Biology UNIT 3 AOS 1 NOTES PDF

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Biology UNIT 3 AOS 1 NOTES...

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BIOLOGY UNITS 3/4

Plasma Membranes KDP - the fluid mosaic model of the structure of the plasma membrane and the movement of hydrophilic and hydrophobic substances across it based on their size and polarity KDP - the role of different organelles including ribosomes, endoplasmic reticulum, Golgi apparatus and associated vesicles in the export of a protein product from the cell through exocytosis KDP - cellular engulfment of material by endocytosis. KDP - the role of different organelles including ribosomes, endoplasmic reticulum, Golgi apparatus and associated vesicles in the export of a protein product from the cell through exocytosis

The plasma membrane Definition: The insoluble boundary that surrounds all living cells Function: O Regulate the inputs and outputs of the cell O Protective barrier that keeps out foreign molecules that could damage or destroy the cell

The Plasma Membrane as a Fluid Mosaic Model: Fluid: the components of the plasma membrane are in constant movement Mosaic: it resembles a mosaic as it is a collage of various components including phospholipids, sterols (cholesterol in animals), proteins and carbohydrates.

Phospholipids O

O

The plasma is structured in a phospholipid bilayer o Hydrophilic (attracted to water) phosphate and glycerol head o Hydrophobic (repelled by water) fatty acid tail The hydrophobic tail turns inwards and away from the aqueous intercellular and extracellular fluid and the hydrophilic heads point outwards to the aqueous fluid, forming a bilayer

Sterols O O

O

Interspersed among the phospholipids Regulate fluidity of plasma membrane in different temperatures o High temperatures – phospholipids have high energy which increases movement – sterols restrict movement of phospholipids and prevents membrane from becoming too fluid o Low temperatures – phospholipids lack energy which decreases movement and makes them pack together tightly– sterols prevent plasma membrane from solidifying by spacing apart phospholipids and increasing fluidity Animal cells – cholesterol/Plant cells – phytosterol

Proteins O

O

Surface proteins – proteins that are bound onto to the membranes surface – they enable cell-cell interaction and communication and the exchange of substances with the external environment (e.g. glycoproteins) Transmembrane proteins – proteins that are embedded in the phospholipid bilayer and are the length of the bilayer – aka integral proteins as they are a permanent part of the membrane structure  Receptor protein o a protein molecule that has receptor sites at the ends of the carbohydrate chains that bind with specific signal molecules (ligands) to trigger a series of chemical reactions within the cell itself  ligands can include lipids, ions and carbohydrates  each receptor is specific for a single or a small number of ligands  each receptor-ligand pair bind with a lock-and-key fit as they are complementarily shaped  once they have successfully bonded, receptor proteins can become either activated or inactivated leading to some form or intercellular response  Transport proteins o Allow movement of specific substances across a membrane o Examples include channel proteins and carrier proteins

Carbohydrates

Lipid and proteins on the cell membrane surface often have short carbohydrate chains protruding out from the cell surface, known as glycolipids and glycoproteins. Glycoproteins O Receptor and recognition proteins that have a carbohydrate group attached to them O Role is to facilitate cellular recognition by allowing immune cells to distinguish between self and nonself-cells Glycolipids O Lipids with a carbohydrate group attached O Role is to maintain the stability of the cell membrane and to facilitate cellular recognition o They allow the immune system to distinguish between the self and non-self-cells.

Movement across the plasma membrane O O

O

O O

The plasma membrane is selectively permeable as it only allows some substances through and not others Plasma membrane is made up of fatty acids, making it hydrophobic and non-polar o Small non-polar substances will diffuse through the plasma membrane easily (O2, CO2) o Small hydrophobic substances will diffuse through the plasma membrane easily (glycerol) Large molecules (glucose), polar molecules (ethanol) and hydrophilic molecules (NaCl) cannot diffuse through the plasma membrane – must enter cell through other forms of transport Along the concentration gradient: movement of substances from an area of high concentration to an area of low concentration (does not require ATP) Against the concentration gradient: movement of substances from an area of low concentration to an area of high concentration (requires ATP)

Other factors affecting permeability of the membrane: o Heat – a temperature exceeding optimum levels denatures (changes the shape of) the membrane proteins increasing membrane permeability o pH – change in pH levels of surrounding liquid beyond the normal range denatures (changes the shape of) the membrane proteins increasing membrane permeability o Ethanol – ethanol dissolves lipid components of the membrane, creating holes in the membrane and increasing membrane permeability

Passive Transport Simple diffusion Definition: passive net movement of small hydrophobic substances and water molecules through the phospholipid bilayer or through ion channels, down their concentration gradient O Diffusion of water is known as osmosis – water can diffuse through the lipid bilayer even though it's polar because it's a very small molecule O Osmosis – the passive net diffusion/movement of water molecules from an area of low solute concentration to an area of high solute concentration until equilibrium is reached

Facilitated diffusion Definition: passive net movement of dissolved hydrophilic/polar substances via channel proteins or carrier proteins down their concentration gradient O Facilitated diffusion does not use any energy (ATP) from the cell o Channel proteins:  Narrow passageways through which small ions can rapidly diffuse down their concentration gradient

o

Carrier proteins:  Bind to specific molecules on one side of the membrane, change conformational shape and release the substance on the other side down the concentration gradient

Factors affecting rate of diffusion O Concentration – greater the difference in concentration gradient the faster the rate of diffusion – when concentration is equal on both sides of the membrane there is no net diffusion O Temperature – higher the temperature, the higher the kinetic energy of molecules resulting in faster rate of diffusion O Particle size – the smaller the particles, the faster the diffusion rate through the membrane

Active Transport Definition: movement of dissolved hydrophilic substances through ion pumps or carrier proteins against the concentration gradients (requires ATP) O Membrane transport proteins use ATP (energy) to move molecules against the concentration gradient

Endocytosis and Exocytosis O

Enables the bulk transport of larger molecules and liquids in and out of a cell o Due to their large size of the molecules this process requires ATP

Endocytosis Bulk transport of large liquid and solid molecules into the cell  In endocytosis, parts of the cell membrane fold around the material being transported and pinch off, enclosing the material in a vesical inside the cell. There are two types of endocytosis:

Phagocytosis: endocytosis of solids (e.g. food)

Pinocytosis: endocytosis of liquids (common in animal cells as it brings nutrient rich extracellular fluid into cell)

Exocytosis Bulk transport of large liquid and solid molecules out of the cell O

O

Membrane bound vesicles that hold large molecules, are formed by the Golgi apparatus. o These vesicles fuse with the cell membrane, open out and spill their contents into the extracellular fluid. Exocytosis takes place to secrete waste from the cell as well as to relocate some of the substances produced in cells (e.g. hormones, mucus, milk proteins and digestive enzymes) elsewhere in the body.

Cell organelles and export of proteins Ribosome Membrane-less small spherical bodies composed of ribosomal RNA (rRNA) and protein – found in both eukaryotes and prokaryotes Function: to synthesise proteins by translating mRNA strands O Found either floating in the cytosol or on the rough endoplasmic reticulum o Ribosomes in the cytosol: synthesise proteins essential for the cell’s survival o Ribosomes on the Rough ER: synthesise proteins that will be secreted from the cell through exocytosis or will be embedded into the cell membrane O Cells with high rates of protein synthesis have many ribosomes

Endoplasmic Reticulum An interconnecting system of thin membrane sheets which divide the cytoplasm in compartments and channels – found only in eukaryotes

Rough endoplasmic reticulum  studded with ribosomes Function: to transport proteins that have been synthesised by ribosomes within the cell to the Golgi Body O Bending and folding (i.e. modification) of the proteins also occurs in the rough ER

Smooth endoplasmic reticulum (not involved in protein synthesis)  does not have ribosomes on its surface O Site of lipid synthesis (i.e. cholesterol, phospholipids, steroid hormones) O Transports substances around the cell

Golgi apparatus Collection of membranes Function: to package proteins into membrane bound vesicles to export from the cell

Vesicles Membrane bound sacs Function: Membrane bound sacs that carries proteins to plasma membrane and fuse with it to release the protein from the cell

Nucleic

acids and proteins

KDP - nucleic acids as information molecules that encode instructions for the synthesis of proteins in cells KDP - protein functional diversity and the nature of the proteome KDP - the functional importance of the four hierarchal levels of protein structure KDP - the synthesis of a polypeptide chain from amino acid monomers by condensation polymerisation KDP - the structure of DNA and the three forms of RNA including similarities and differences in their subunits, and their synthesis by condensation polymerisation KDP - the genetic code as a degenerate triplet code and the steps in gene expression including transcription, RNA processing in eukaryotic cells and translation.

The proteome  The proteome is the whole set of proteins in an organism o Proteins contained in a proteome are diverse in function  Structural – i.e. collagen, actin, keratin  Transport – i.e. haemoglobin for the transport of oxygen, channel proteins,  Regulatory – i.e. hormones  Enzymes – i.e. catalyse biological reactions  Immunological – i.e. antibodies Proteins can be classified as either fibrous or globular – O Fibrous – elongated and insoluble (i.e. collagen) O Globular – compactly folded and soluble – enzymes and hormones

The four hierarchal levels of protein structure

Primary structure  A sequence of amino acids in a polypeptide chain o Amino acid  a small molecule containing a central carbon which is attached to a hydrogen atom, an amine group (NH2), a carboxylic acid group (COOH) and a unique R group.  The different R groups distinguish one amino acid from another and gives each amino acid its particular chemical properties (i.e. polarity, electrical charge, solubility, etc.)

Amino acids are monomers of the protein which is a polymer Synthesis of proteins occurs through condensation reactions o Condensation reactions  reactions in which smaller monomers react to form larger molecules, resulting in the release of water  Condensation reactions are anabolic (building up) and endergonic (energy is absorbed) Condensation polymerisation  The carboxylic acid group (-COOH) of one amino acid reacts with the amine group (-NH2) of another amino acid to form a peptide bond  Breakdown of polymers occurs through hydrolysis reactions o Water is added to break down a larger molecule/polymer into its monomers o Hydrolysis is catabolic (breaking down) and exergonic (energy is released) O O

Secondary structure Local coiling and folding the polypeptide chain into alpha-helices and beta-pleated sheets held together by hydrogen bonds o Tight coils are known as alpha-helices o Formed when hydrogen bonds form between amine and carboxyl groups of adjacent amino acids forming a helical shape o Flattened folding forms are b-pleated sheets o Formed through the hydrogen bonding between amine and carboxyl groups of adjacent amino acids in the polypeptide chain – causes chain to fold back on each other o Some parts of the polypeptide chain do not fold into defined arrangements and are called random coils

Tertiary structure Overall three-dimensional shape of the protein determined through the intermolecular interactions between different amino acid R groups O Hydrogen bonding – between atoms in some R groups or between atoms of hydrophilic amino acids and surrounding water

O O O

Ionic interactions– between R groups with opposite electrical charges Disulphide bridge– between the sulphur atoms in the cystine R group Hydrophobic interactions with surrounding aqueous environment – R groups that are hydrophobic are repelled by water and thus tucked away within a protein molecule whereas polar amino acids and hydrophilic and therefore tend to be on the outer surface of the protein

O

The tertiary structure that determines the function of the protein

Quaternary structure When two or more polypeptide chains join through intermolecular bonding to form a singular functional protein o Each polypeptide chain is described as a subunit of the protein O Not all proteins are found in quaternary structure – only large and complex proteins (i.e. haemoglobin consists of four polypeptide chains)

DNA vs RNA Nucleic acid  large, linear polymers that form when monomers (nucleotides) bond together – there are two nucleic acids; DNA and RNA Function of DNA  universal code Function of RNA Property DNA RNA Number of One Two strands O O O

Nucleotide

A phosphate group projects from one end of a strand which is called the 5’ end A hydroxyl group projects from the other end of a strand which is called the 3’ end Antiparallel arrangement - 5’ end of one strand comes together with the 3’ end of the complementary strand

O O O O

Pentose sugar – deoxyribose (Doesn’t have oxygen on 2’ carbon of pentose sugar) Negatively charged phosphate group giving DNA an overall negative charge Nitrogenous base (A, T, C, G)

Pentose sugar – ribose (has oxygen on 2’ carbon of pentose sugar)

O O

Bases

Adenine, Thymine, Guanine, Cytosine o o o o

A pairs with T with two hydrogen bonds C pairs with G with three hydrogen bonds Thymine and Cytosine are pyrimidines as they only have one carbon ring Adenine and Guanine and purines as they have two carbon rings

Negatively charged phosphate groups giving RNA an overall negative charge Nitrogenous Base (A, U, C, G)

Adenine, Uracil, Guanine, Cytosine o o o o

A transcribes to U T transcribes to A G transcribes to C C transcribes to G

Three forms of RNA  Messenger RNA (mRNA) – RNA strand that carries the copied DNA code to the ribosome for the purpose of polypeptide synthesis.  Transfer RNA (tRNA) – carries amino acids to ribosome for synthesis of polypeptide chain – anticodon on tRNA binds to complementary mRNA codon and the amino acids on tRNA are joined by condensation polymerisation forming a polypeptide chain o There can be more than one anticodon that corresponds to any one amino acid  Ribosomal RNA (rRNA) - serves as a structural component of the ribosome

Condensation polymerisation of nucleic acids

O O

A nucleotide is a monomer of the DNA polymer The nucleotides are linked through condensation polymerisation o The -OH group on the 3’ carbon atom of pentose sugar of one nucleotide joins with phosphate on the 5’ carbon of the pentose sugar of the other nucleotide to form water, which is released o Resulting nucleotides form phosphodiester bonds forming a long sugar-phosphate backbone

Transcription and Translation of DNA into a protein Transcription 1. DNA in the region of the gene unwinds exposing two single strands of DNA with unpaired bases 2. RNA polymerase recognises the promoter region (beginning of the gene) and attaches to the DNA template strand 3. RNA polymerase uses free nucleotides to assemble a new chain of nucleotides from a 5’ to 3’ direction to produce a complementary pre-mRNA strand 4. Once a pre-mRNA molecule is formed, the DNA returns to normal

RNA processing O

A pre-mRNA molecule consists of sections known as introns and sections known as exons o Intron sections of pre-mRNA must be removed and discarded, leaving only exon sections

During RNA processing: O Introns are spliced out of leaving only exon sections O Methyl cap is added to the 5’ end O Poly-A-tail is added to the 3’ end o The addition of these structure protects mRNA from degradation o Methyl 5’ cap assists the ribosome in recognising the region to begin translating O After RNA processing, pre-mRNA turns into mRNA

Alternative splicing: O During RNA processing, different exons may be removed along with introns to produce mRNA molecules of different length and sequence – this is known as alternative splicing o o

Polypeptides translated from the alternate mRNA molecules are of different sizes, have different sequences and have their own unique functions Explains why we have more proteins produced than genes  One gene could produce one protein at one stage of development but a different protein at another stage of development  One gene could produce

The genetic code O O

mRNA molecule serves as a linear sequence of instructions for making the primary structure of proteins Codon - a three-base sequence (i.e. AUG) in an mRNA molecule that codes for specific amino acids in a ribosome o There are 64 codons and 20 amino acids O Genetic code is degenerate - the same amino acid can be coded by multiple codons O Genetic code is unambiguous - One codon will only even code for one particular amino acid O Genetic code is universal - All organisms in the world have the same codons and the same amino acids coded from these codon

Translation mRNA leaves the nucleus through nuclear pores and travels to the ribosome 1. Ribosome binds to the mRNA strand and begins reading the strand mRNA starting from start codon (AUG) 2. tRNA carry specific amino acid to ribosome and pair with mRNA codon because they have a complementary anticodon 3. Peptide bonds are formed between neighbouring amino acids through condensation polymerisation creating a polypeptide chain 4. Translation continues to occur in a 5’ to 3’ direction until stop codon (UAG, UGA, UAA) is reached O O

As peptide bonds between the amino acids form, the amino acid detaches from the tRNA making it an uncharged tRNA molecules The mRNA strand can then be recycled to produce more protein molecules

Transcription and translation overall diagrams

Gene structure and

regulation

KDP - the functional distinction between structural genes and regulatory genes KDP - the structure of genes in eukaryotic cells including stop and start instructions, promoter regions, exons and introns KDP - use of the lac operon as a simple prokaryotic model that illustrates the switching off and on of genes by proteins (transcriptional factors) expressed by regulatory genes.

Genes  A gene is the basic unit of heredity  It is the section of DNA that controls the ...