162.101 Biology of Cells PDF

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Summary

biology of cellsthe aim of science is to understand how the world is structured and behaves. scientific enquiries can be done by two methods or involve both of the following...DISCOVERY SCIENCE:describes nature by making repeatable observations and measurements, both qualitative and quantitative. th...

Description

biology of cells the aim of science is to understand how the world is structured and behaves. scientific enquiries can be done by two methods or involve both of the following… DISCOVERY SCIENCE: describes nature by making repeatable observations and measurements, both qualitative and quantitative. this involves inductive reasoning (going from specific instances to general conclusions). HYPOTHESIS-BASED SCIENCE:

seeks to explain nature by forming questions, hypotheses and tests. this involves deductive reasoning; from general principles to specific conclusions. Hypotheses are possible explanations of an observation. • it must be testable • it must be falsifiable, or able to be proven incorrect. • can be supported but cannot be proven, as there is always an area of doubt. CONTROLLED EXPERIMENTS take the experimental sample and compare it against control groups in which all variables are the same except the one being tested.

• Positive controls have an expected response • Negative controls expect no response. Many cells are too small to see with the naked eye. Eukaryotic cells are between 10-100μm in diameter, while prokaryotic cells are only 1μm. Microscopes are required to observe them. RESOLUTION: measures the clarity of an image

light microscopy BRIGHT FIELD: specimens stained with dyes to enhance contrast are examined under white light. if unstained, the light passes straight through. Can resolve detail down to 0.2μm. FLUORESCENCE: specimens stained with fluorescent dyes which are visible when excited by UV light. This UV light has a shorter wavelength than white light, so limit of resolution is better, about 0.17μm. CONFOCAL: allows us to see cells in 3-dimensions

electron microscopy uses an electron beam, rather than visible light, with a much shorter wavelength and resolution of 0.002μm. the electron beam is focused by electromagnet lenses. TRANSMISSION E.M: a thin section of specimen is viewed and can even reach internal ultrastructures of the cells. with high magnification and resolution. SCANNING E.M: scans the surface of a specimen with a very fine beam of electrons and transmits a 3D image to a screen which gives a better depth of field than TEM but less magnification

the cell theory 1. 2. 3.

all living organisms are composed of cells cells are he basic unit of all life (components of cells are not alive) every cell arises by division of pre-existing cells

there are three major domains of organisms: archaea, bacteria and eukarya.

• archaea and bacteria consist of prokaryotic cells • all other eukarya organisms; plants, animals, fungi and protists consist of eukaryotic cells PROKARYOTIC CELL

EUKARYOTIC CELL

no nucleus

contain a nucleus (eu- genuine, karyote- nucleus)

no membrane-bound organelles

contains membrane-bound organelles for specific functions

no cytoskeleton system

contain a cytoskeleton network of protein cables

circular chromosomes

linear chromosomes

macromolecules there are four classes of macromolecules that are vital for cells: nucleic acids, proteins, carbohydrates and lipids. these are often polymers; chains of covalently-joined monomer units. despite the different structures of the polymers, they all share common mechanism of synthesis and break down - known as the THE BUILDING BLOCK PRINCIPLE… POLYMER SYNTHESIS - dehydration reactions remove H2O from two molecules (-H and -OH) and a new bond forms - energy is added to a monomer to create an activated monomer prior to this. - one monomer is added per dehydration reaction - enzymes catalyse the dehydration reaction POLYMER BREAKDOWN - hydrolysis reaction splits a longer polymer by adding H2O across a bond - H- will add to one side of the bond, -OH will add to the other side - one monomer is removed at a time - energy is released when the polymer bond breaks

nucleotides nucleotides are the building blocks of nucleic acids like DNA and RNA. they are made of three components: a nitrogenous base, pentose sugar, and a phosphate group. PENTOSE SUGARS have four carbons, numbered clockwise from an oxygen atom. • C1: has a nitrogenous base bonded • C2: has -OH or -H bonded (depending whether it is ribose or deoxyribose) • C3: has -OH bonded • C4: has a methyl group (C5) which has a phosphate group in DNA, the pentose is called deoxyribose because there is a hydrogen where a hydroxyl group could be, therefore lacks an oxygen.

NITROGENOUS BASES have two structures; double-ringed purine (A and G) or single-ringed pyrimidine (C, T and U). the backbone is repetitive; the difference along the polymer is the bases.

dna BACKBONE: the pentose of one nucleotide is covalently bonded to the phosphate of the next nucleotide, such that a phosphate-pentose backbone forms, with bases extending out. COILS: polynucleotide molecules usually exist as two strands coiled around one another, rather than a single strand. the polar backbone is on the outside while the hydrophobic bases stack on the interior. the three-dimensional double helix structure was proposed by Watson and Crick in 1953. BASE PAIRING: the bases in one strand are linked by hydrogen bonds to the bases in the opposing strand according to a base pairing rule:

- one purine will bind with a pyrimidine; form G-C pairs and A-T pairs - purine to purine pairing is too wide for the helix - pyrimidine to pyrimidine pairing is too narrow for the helix PRIMES: the polymer strands have directionality so one end is called 5’ and the other is 3’. the strands in a double helix are anti-parallel so one runs 5’ to 3’ while the other runs 3’ to 5’. specific sequences of nucleotides in DNA code for various genetic information. the information in DNA is used to direct the synthesis of polypeptides by specifying their animo acid sequence.

rna the general structure is similar to DNA, with some important differences - it is a single linear strand - it has adenine, cytosine and guanine bases, but thymine is replaced with uracil - the sugar is ribose RNA is more flexible and can fold into many shapes, stabilised by base pairing, for different functions. RNA is thought to be the original informational molecule of life as it can self-replicate, encode proteins, act as an enzyme. It acts as a working copy of genetic information. It has a structural role (ribosomes) and catalytic role (ribozymes).

weak interactions weak interactions are important to allow molecules to interact and maintain structure - occur both within and between molecules. - they have a cumulative effect; become strong in numbers. - reversible so processes can repeat - transient or short-lived - four types of weak interactions:" 1. IONIC INTERACTIONS" " between any two charged groups." interactions between ions in solution are not as strong as in crystal due to a salvation shell of water molecules" " 2. HYDROGEN BONDS! ! electronegative atoms like O, S and N attract electrons more strongly than C and H, which creates partial -ve and +ve regions in the molecule" water molecules will form H-bonds with polar groups on other molecules in water, the bonds are continually breaking and reforming as molecules move. this linked pattern is the water matrix. 3. HYDROPHOBIC INTERCTIONS " the tendency for non-polar or non-ionic molecules to congregate in water. they do not bond with H2O molecules." 4. VAN DER WAALS INTERACTIONS" " between any type of closely positioned atoms and usually stabilise other weak interactions. these interactions are very dependent on the distance between molecules

proteins proteins are the working molecules of life - every function of a living system has proteins involved. they are polymer sequences of amino acid monomers. proteins function in support and structure (e.g. feathers made of keratin), movement, receiving signals, protecting against disease, storing energy, transport and catalysing reactions (enzymes). AMINO ACIDS: consist of an amine group (n-terminal), a carboxyl group (c-terminal) and an -R side chain which can be hydrophilic (polar and charged) or hydrophobic (non-polar), and an also vary in size and shape.

• • • •

amino acids are joined by dehydration reactions to make polypeptide chains. each amino acid is added to the c-terminal - or carboxyl end - with a covalent peptide bond. chains are broken by hydrolysis; removal of water. proteins are made when one or more polypeptides are folded into a certain 3D conformation.

a molecule’s biological function is dependent on the correct shape. in order to interact, they must also fit together; so incorrect shape leads to incorrect function or no function at all. the function of a protein is determined by its structure which, in turn, is determined by the level of both covalent bonds and weak interactions. there are four levels of protein structure… 1o STRUCTURE: "

- linear polypeptide chain (unique specific sequence of amino acids linked by peptide bonds). - they are determined by genes; proteins are macromolecules built to a plan. - altering just one acid has significant effects. 2o STRUCTURE: "

- regular folding / coiling due to hydrogen bonds forming between amino acids in backbone - α HELIX: when N-H hydrogen bonds to a C=O a few amino acids down the backbone, it coils. - β PLEATED SHEET: when two or three beta strands fold and laterally form hydrogen bonds. " each strand within a folded chain is about 3-10 amino acids long. 3o STRUCTURE:"

- irregular folding of the polypeptide due to weak interactions between R groups. • ionic bonds - form between charged side chains • hydrophobic + van der waals interactions • disulphide bridges - form between sulphur atoms of two side chains • hydrogen bonds - with electronegative atoms like oxygen and nitrogen - folding is irregular because the sequence of R groups is irregular - most non-polar chains are on inside, while polar chains are on outside - many proteins are complete at tertiary level 4o STRUCTURE:

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creation of an oligomeric protein two or more separate polypeptide chains join not all functioning proteins have quaternary structures; some have just one chain haemoglobin is a protein with four sub-units: two alpha and two beta collagen is a fibrous protein with three polypeptide chains coiled like rope

DENATURATION: the unfolding of a protein due to environmental changes, which causes a loss in biological function. this deactivation is often reversible, but sometimes permanent. ENZYMES: proteins that interact with reactants to lower the activation energy and ease reactions. 1. substrate enters the active site on an enzyme. 2. substrate is held in place by weak interactions. 3. undergoes a reaction more easily and quickly than without the enzyme. 4. product is released. 5. the enzyme itself doesn’t change, so active site remains for other reactants to enter enzymes only function under optimal pH and temperature ranges. "

- changes in acidity can impact bonds between charged side chains, while heat can disrupt almost all interactions.

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carbohydrates SIMPLE SUGARS"

- “sugar” is a general term applied to simple carbohydrates like monosaccharides (glucose) and disaccharides (sucrose, maltose and lactose). "

- monosaccharide rings are joined by glycosidic linkages. - monosaccharides and disaccharides are readily available fuel and carbon sources for cells POLYSACCHARIDES polymer chains of glucose which have two functions - they store energy and provide cell structure energy storage

structural support

in plants

STARCH

CELLULOSE

in animals

GLYCOGEN

CHITIN (arthropods)

glucose monomers differ in their 3D configuration:"

- α glucose: the -OH group on the first carbon is pointed down (chains form starch and glycogen)"

- β glucose: the -OH group on the first carbon is pointed up (chains form cellulose)" " " CELLULOSE: is a linear polymer of β glucose." the -OH groups in cellulose alternate around the ring, making the sugar molecules more polar and allowing them to undergo hydrogen bonding between separate strands and form strong fibres - used as structural polysaccharides in plant cell walls.

lipids lipids are non-polar therefore are hydrophobic / not attracted to water. lipids are not true polymers, as they do not contain identical repeating monomer subunits.

- they contain fatty acid and glycerol subunits which are not joined one after the other in a chain. FATS created by linking three fatty acid tails to one glycerol molecule —> triacylglycerol

• three dehydration reactions occur and remove three molecules of H2O • the carboxylic acid groups of the three fatty acid molecules bond to the three -OH groups on one glycerol molecule, forming ester linkages.

unsaturated fat: the fatty acid tails contain one or more double bonds.

• the double bond is usually in cis configuration which puts a kink in the tail • cannot pack closely • liquids at room temperature (oils) saturated fat: contain no double bonds in the fatty acid tails; because C’s are saturated with H’s

• tails are straight so can pack closely • easily solidify at room temperature (butter, cheese, lard, fatty meat) PHOSPHOLIPIDS amphipathic: have both hydrophobic and hydrophilic regions which have a self-organising behaviour in aqueous solution" have one phosphate head (hydrophilic) and two fatty acid tails (hydrophobic) they are the main component of cell membranes; forming a phospholipid bilayer. the hydrophilic phosphate heads contact water and keep it from entering the internal hydrophobic tail region.

cellular membranes main functions: 1. maintain cell structure 2. regulate flow of material 3. receive information (on internal and external surfaces) 4. contain important proteins phospholipid bilayer: two layers of phospholipids arranged with their tails shielded from the aqueous environment by the hydrophilic phosphate heads. FLUID-MOSAIC MODEL:

- the phospholipid bilayer has a fluid nature; its components move laterally within one layer of the membrane. cholesterol embedded in the membrane controls this fluidity."

- membranes contain a mosaic of different shaped and sized proteins for various functions. - some are grouped for specific function - some move around - some are anchored in place - some are peripheral (on surface of one layer) - some are integral (cross both layers) membrane proteins can function in transporting molecules from one side to the other, enzymatic activity, intercellular joining, cell-cell recognition, signal transduction and attachment to the extracellular matrix. there are three general ways in which molecules and ions cross cellular membranes… 1. diffusion: very small hydrophobic and uncharged polar molecules (e.g. O2 and CO2) 2. transport proteins: pumps and channels allow hydrophilic molecules to cross, either with or against the gradient of the cell. 3. bulk transport: of large molecules via exocytosis and endocytosis with vesicles

cell components PROKARYOTIC CELLS (bacteria)"

• rod-shaped" • FLAGELLA: extend from cell interior to allow them to swim

• FIMBRIAE: short surface appendages •

for attachment NUCLEOID: unenclosed region of circular chromosomes PLASMA MEMBRANE: encloses the cytoplasm CAPSULE: sticky outer layer covering a rigid CELL WALL!

• • !

unlike other organisms, bacterial cell walls are made of peptidoglycan which have polysaccharide chains covalently cross-linked by short chains. the bacterial cell wall is used in antibiotics like penicillin.

EUKARYOTIC CELLS (plants, fungi, protists, animals) • membrane-bound nucleus • the interior (except the nucleus) is called the cytoplasm; containing a semi-fluid cytosol. - there is complex compartmentalisation in the cytoplasm of various membrane-bound organelles for different functions."

• MITOCHONDRIA: site of cellular respiration - converts food into chemical energy. - it has an outer membrane and a folded inner membrane which forms the internal matrix compartment.

- contain circular DNA - ribosomes in the mitochondrial matrix help to translate mtRNA from mtDNA. - folds are called cristae and increase the surface area for chemical reactions, i.e. more ATP produced.

• plant cells have two main features that differentiate from animal cells; they have a cell wall which encloses the plasma membrane and have an extra type of organelle - chloroplasts."

• CHLOROPLASTS: convert light energy and convert it into sugars via photosynthesis. - they have an outer and inner membrane which encloses aqueous fluid called stroma. - membranous sacks called thylakoids contain light-absorbing chlorophyll pigment - 10-20 thylakoids are stacked into grana which are connected by lamellae • PEROXISOMES: have a range of oxidative functions. - detoxify oxygen radicals by converting them into hydrogen peroxide and then into water. - also play a role in breaking down long fatty acid chains into shorter ones." • NUCLEUS: stores and protects the cell’s genetic information, and separates the DNA from ribosomes in the cytoplasm (in turn, separating transcription and translation). also carries out RNA processing in which non-coding intron sequences are cut out of the pre-RNA to make mature mRNA containing mainly exons." " there are four main components of the nucleus with different forms and functions…"

- NUCLEOLUS is a dark staining region of the nucleus and the site where ribosomes are synthesised."

- NUCLEAR ENVELOPE has a double membrane and encloses the DNA for protection" - NUCLEAR PORES are cylindrical protein structures which control the movement of molecules int and out of the nucleus"

- NUCLEAR LAMINA is a net of protein filaments lining the envelope and supports nuclear shape

- the complex of loosely packed DNA and histone proteins is called chromatin. • euchromatin loosely packed 10-nm and 30-nm fibres - transcriptionally active • heterochromatin tightly packed - transcriptionally inactive"

- packaged into negatively charged DNA wrapped around small positively charged histone proteins. each “bundle” is a nucleosome like beads on a string."

- this chromatin complex condenses into visible chromosomes during division

endomembrane system regulates protein traffic and performs metabolic functions in the cell ENDOPLASMIC RETICULUM extensive network of membranes, tubes and sacs that is continuous with the nuclear envelope

• SMOOTH: tubular reticulum which lacks ribosomes, hence a smooth appearance - contains many enzymes to synthesise lipids, store calcium ions, detoxify drugs and poisons - especially abundant in liver cells • ROUGH: sheet-like reticulum covered in ribosomes, gives a granular appearance - aids in sorting proteins destined to be secreted, packaged into vesicles for internal use or be inserted into membranes,.

- adds carbohydrates to proteins to make glycoproteins (glycosylation) - produces new membrane

1. protein synthesis begins on free ribosomes in the cytoplasm. 2. proteins destined to be secreted or remain in endomembrane system have a signal peptide; the first part of the polypeptide chain that is made in translation 3. when this signal end emerges, a signal recognition particle (SRP) binds to it and blocks further translation. 4. the SRP will take this ribosome (with the emerging peptide chain) to the rough ER membrane. 5. the SRP takes the ribosome-peptide complex to the ER membrane where it docks. 6. after docking, the synthesis resumes and the polypeptide chain is fed through a channel into the ER lumen for packaging or will remain in the membrane.

GOLGI APPARATUS a series of 5 to 8 flattened sacs stacked together"

• the “cis” side is closest to th...