Molecules, Cells and Genes Notes

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    Revision Notes, Molecules, Cells And Genes

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    Cells – The Building Blocks of LifeThe cell is an organism’s basic unit of structure and function. 

      All cells share certain characteristics: enclosed by membrane that regulates passage of materials

    between cell and surroundings, contains DNA as genetic information

      Two main forms of cells: prokaryotic and eukaryotic

     

    Bacteria and archaea are prokaryotic cells  All other life forms are eukaryotic cells

      Eukaryotic cells

    o  Subdivided by internal membranes into several membrane-enclosed organelles

    o  Generally, largest organelle is the nucleus which contains cell’s DNA 

    o  Other organelles located in cytoplasm (entire region between nucleus and outer membrane of

    cell)

      Prokaryotic cells

    o  Simpler and smaller than eukaryotic cells

    o  DNA not separated from rest of cell in membrane-bound nucleus

    The continuity of life is based on heritable information in the form of DNA.

      Chromosomes contain almost all of cell’s genetic material 

      DNA is the substance of genes

      Genes encode information necessary to build other molecules in the cell esp proteins

      Proteins play structural roles and are responsible for carrying out cellular work

      DNA made up of two strands arranged in a double helix

      Four kinds of chemical building blocks (nucelotides)

    o  Adenine

    o  Guanine

    o  Cytosine

    o  Thymine

      Three components of a nucleotide: pentose sugar, phosphate group, nitrogenous base

      RNA is an intermediary – sequence of nucleotides along gene is transcribed into RNA, which is then

    translated into a specific protein

      Differences between organisms reflect differences between nucleotide sequences

    Feedback mechanisms regulate biological systems.

      Negative feedback – accumulation of an end product of a process slows that process (most common)

     

    Positive feedback – end product speeds its own production

    Fundamental characteristics of life

      Reproduce

      Grow and develop

      Metabolise

      Respond to environmental changes

    o  Respond to stimuli, changes in surrounding

      Possess the chemicals of life

    o  Carbohydrates

    Proteins – polymers formed from linking amino acids with peptide bonds

    o  Lipids – fats/oils/waxes, energy storage

    o  Nucleic acids (genetic material) – polymers formed from linking nucleotides, used to store and

    transfer genetic information

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      Have cells

    How is life classified?

    The three-domain system of classification is currently used (replaced five-kingdom system).

      Bacteria (prokaryotes)

      Archaea (prokaryotes)

      Eukarya (eurkaryotes)

    Includes three multicellular kingdoms: plantae, fungi, animalia

    Bacteria, Archaea and Eukarya

    Bacteria & Archaea Eukarya

    Similarities - Plasma membrane

    - Semifluid substance cytosol (fills the

    cytoplasm, contains salts, minerals, organix

    compounds)

    - Chromosomes

    - Ribosomes (make proteins)

    - Plasma membrane

    - Semifluid substance cytosol

    - Chromosomes

    - Ribosomes (make proteins)

    Differences - Simpler and smaller

    - No nucleus- No membrane-bound organelles

    - DNA in unbound region “nucleoid” 

    - Cytoplasm bound by plasma membrane

    - Unicellular

    - Cell wall

    - Eukaryotic cell has membrane-enclosed

    organelles (the largest being the nucleus)- Multicellular

    Structure and

    Features

    Fimbriae: attachment structure on the surface

    of some prokaryotes

    Nucleoid: region where DNA is located (not

    enclosed by membrane

    Ribosomes: complexes that synthesis proteins

    Plasma membrane: membrane enclosing thecytoplasm

    Cell wall: rigid structure outside the plasma

    membrane

    Capsule: jellylike outer coating of many

    prokaryotes

    Flagella: locomotion organelles on some

    bacteria

    Cytoplasm: region between the membrane and the

    nucleus, contains organelles of the cell 

    Nucleus: nuclear envelope – surrounds nucleus

    separating it from the cytoplasm, selectively

    permeable; nucleoplasm – fluid interior portion;

    chromosome – DNA molecule; chromatin – totalcollection of DNA molecules and associated

    proteins, make up eukaryotic chromosome;

    nucleolus – within nucleus, non-membrane bound,

    composed of protein and nucleic acid,

    manufactures ribosome’s (site of RNA

    transcription)

    Ribsomes: molecular machines that catalise the

    assembly of individual amino acids (carried by

    messenger RNA) into polypeptide chains (proteins).

    Endoplasmic reticulum: continuous with the outer

    membrane of the nuclear envelope, a mesh ofinterconnected membranes, ribosome’s cluster on

    the ER.

    Two types of endoplasmic reticulum:

    1. Rough ER – mRNA travels to ribosome’s through

    rough ER, involved in protein synthesis and

    transport

    2. Smooth ER – lipids made inside the SER (fatty

    acids, phospholipids, sterols), involved in

    cholesterol metabolism and membrane synthesis

    Golgi body: modifies proteins and lipids, receives

    transport vesicles from the ER on onde side of theorganelle

    Lysosomes: small organelles that contain enzymes

    Membrane: structure separating the inside from

    the outside of the cell, controls traffic of materials

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    into and out of the cell

    Transport vesicles: small membrane bound sac,

    Cytoskeleton: network of protein filaments and

    microtubules that control cells shape, maintains

    intracellular organisation and involved in cell mvt

    Mitochondria: membrane-enclosed organelle,

    generals cell’s ATP supply, involved in other

    processes e.g. signaling cell cycle, growth, death

    Chloroplast: membrane-bound organelles found in

    plant cells, algae and some bacteria,

    photosynthesis (absorb light and use it with water

    and CO2 to produce sugars)

    The Endomembrane System:

    The eukaryotic cell’s endomembrane system is a

    manufacturing and material transport network that

    enables the cell to make, move and break down

    cellular products.

    Reproduction - Prokaryotes reproduce by binary fission – 

    offspring cells are generally identical.

    During binary fission, chromosome replicates

    and two copies pulled apart as cell grows

    - Prokaryotes have genetic variation due to:

    rapid reproduction, mutation and genetic

    recombination.

    Bacteria Vs.

    Archaea

    Bacteria Archaea

    - Cell membrane contains ester bonds

    - Cell wall made of peptidogylcan

    - One RNA polymerase

    - Ribosomes sensitive to antibiotics (archaeal

    are not)

    - Ubiquitous

    - Cell membrane contains ether linkages

    - Cell wall lacks peptidoglycan

    - Genes and enzymes behave more like eukaryotes

    - 3 RNA polymerases (like eukaryotes)

    - Typically extremophiles

    Extremophiles archaea that live in extreme

    environments. Extreme halophiles live in highly

    saline environments. Extreme thermophiles thrive

    in hot environments. Methanogens live in swamps

    and marshes and produce methane as a waste

    product. Strict anerobes, poisoned by oxygen.

    How did we get here?

    Evolution is the process of change that accounts for unity and diversity of life.

    There are several conditions on early Earth that made the origin of life possible.

      Chemical and physical processes produced simple cells through a series of stages

    o  Abiotic synthesis of small organic molecules

    Joining of these small molecules into macromoleculeso  Packaging of molecules into “probionts” 

    o  Origin of self-replicating molecules

      Fossil records show macroevolutionary changes over large time scales

    Nuclear envelope isconnected to rough ER,

    which is alsocontinuous with

    smooth ER

    Membranes andproteins produced byER flow in the form of

    transport vesicles to theGolgi

    Golgi pinches oftransport vesicles andother vesicles that giverise to lysosomes, otherspecialised vesicles and

    vacuoles

    Lysosome is availablefor fusion with another

    vesicle for digestion

    Transport vesiclecarries proteins to

    plasma membrane forsecretion

    Plasma membraneexpands by fusion ofvesicles and proteinsare secreted from the

    cell

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    There is unity in the diversity of life.

      DNA is the genetic language common to all organisms

      Unity evident in many feature of cell structure e.g. anatomical similarity in embryos

    Evolution and Selection

    Charles Darwin and the theory of natural selection made two main points.

      Species showed evidence of “descent with modification” from common ancestors 

      Natural selection is the mechanism behind “descent with modification” 

      Explained duality of unity and diversity

    Evolutionary theory and Darwin’s four postulates. 

      Darwin showed life evolves over time and natural selection was reason for change

      Darwin’s four postulates 

    o  Individuals within a species are variable

    o  Some of these variations are passed on their offspring

    o  In every generation more offspring are produced than can survive

    Survival and reproduction are not random

    Endosymbiosis

    The process in which unicellular organisms engulf other cells which, become endosymbionts (cells living within

    other cells) and ultimately organelles in the host cell.

      Endosymbiont theory: the theory that mitochondria and plastids, including chloroplasts, originated as

    prokaryotic cells engulfed by an ancestral eukaryotic cell

    o  The engulfed cell and host cell then evolved into a single organism

      Evidence supporting an endosymbiotic origin of mitochondria and plastids:

    o  Similarities in inner membrane structures and functions

    Division is similar in these organelles and some prokaryotes

    o  Organelles transcribe and translate their own DNA

    o  Ribosomes are more similar to prokaryotic than eukaryotic ribosomes

    MacromoleculesElements are made up of atoms.

      Chemical bonding of atoms makes molecules

      Biomolecules: are the principle molecules that account for the structural complexity and diversity of

    living organisms  Organisms consist of organic molecules, primarily – H C O N P S components for synthesis of

    macromolecules

    Macromolecules: giant molecules formed by joining of smaller molecules, usually by a dehydration reaction.

      Four classes of macromolecules:

    o  Carbohydrates

    o  Lipids

    o  Proteins

    o  Nucleic acids

     

    Macromolecules (except for some lipids) are polymers

      Polymers: long molecules consisting of many similar/identical subunits (monomers)

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    Macromolecule Monomer (Subunit) 

    Carbohydrate Monosaccharides (simple sugars)

    Lipid Fatty acids (not all classified as polymers)

    Protein Amino acids

    Nucleic acids Nucleotides (with nitrogenous acids G, A, T, C, U)

    The synthesis and breakdown of polymers

      Synthesis  – water molecule is lost in a dehydration reaction to form a new covalent bond

      Breakdown  – water molecule is added to break a covalent bond, known as hydrolysis

    Carbohydrates

      Monosaccharides e.g. glucose

      Disaccharides (two monosaccharides joined by a glycosidic bond) e.g. maltose

      Polysaccharides (polymers with hundreds of monosaccharides joined by glycosidic bonds) e.g. starch

     

    Polysaccharides divided into two groups: storage and structuralo  Storage

      Starch (polymer of glucose): stored by plants as granules within carious cellular

    structure, this stored energy can be accessed later via hydrolysis

      Glycogen (highly branched polymer of glucose): stored by animals in liver and muscle

    cells, hydrolysis of glycogen releases glucose when demand for energy increases

    o  Structural

      Cellulose (polymer of glucose): major component of plant cell walls

      Chitin (polymer of glucose with nitrogen groups): exoskeletons of anthropods

    Lipids

     

    Hydrophobic (non-polar), don’t mix with water 

      Many forms and functions:

    o  Energy storage and transport e.g. fats, triacylglycerols (TAG)

    o  Structure – phospholipids, sterols

    o  Chemical messengers – steroids, glycolipids

    o  Photoreceptors – carotenoids

    o  Coverings – waxes

      To make a fat:

    o  Three fatty acid molecules are each joined to glycerol by an ester bond

    o  Results fat called TAG or triglyceride

     

    Saturated fatty acids – no double bond between carbon and hydrocarbon chains

      Unsaturated fatty acids – one or more double bonds, causes kinks in molecule

      Phospholipids

    o  Make up cell membrane

    o  Hydrophilic (polar) head and 2 hydrophobic tails

    o  Similar in structure to TAG but phosphate and polar group (e.g. choline) replace one of three

    fatty acids

    Proteins – biologically functional molecule that consists of one or more polypeptides

      Polymers of amino acid monomers (polymers known as polypeptides)

     

    Protein consists of one or more polypeptide, folded into 3D structure  20 different amino acids, common structure of amino acids:

    o  Carbon atom attached to:

      Amino group

      Carboxyl group

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      Hydrogen atom

      Side chain ‘R’ 

      Protein synthesis:

    o  Amino acids linked by peptide bonds to form polypeptide chain

    o  Proteins consist of backbone of peptide bond

    o  Polypeptide folds to give 3D structure – determines function of the protein

      Four levels of protein structure:

    o  Primary

    Secondary

    o  Tertiary

    o  Quarternary (arises when protein consists of 2 or more polypeptide chains)

    Protein function Protein Example

    Structural Collagen, keratin

    Storage Casein, ovalbumin

    Transport Haemoglobin, albumin

    Hormones Insulin

    Defence Antibodies

    Movement Actin and myosinGrowth factors Human growth factor

    Enzymes Amylase

      Enzymes – catalytic proteins that speed up chemical reactions without being consumed

    o  Affected by: temperature, pH, concentration of enzyme, substrate (reactant on which an

    enzyme works)

    o  Substrate associates with special region of enzyme called active site where catalysis occurs

    o  Enzymes lower activation energy   increasing rate of reaction CALLED CATALYSIS

    Do not affect equilibrium of free energy change

    Nucleic acids

      Store and transmit hereditary information

      Two types of nucleic acids: DNA and RNA

      DNA: direction for replication; DNA directs RNA synthesis and  controls protein synthesis

      Amino acid sequence of polypeptide is determined by genes (composed of DNA)

      Nucleic acids are polymers of nucleotides – known as polynucleotides

    Cytoskeleton  – describe the functions of the cytoskeleton, compare structure/functions of

    microtubules, microfilaments and intermediate filaments, explain how ultrastructure of cilia andflagella relate to their functions

    The cytoskeleton is a network of fibrous proteins distributed throughout the cytoplasm of eukaryotic cells.

      Linked to organelles and the plasma membrane

      Made up of 3 molecular structures:

    o  Microtubules

    o  Microfilaments

    o  Intermediate filaments

      Functions:

    Maintain cell shapeo  Organising and moving organelles and macromolecules within cells

    o  Linking cells together in multi-cellular organisms

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    Microtubules

      Long hollow tubules

      Made of polymers of tubulin

      Directional (have a positive and a negative end)

      Form tracks for molecular motor proteins to move organelles and other structures

      “Powerhouse” for flagella and cilia 

      Crucial role in mitosis (separation of chromosomes)

     

    Shape and support the cell  Centrosomes

    o  Microtubules generated from centrosomes (microtubule organizing centres)

    Microfilaments (Actin filaments)

      Made of actin in twisted double chain

      Maintain shape of cell (bears tension)

      Involved in:

    o  Membrane “pinching” process in cell division 

    o  Formation of pseudopodia

    o  Muscle contraction

     

    Actin filaments arranged parallel on muscle, interlocked with myosin contraction of

    muscle results from actin and myosin filaments sliding past one another  shortening

    the cell

      Myosin uses ATP energy and moves along actin microfilament tracks

    Intermediate filaments

      Found only in multicellular organisms

      Composed of fibres of keratin

      More permanent structure which therefore help:

    o  Stabilize cell structure and shape

    Anchor organelles

    Molecular motor proteins

      Proteins whose structures allow them to “step” along microfilaments or microtubules by changing

    their shape

      Shape changes are reversible

      Shape changes require energy from ATP (adenosine triphosphate)

      ATP:

    o  Organic compound which is used in cells as a way of storing “energy” 

    o  When it is broken down (to ADP or AMP) energy is released

    Kinesins and Dyneins are molecular motors

      Move organelles and vesicles with the cell in a positive or negative direction along MT

    o  Kinesin – positive direction

    o  Dynein – negative direction

    Cell movement

      Movement of MT power movement of eukaryotic cells using flagella and cilia

      Dynein bends bundles of MT to move flagella and cilia

    Maintaining Cell Integrity

    Members of the Membrane

      Lipids

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    o  Phospholipids

      Amphipathic – both hydrophyllic/phobic region

    o  Cholesterol

      Protein

    o  Peripheral

    o  Integral – penetrate the hydrophobic interior of the lipid bilayer

      Transmembrane proteins – span the membrane but have different domains on each

    side of the membrane

     

    Carbohydrate (CHO)

    o  Glycolipids – covalently bonded to lipids

    o  Glycoproteins – covalently bonded to proteins

    o  Membrane carbohydrates are involved in cell-cell recognition

    o  Cells recognize other cells by binding to molecules containing carbohydrates on extracellular

    surface of the plasma membrane

    o  Membrane carbohydrates function as markers that distinguish one cell from another (on the

    outer part of the membrane)

      Structure of Membranes:

    o  Fluid mosaic model

     

    Membrane is a fluid structure with “mosaic” of various proteins attached to double

    layer (bilayer) of phospholipids

      “Sidedness” – asymmetrical distribution of proteins, carbohydrates and lipids between

    two sides of membrane

      Plasma membrane has distinct cytoplasmic and extracellular faces (topically

    equivalent to inside face of ER, Golgi, lysosome and vesicle membranes)

      Fluidity: refers to the rapid movement of lipids and proteins laterally in the plane of the

    membrane

    Membrane Permeability (diffusion, osmosis, facilitated transport)

     

    Phospholipid bilayer is permeability barrier to most molecules  Hydrophobic molecules will dissolve in the hydrophobic core and diffuse across the membrane

      Small molecules (e.g. O2, CO2, H2O) cross membranes by diffusion

      Ionised, polar and large molecules will NOT cross membranes unless specific transport mechanism

    (protein transporter) is present

      Diffusion:

    o  Molecules that can diffuse across a membrane will move in both directions

    o  Difference in concentration between the two sides of the membrane there will be NET movt

    down the concentration gradient until equilibrium is reached

    o  Known as passive transport because the cell does not expend energy in the process

     

    Osmosis is the passive transport of water:o  Isotonic: no net movt across the plasma membrane, diffuses across membrane but at the same

    rate in both directions; flaccid in plant cells

    o  Hypertonic (more, refers to non-penetrating solns): cell will lose water, shrivel and die;

    plasmolysed in plant cells

    o  Hypotonic (less): water will enter cell faster than its leaves and the cell will swell and lyse

    (burst); turgid (normal) in plant cells

    Nutrient and Ion Transport Enzymes

     

    Facilitated transport/diffusion integral membrane proteins can allow transport down concentrationgradient

    o  Transport proteins assist movement molecules down the concentration – no energy reqd 

    passive transport

    o  Channel proteins: allow direct passage from one side to the other

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      Channel proteins that transport ions are called ion channels

      Gated channels – channels/transporters may require another type of molecule to be

    bound to a specific site before they function

    o  Carrier proteins: binding of solute on one side produce conformational change in proteins

    moving solute through

      Alternate between 2 shapes, moveing solute across membrane during shape change

      Transport is directional – energy released by ATP hydrolysis allows transport against concentration

    gradient

    An Introduction to MetabolismParts of Chapter 8&9

    Extracting Energy from FoodParts of Chapter 9

    Photosynthesis

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