Biology UNIT 3-4 Notesssssd PDF

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Biology notes unit 3/4 - Chiara Braida

Cell Theory: - All living organisms are composed of one or more cells - Cells are the basic functional unit of life - All new cells arise from pre-existing cells Characteristics of living things: -

Responsiveness to the environment Growth and change Ability to reproduce Have a metabolism and breathe Being made of cells Maintain homeostasis Passing traits onto offspring

Classification: -

Prokaryotes: unicellular organisms that lack membrane bound organelles, have no nucleus. Instead DNA is found as either a plasmid or the nucleoid, a region with no membrane - Bacteria – can have a polysaccharide capsule and peptidoglycan membrane - Archaea – have S-layer (regularly structured layers of proteins or glycoproteins) as cell wall

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Eukaryotes: consist of all non-bacterial cells. These cells contain a nucleus, membrane bound organelles and are multicellular - Different kingdoms: - Animals – have no cell wall - Plants – have a cellulose cell wall and are autotrophs - Fungi – have a chitin cell wall and are heterotrophs

- Protists – eukaryotes that don’t fit into other categories, eg algae or invertebrates Autotrophs: able to make own food (glucose) – photosynthesis

Heterotrophs: require food (glucose) produced by autotrophs

Plasma membranes: -

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Plasma membrane: Encloses the contents of cells and allows the cytosol to have different composition from surrounding external environment by selectively regulating movement of substances into and out of the cell. Membrane is semi-permeable - Composed of a double layer of phospholipids, AKA phospholipid bilayer -The hydrophilic heads face out - Hydrophobic tails face inwards Fluid mosaic model: The term ‘fluid’ comes from the fact that the fatty acid chains of the phospholipids act like a thick, oily fluid, and the term ‘mosaic’ comes from the fact that the external surface (when viewed from above) has the appearance of a mosaic because of the embedded proteins set in a uniform background

Movement: -

Hydrophobic: Very small hydrophobic molecules can pass through the gaps between the phospholipids,

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they can dissolve in the hydrophobic tails Hydrophilic: Hydrophilic substances use facilitated diffusion. Ions and large, polar molecules use this method

Types of movement: Diffusion: the net passive movement of particles from an area of high concentration to low concentration

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Osmosis: net movement of water molecules across a semi-permeable membrane from a region of low solute concentration to a region high solute concentration. Affects the tonicity of the solution (hypo, hyper, iso) -hypotonic: when the concentration of water outside the cell is greater than inside, and results in osmosis INTO the cell, causing it to undergo lysis (burst) -hypertonic: when the concentration of water outside the cell is less than that of inside, which results in osmosis OUT OF the cell, causing crenation (shrivel up) - Isotonic: when cell and environment have the same concentration of water In plants: -Plasmolysis is when the plasma membrane falls away from the cell wall (hypertonic) - Turgor is when the vacuoles of plants are so full of water they push up against the cell wall and support the plant (hypotonic)

Concentration gradient: the gradual difference in concentration of a dissolved substance in a solution between an area of high and low density -

Simple diffusion: requires no energy, follows the concentration gradient facilitated diffusion: protein mediated transport - Passive transport: no energy required, follows concentration gradient - Channel proteins: open on both sides with a central filled water pore. Requires no energy to pass through

- Active transport: molecules moving against their concentration gradients, from an area of low concentration to high concentration. Requires energy in the form of ATP Primary active transport uses ATP secondary active transport is powered by the movement of ions down an electrochemical gradient - Gated proteins: Open via nerve impulses, require energy to pass substances through the membrane - Carrier proteins: only used by a specific molecule. When the molecule enters, the protein changes shape to allow it through - Coupled carrier: when a carrier protein allows two different molecules pass through. Either symport (same way) or antiport (opposite ways)

Bulk Transport: Endocytosis: the bulk entry of substances into the cell by the formation of a vesicle from the plasma membrane - Phagocytosis: large macromolecules or whole structures are endocytosed (cellular eating)

- Pinocytosis: fluid with only small dissolved molecules are endocytosed (cellular drinking) Exocytosis: The movement of materials out of a cell via secretory vesicles

Secretory pathway of proteins: 1. A protein is synthesised in the ribosome within the rough endoplasmic reticulum by the process of translation 2. The protein is transported along the membranes of the rough ER and is modified throughout 3. The protein is transported via a vesicle to the Golgi apparatus, where it is modified and packaged into another vesicle 4. The vesicle is transported to the cell membrane, where the protein is secreted by exocytosis

Structure

Nucleus

Centrioles

Function control centre (controls all cell activities) contains the genetic information (DNA) its membrane called the nucleus envelope has gaps called nuclear pores for movement of molecules between nucleus and cytoplasm nucleolus is the dark region of condensed genetic material within the nucleus, contains rRNA, and assists in the synthesis of ribosomes Pair of small cylinders called microtubules. Involved in separating chromosomes during cell division

Anima l (Y/N)

Plant (Y/N)

Yes

Yes

Yes

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Cytoplasm

The contents of the cell (contains 90% water, and contains ions, salts, enzymes etc)

Yes

Yes

Cytosol

Fluid component of cytoplasm

Yes

Yes

Endoplasmic Reticulum

Rough: composed of folds of the plasma membrane, studded with ribosomes. The rough ER is involved in the synthesis and export of proteins outside of the cell Smooth: is involved with steroid synthesis and, in muscle cells, calcium storage Sorting, storing and modification of materials for transport

Yes

Yes

Yes

Yes

Golgi Apparatus

Lysosomes

Containing powerful enzymes that break down debris and foreign material

Plastids (amyloplasts) Ribosomes

Stores starch in roots and stores tissue, responsible for geotropism and chromoplasts ( what gives colour to petals/fruits) Small organelles in Cytosol and sometimes found in endoplasmic reticulum- site of protein synthesis Maintains what travels in and out of vacuoles

Tonoplasts Vacuoles

Vesicles

Membrane bound space containing liquid in plants, physically support through turgor pressure/storage. Other cells digest (food vacuoles) or involved in water maintenance ( contractile vacuoles) Involved in transport activity in cells

Yes

-

-

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Table of organelles:

Nucleic acids and proteins: Organic molecules (biomacromolecules): All biomacromolecules are synthesised via condensation reactions Nucleic acids Carbohydrates Lipids Proteins

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Carbohydrates: Most abundant organic compounds in nature energy source/storage - structural components - part of both DNA and RNA form glycoproteins and glycolipids as in cell membranes Composed of C, H and O

  

Monosaccharide – basic subunits of carbohydrates, meaning “single sugar” Disaccharide – two sugars joined together, meaning “two sugars” Polysaccharide – many sugars joined together, meaning “many sugars”

Proteins: proteins are polymers (made up of repeating subunits). The subunits of a polymer are called monomers. The monomers of proteins are amino acids. Amino acids: different amino acids have different R groups, different names, and different abbreviated names. Some R groups are polar, others non. Two amino acids can combine to form a dipeptide. The linkage that joins the two amino acids is called a peptide bond. Combining numerous amino acids forms a polypeptide chain. Joining of monomers occurs via condensation polymerisation, where a molecule of water is released for every bond made between two monomers. A polypeptide chain is called a protein when it’s extremely long, has multiple separate amino acid chains, or the molecule is globular

Four levels of protein structure: -

Primary: the specific sequence of amino acids in the polypeptide chain. Peptide bonds hold the primary

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structure together (which are covalent) Secondary structure: Consists of localised coiling and folding of segments of the polypeptide chain. Hydrogen bonding between nearby peptide groups keep it together. 3 types of coils and folds: - Alpha helices - Beta pleated sheets - Random coils

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Tertiary structure: the specific 3D structure of the protein due to global coiling and folding. A variety of interactions keep the shape together, including: - Hydrogen bonding -ionic interactions -covalent bonding (disulphide bridges) -hydrophobic interactions

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Quaternary structure: only in proteins with multiple polypeptide chains

The role of proteins in cells -

Catalytic – enzymes Structural – collagen, plasma membrane Contractile elements – actin and myosin fibres Transport – haemoglobin, protein channels Regulatory – hormones Immunologic – antibodies Cell recognition and signal transduction – marker proteins, receptor proteins

Proteome – all the functional proteins produced by an organism (i.e., the products of the genome) Lipids -

‘Fatty’ substances which are non-polar, hydrophobic molecules Major components of cell membranes Lipids: – store energy – Structural components (form effective barriers b/n two watery environs.) – form steroids - Simple lipids – composed of C, H and O - Compound lipids – contain fatty acids, glycerol and other elements - Saturated fat – has maximum number of H atoms with no double bonds between carbon atoms - Unsaturated fat – has at least one double bond between carbon atoms in chain

Nucleic acids: either DNA (deoxyribonucleic acid) or RNA (ribonucleic acid)

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DNA: chemical that encodes how organisms are made, present in the nucleus, and is the blueprint for

every protein in the body

- RNA: mRNA: when a cell wants to make a protein from a segment of DNA, the code in that segment is transported into the ribosome via mRNA (transcription) tRNA: carries amino acids to the ribosome for protein synthesis (translation) rRNA: structural component of ribosomes, also found in the nucleus The monomers of DNA and RNA are nucleotides. -

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DNA nucleotides are composed of: - Deoxyribose - Phosphate - Nitrogenous base RNA nucleotides are composed of: - Ribose -phosphate -nitrogenous base

DNA is formed when two nucleotides join together, the phosphate group of one covalently bonds to the deoxyribose sugar of the next. DNA is directional, the end with a free phosphate group is called the 5’ end, and the other is the 3’ end. DNA is composed of two strands that run anti-parallel, one strand runs 5’  3’, the other 3’  5’. Hydrogen bonds between opposing nitrogenous bases hold the strands together. AT, GC

RNA - Single stranded - Equivalent of thymine is uracil - Has ribose sugar C)

DNA - Double stranded - Has guanine, adenine, cytosine and thymine - Has deoxyribose sugar

Purines: bases with a double ring structure (A and G) Pyrimidines: bases with a single ring structure (T and

Gene expression and regulation: Gene: a length of DNA which codes for a specific protein. The ‘code’ is the sequence of amino acids, and is read by groups of 3, known as triplets on DNA. Each group of 3 codes for a given amino acid.

Every protein that is made in our body has a corresponding gene associated with it

Protein synthesis from genes: Gene expression: the ‘journey’ from a gene to a functioning protein

Transcription: To form an RNA copy of a gene, the enzyme helicase unwinds the DNA double helix and RNA polymerase synthesizes an RNA complementary to the 3’5’ (template) strand. The RNA nucleotides will anneal to the complementary bases, and RNA polymerase will join the nucleotides together to form an RNA strand. This strand is called pre-mRNA.

Post-transcription modification: -

Introns that are in the pre-mRNA will be spliced and removed, and the remaining exons will be joined together A methyl ‘cap’ is added to the 5’ end of the RNA strand A poly-A tail is added to the 3’ end The product of this is mRNA

The strand that goes in the 5’3’ is called the sense strand, because resembles the RNA sequence of the pre-mRNA strand. Codon is the mRNA triplet. 3’5’ is called the antisense strand.

Translation: RNA involved is called tRNA, which has an amino acid attached to one of its ends, and a group of 3 anticodons found at the bottom of the molecule. Each anticodon corresponds to a different amino acid. What occurs? -

The mRNA arrives at the ribosome The tRNA molecules with the amino acids attached anneals to the mRNA codon via their complementary tRNA anticodons The amino acids that arrive at the ribosome on their tRNA detach, and are joined together via peptide bonds to form the polypeptide chain

Gene regulation: All cells contain the same genome, except they do very different things. This is because cells express different genes, some are switched ‘on’ while others ‘off.’ Structural genes: genes that produce proteins that become part of the structure and functioning of an organism

Regulatory genes: produce proteins that control the expression of other genes in the same cell they were produced in Why does gene regulation occur: To prevent the cell from producing proteins that are not needed by the cell, therefore saving energy and ATP. Also stops the cell from inappropriately producing proteins that can harm the organism How does gene regulation occur? -

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Some genes are expressed, producing proteins whose function it is to bind to the upstream region of the DNA (DNA binding proteins), which may either impair or promote the binding of RNA polymerase to the DNA via its promoter region DNA binding proteins that affect the rate of transcription are called transcriptional factors. Transcription factors are coded for by regulatory genes The promoter region is the segment of DNA, immediately before the transcribed part of the gene, onto which RNA polymerase and transcription factors bind Signalling molecules may bind to receptors on the cell, which may cause expression of a gene, or the inhibition of that gene Operator is where the DNA binding proteins bind to the DNA

Lac Operon: The mechanism by which a bacterial gene that synthesizes lactose is regulated. Operon: a group of linked structural genes with a common promoter and is transcribed as a single unit

When there is no lactose, the inhibitory transcription factor binds onto the operator. This inhibits the ability of the RNA polymerase to bind onto the promoter, which in turn inhibits transcription. However, when lactose is present, it binds to the repressor and changes its shape, allowing RNA polymerase to bind to the promoter region and transcribe the gene.

Structure and regulation of biochemical pathways: Role of enzymes as protein catalysts: Chemical reactions in our bodies are very slow, however if metabolic reactions occurred at slow rates, life could not be sustained. Activation energy is the minimum amount of energy required to break the bonds between reactant molecules Enzymes are a type of catalyst. Catalysts increase the reaction rate by lowering the activation energy. Enzymes: -

Are biological catalysts because they are proteins Act by binding to the substrate

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Can only catalyse specific metabolic reactions because they can only bind compounds that have a complementary shape to their active site Only work at a specific temperature or pH

Lock and key mode: active site exactly complementary to substrate shape Induced fit model: enzymes shape changes to bind to substrate Metabolism: is the overall chemical activity of cells. Anabolic: reactions that build things up. Require an input of energy, endergonic Catabolic: reactions that break things down. Produce energy, exergonic

Factors that affect enzyme function: -

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Temperature: if the enzyme is in an area with too low temperature, its activity is lowered. This is because the enzymes are moving slower, and therefore collide with the substrate less frequently. If the temperature is higher than the enzymes optimum temperature, the activity is significantly lowered, because excessively high temps break the hydrogen bonds in the secondary and tertiary structures. The active site changes due to this, and the enzyme has been denatured, as it can no longer bind to its complementary substrate pH: Altered pH changes the location and strength of the ionic interactions between the R groups. This changes the tertiary structure and everything that follows it, causing it not to be able to bind to its complementary substrate concentration of enzyme: the higher the concentration of the enzyme, the more frequently enzyme-substrate complexes will be forming, and therefore there will be a higher reaction rate Concentration of substrate: as the concentration of substrate initially increases, so does the rate of the enzyme-substrate complexes forming, and thus the reaction rate. However, there will be a point where there us so much substrate that all of the enzymes are ‘full’, and thus they have become saturated with substrate, and the reaction rate will remain constant

Inhibition: Competitive inhibitor (reversible): chemicals that have a similar shape to the substrate can also bind to the enzymes active site. They ‘block’ substrate from binding, thus slowing down the reaction rate. By increasing substrate concentration, you can increase the reaction rate, since the substrate can ‘compete’ better Non-competitive inhibitor: Binds to a site other than the active site of the enzyme and changes the shape of the active site (the site in which the inhibitor binds is called the allosteric site – can be reversed)

Coenzymes: Coenzymes: small organic molecules that are required for the function of an enzyme ATP: Adenosine triphosphate – the synthesis of a protein from amino acids, protein has a higher chemical energy than the amino acids so it requires an energy input. ATP is a molecule that supplies energy for endergonic reactions NAD+/NADP+: Used to add or removed electrons and protons from a substrate. NAD+/NADP+ removes electrons from substrate to produce NAD and NADP. NAD/NADP donate electrons to substrate to convert to NAD+/NADP+ Oxidation: removal of electrons from a substrate to form the product Reduction: addition of electrons to a substrate to form the product

Photosynthesis:

Purpose: to convert solar energy into chemical energy via the reduction of CO2 to glucose, and to store this glucose for future use

Chloroplast: the site where photosynthesis o...