

• Managed by controlling diet to eliminate proteins containing phenylalanine

•

Disease is tested by drops of blood taken from the baby

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Biology Revision Notes Custom (Part 1 of part two)

Large Molecules

• Monomer (-OH) + Monomer (-H)→ Polymer + H2O(l)

o Condensation: monomers (e.g. amino acids) join to form polymers (e.g. proteins)

o Glycosidic bond forms when two carbohydrate monomers join together

o Hydrolysis: break down of a polymer; reverse reaction

• Polymers are also called macromolecules (e.g. starch, proteins, triglyceride)

Carbohydrates

• Organic molecules in which C, H and O bind together in the ratio Cx(H2O)y

• Serve as an energy source important for the brain and cellular respiration

• Plants produce carbohydrates by using energy from sunlight

o 6CO2 + 6H2O + energy (from sunlight)→ C6H12O6(carbohydrate) + 6O2

•

Animals eat plant materials to obtain the produced carbohydrates

• They can then be used in animal metabolism to release energy

o C6H12O6 + 6O2→ 6CO2 + 6H2O + energy

Monosaccharides

Triose (3 carbons) Product of respiration and photosynthesis

Pentose (5 carbons)

- Ribose

- Deoxyribose

Found in RNA and DNA

nucleic acids

Hexose (6 carbons)

- Glucose

- Fructose

- Galactose

Source of energy in respiration

Main energy source in brain

Found in sweet-tasting fruits

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Disaccharides (two sugar residues)

Sucrose (glucose + fructose) Transport carbohydrates in plants

Maltose (glucose + glucose) Formed from digestion of starch

Lactose (glucose + galactose) Carbohydrates found in milk

Polysaccharides (many sugar residues)

Starch (alpha-glucose) Main storage of carbohydrates

- in plants

Glycogen (alpha-glucose) - in humans and animals

Cellulose (beta-glucose) Important component of the plant cell wall

Starch

• Consists of amylopectin and amylose (both are made of α-glucose)

o Amylopectin is branched via 1,6-glycosidic bonds

o Amylose forms a stiff helical structure via 1,4-glycosidic bonds

o Both are compact molecules→ starch can be stored in small space

• The ends are easily broken down to glucose for respiration

• Does not affect water potential as it is insoluble

•

Readily hydrolysed by the enzyme amylase found in the gut and saliva

• Major carbohydrate used in plants

o Found as granules (chloroplast)

o Each granule contains amylopectin combined by a larger amount of amylose

• Commonly used sources are corn (maize), wheat, potato, rice

Glycogen

•

Branched, storage, polymer of glucose linked via glycosidic bonds

• Found in skeletal muscle and in the liver

• Chains are linked by alpha-1,4-linkage, branches are linked by alpha-1,6-linkages

• Glycogen is broken down to glucose by glycogenolysis (glycogen phosphorylase)

• Major site of daily glucose consumption (75%) is the brain via aerobic pathways

• Most of the remainder is utilized by erythrocytes, skeletal muscle, and heart muscle

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• Glucose is obtained from diets or from amino acids and lactate via gluconeogenesis

• Storage of glycogen in liver are considered to be main buffer of blood glucose levels

Cellulose

• Polysaccharide consisting of long beta-glucose chains

• Linked together by hydrogen bonds to form microfibrils

• Structural function is a important component of plant cell walls

• Its tensile strength helps plant cells in osmosis //cell does not burst in dilute solutions

Proteins

Structure

• Proteins are polymers of amino acids

• Proteins are made up by different combinations of 20 amino acids

o They have a general structure:

o The difference between different amino acids is found in the R-group

o

When two amino acids join together, they release -H and -OH groups highlighted in redbelow

o Peptide bond is formed between alpha-carbon and nitrogen

o Condensation reaction

• Primary structure of a protein

o Sequence of amino acids

o Joined together by covalent peptide bonds

• Secondary structure

o

Hydrogen bonds between amino acids

o Made of a combination of alpha-helices and beta-pleated sheets

o Proportion of α-helix and β-sheet depends on sequence (primary structure)

• Tertiary structure

o Complex globular shape

o Folding and twisting of polypeptides (H-bond)

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o Polypeptides contain many peptide bonds

• Quaternary structure

o Several polypeptide chains //several tertiary structures combined

o Haemoglobin has 4 polypeptide chains

o Collagen has 3 polypeptide chains, twisted around each other

o Globular proteins are soluble and has folded chains

o Fibrous proteins are insoluble and long, thin, twisted chains

• Same amino acid sequence→ same shape always

Bonds Found in Proteins

•

Hydrogen bonds

o Between R-groups are easily broken, but are numerous

o The more bonds, the stronger the structure

• Disulphide bonds

o Between sulphur-containing amino acid cystine

o Strong bonds found in skin and hair

• Denaturation

o Destruction of tertiary structure, can be done by heat

o

Protein structure is lost and cannot reform→ dysfunctional

Absorption and Function

• Absorption of proteins in the digestive tract

o Proteins are taken in as food

o They are broken down in the digestive tract into their individual amino acids

o Amino acids are recombined in the body to form different proteins

o Good food sources include beans, milk, cheese, fish, meat

• Several substances are composed of proteins with distinct functions

o Keratin, collagen are main components in hair, muscles, tendons, skin

o Enzyme amylase digests starch

o Haemoglobin transports O2 in the blood stream

o Insulin regulates glucose storage

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Lipids

• Easily dissolved in organic solvents but not in water

• Triglycerides (fats and oils)

o Serves as an energy reserve in plant and animal cells

o

Consists of 3 fatty acids linked by ester bonds to glycerol

o Excess energy available from food/photosynthesis is stored as triglycerides

o Can be broken down later to yield energy when needed

o Fats and oils contain twice as many energy stored per unit of weight as carbohydrates

o Triglycerides (TG) are also called triacylglycerides (TAG)

• Saturated fatty acids

o -COOH group without double bonds in the carbohydrate chain

o May cause blockage of arteries which can lead to strokes and heart attacks

o

High melting point / solid at room temperature (fats) / typical animal fats

• Unsaturated fatty acids

o -COOH group with double bonds in the carbohydrate chain

o Low melting point / liquid at room temperature (oils)

o Found in plants

• Phospholipids

o Formed by replacing one fatty acids in a triglyceride with a phosphate group

o Phosphate is polar / hydrophilic / does mix with H2O

o Fatty acid tails remain non-polar / hydrophobic / insoluble, does not mix with H2O

o Form a ball called a micelle when placed in a polar solution (e.g. water)

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Fluid-mosaic model

• Plasma membrane consists of a phospholipid bilayer studded with proteins, polysaccharides, lipids

• The lipid bilayer is semipermeable

o Regulates passage of substances into and out of the cell

o

H2O and some small, uncharged, molecules (O2, CO2) can pass through• Phospholipids have two parts

o "Head": hydrophilic → attracts and mixes with H2O

o Two "fatty acid tails": hydrophobic

Function of proteins

• Carrier (change shape for different molecules) for water-soluble molecules such as glucose

•

Channels for ions (sodium and chloride ions)

• Pumps use energy to move water-soluble molecules and ions

• Adhesion molecules for holding cells to extracellular matrix

• Receptors enable hormones and nerve transmitters to bind to specific cells

• Recognition sites, which identify a cell as being of a particular type

• Enzymes, which speed up chemical reactions at the edge of the membrane

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• Adhesion sites, which help some cells to stick together

• E.g. glycoprotein acts as a receptor and recognition site

Passive transport• Uses energy from moving particles (Kinetic Energy)

Diffusion

• Substances move down their conc. gradient until the conc. are in equilibrium

• Microvilli are extensions of the plasma membrane

o They increase the surface area of the membrane, therefore

o

They accelerate the rate of diffusion

• Fick's law → rate of diffusion across an exchange surfaces (e.g. membrane, epithelium) depends

on

o surface area across within diffusion occurs (larger)

o thickness of surface (thinner)

o difference in concentration gradient (larger)

o Fick’s law = (surface area x difference in conc gradient) / thickness of surface

• Temperature increases rate of diffusion due to increasing K.E. (kinetic energy)

Facilitate diffusion

• Transmembrane proteins form a water-filled ion channel

o Allows the passage of ions (Ca2+, Na+, Cl-) down their conc. gradient //passive - no ATP

requiredo Some channels use a gate to regulate the flow of ions

o Selective permeability - Not all molecules can pass through selective channels

• How do molecules move across the membrane?

o Substrate (molecule to move across the membrane) binds to carrier protein

o Molecule changes shape

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o Release of the molecule (product) at the other side of the membrane

• Example

o If you want to move a muscle a nerve impulse is sent to this muscle

o The nerve impulse triggers the release of a neurotransmitter

o Binding of the neurotransmitter to specific transmembrane proteins

o Opens channels that allow the passage of Na+ across the membrane

o In this specific case, the result is muscle contraction

o These Na+ channels can also be opened by a change in voltage

Osmosis

• Special term used for the diffusion of water through a differentially permeable cell membrane

•

Water is polar and able to pass through the lipid bilayer

• Transmembrane proteins that form hydrophilic channels accelerate osmosis, but water is still able

to get through membrane without them

• Osmosis generates pressure called osmotic pressure

o Water moves down its concentration gradient

o When pressure is equal on both sites net flow ceases (equilibrium)

o The pressure is said to be hydrostatic (water-stopping)

Water potential

• Measurement of the ability or tendency of water molecules to move

• Water potential of distilled water is 0, other solutions have a negative water potential

•

Measured in kPa - pressure

• Hypotonic

o Solution is more dilute / has a lower conc. of solute / gains water by osmosis

o Cells placed in a hypotonic solution will increase in size as water moves in

o For example, red blood cells would swell and burst

o Plant cells are unable to burst as they have a strong cellulose cell wall

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• Hypertonic

o Solution with a higher conc. of solutes / loses water by osmosis

o Cells will shrink in hypertonic solutions

• Isotonic

o Solutions being compared have equal conc. of solutes

o Cells which are in an isotonic solution will not change their shape

o The extracellular fluid of the body is isotonic

• Molecules collide with membrane / creates pressure, water potential

• More free water molecules, greater water potential, less negative

• Solute molecules attract water molecules which form a "shell" around them

o water molecules can no longer move freely

o

less "free water" which lowers water potential, more negative

Active Transport

• Movement of solute against the conc. gradient, from low to high conc.

• Involves materials which will not move directly through the bilayer

• Molecules bind to specific carrier proteins / intrinsic proteins

• Involves ATP by cells (mitochondria) / respiration

o

Direct Active Transport - transporters use hydrolysis to drive active transporto Indirect Active Transport - transporters use energy already stored in gradient of a directly-

pumped ion

• Bilayer protein transports a solute molecule by undergoing a change in shape (induced fit)

• Occurs in ion uptake by a plant root; glucose uptake by gut cells

Endocytosis and Exocytosis

•

Substances are transported across plasma membrane in bulk via small vesicles

• Endocytosis

o Part of the plasma membrane sinks into the cell

o Forms a vesicle with substances from outside

o Seals back onto the plasma membrane again

o Phagocytosis: endocytosis brings solid material into the cell

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o Pinocytosis: endocytosis brings fluid materials into the cell

• Exocytosis

o Vesicle is formed in the cytoplasm //May form from an edge of the Golgi apparatus

o Moves towards plasma membrane and fuses with plasma membrane

o Contents are pushed outside cell

o Insulin is secreted from cells in this way

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Biochemistry of Respiration

• Oxidative breakdown of organic molecules to store energy as ATP

• Animals and plants respire; FAD and NAD are coenzymes

Aerobic respiration

• C6H12O6 + 6O2→ 6CO2 + 6H2O + energy

• Complete oxidation of an organic substrate to CO2 and H2O using free O2

• Production of CO2, NADH + H+ and FADH + H+, 38ATP

1) Glycolysis→ cytoplasm

• Glucose enters cell by facilitated diffusion

• ATP activates glucose to produce 2 unstable compounds

• Substrate-level phosphorylation produces 4ATP

• Net yield of 2ATP and 2reducedNAD per glucose molecule

2) Link reaction→ matrix of mitochondria

•

Pyruvate enters matrix of mitochondrion for further reaction

• Net yield of 2reducedNADH per glucose

3) Krebs cycle→ matrix of mitochondria

• Citrate is gradually broken down to re-form oxaloacetate

• Substrate-level phosphorylation forms 2ATP

• Removal of hydrogen from respiratory substrate

•

Net yield of 2ATP, 2reducedFADH, 6reducedNADH per glucose

4) Electron Transport Chain ETC→ inner membrane/cristae of mitochondria

• Reduced coenzymes arrive at ETC

• Split into coenzyme + 2H+ + 2e- by hydrogen carriers

• 2e- are transferred to electron carriers (cytochrome)

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• Pass down ETC by redox reaction and release energy as they go

• Energy produces ATP by oxidative phosphorylation

• Final electron acceptor 1/2O2 is reduced by 2H+ and 2e- to produce H2O

• Net yield of 34ATP (30NADH, 4FADH) per glucose

• //Cytochromes are iron-containing proteins→ cytochrome a3 also contains copper and is

irreversibly damaged by cyanide

IMG 5-14-8

Anaerobic respiration (fermentation)

• Substrate-level phosphorylation: 2ADP + 2Pi→ 2ATP directly by enzymes in glycolysis

• No O2 to accept electrons from NADH + H+→ no Krebs cycle or ETC

• NADH + H+ reduces (gives off H+ ions to) pyruvate to produce

o Lactate C3 in animal cells→ can be re-oxidised

o Ethanol C2 in yeast cells→ irreversible, CO2(g) lost

•

Regenerates NAD• NAD can be re-used to oxidise more RS/allows glycolysis to continue

• Can still form ATP/release energy when O2 is in short supply

Role of ATP

• Adenosine (ribose + adenine) triphosphate (3 phosphate groups)

•

Produced by adding Pi to ADP→

phosphorylation• Breaks down to ADP (adenosine diphosphate) and Pi (inorganic phosphate ion) by hydrolysis

• ATP is useful as an immediate energy source/carrier because

o Energy release only involves a single reaction

o Energy released in small quantities

o Easily moved around inside cells, but cannot pass through cell membranes

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• Light-dependent reaction cannot be the only source of ATP

o "Photosynthesis cannot produce ATP in the dark

o Need more ATP than can be produced in photosynthesis

o Cannot be produced in plant cells lacking chlorophyll

o ATP cannot be transported"1

• Central molecule in metabolism (ATP hydrolysis)

o Muscle contraction→ changes of position of myosin head relative to actin

o Protein synthesis→ ATP "loads" amino acids onto tRNA

o Active transport→ driven by phosphorylation of membrane-bound proteins

o Calvin Cycle→ cyclic reduction of CO2 to TP

o Nitrogen fixation→ involves ATP-driven reduction of molecular nitrogen

•

ATP in liver is used for active transport / phagocytosis / synthesise of glucose, protein, DNA, RNA,lipid, cholesterol / urea in glycolysis / bile production / cell division

Brown fat

• White fat insulates the body and reduces heat loss

• Brown fat cells in mitochondrial membrane produce heat

•

Mitochondria in other tissue / chemiosmosiso H+ ions pass back from space between two mitochondrial membranes into matrix

o Through pores which are associated with the enzyme ATP synthetase

o Energy from the ETC will be used to produce ATP

• Mitochondria in brown fat

o H+ ions flow back through channels not associated with ATP synthetase

o Energy produces heat instead of ATP

o Found in chest, larger arteries for heat distribution round the body or in hibernating

mammals

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Biology Revision Notes Custom Part 1