Cell Biology

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Cell Biology

• Achievement Standard 2.8
• 90464

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Cells

• All living things are made up of 1 or more cells
• Cells vary in shape but they are always small
• Small size is due to difficulty in diffusing
  substances
• Cells can be divided into 2 types
• Prokaryotes
• Eukaryotes

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Cell Organelles

• There are some organelles in cells that are
  present in both plant and animal cells, and
  others that are present only in one or the other
• Cell wall (plant only)
• Cell membrane
• Cytoplasm
• Nuclear membrane
• Nucleus
• Chromosomes
• Mitochondria
• Chloroplast (plant only)
• Centriole
• Vacuole
• Ribosome
• Endoplasmic reticulum (smooth and rough)
• Lysosome
• Golgi body

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Nucleus contains inherited information The total
collection of genes located on chromosomes in the
nucleus has the complete instructions for
constructing a total organism.
Cytoplasm The nucleus controls cell metabolism
the many chemical reactions that keep the cell
alive and performing its designated role.
Structure of the nucleus
Nuclear pores are involved in the active
transport of substances into and out of the
nucleus
Nuclear membrane encloses the nucleus in
eukaryotic cells
Nucleolus is involved in the construction of
ribosomes
Chromosomes are made up of DNA and protein and
store the information for controlling the cell
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• Eukaryotes have two types of organelles with
  their own DNA
• mitochondria
• chloroplasts
• The DNA of these organelles is replicated when
  the organelles are reproduced (independently of
  the DNA in the nucleus).

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Unicellular Organisms

• Unicellular organisms carryout all their life
  functions inside a single cell. While some of
  their organelles are the same as that of
  eukaryotes there are some that are found only in
  unicellular organisms. These are
• Oral Groove Ciliated channel on one side of the
  cell where food particles are taken in
• Anal Pore Specialised region of the cell
  surface where food vacuoles attach an rupture to
  the outside
• Eyespots Is used in light detection and
  phototaxic responses
• Contractile Vacuoles used to regulate the
  amount of water inside the organism by expelling
  it to the outside
• Food Vacuole space that contained ingested food
  particles
• Pseudopodia false legs to aid in ingestion of
  food particles

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Unicellular Organisms cont..

• As well as having specialised organelles, some of
  the cellular processes are significantly
  different to those of multicellular organisms.
• Gas Exchange
• This is usually by diffusion across the cell
  membrane. To increase efficiency, the organism
  is usually long and/or flat in shape increasing
  the surface area to volume ratio.
• Ingestion and Feeding
• All unicellular organisms that cannot
  photosynthesise must ingest small food particles
  as their food supply. Food particles cross the
  membrane by phagocytosis to form a food vacuole
  which is digested. Any indigestible material
  left in the food vacuole is discharged to the
  outside through the anal pore.
• Some unicellular organisms do not have an oral
  groove so they use pseudopodia to engulf the food
  particles.
• Excretion
• In unicellular organisms, the main waste product
  formed is ammonia. This is very toxic so it must
  be diluted by large volumes of water before being
  excreted. Contractile vacuoles aid in the
  collection and removal of wastes.

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Unicellular Organisms cont..

• Water regulation
• Since many unicellular organisms live in fresh
  water and are enclosed by semi-permeable
  membranes water is constantly moving into them.
  Contractile vacuoles work to collect and remove
  the water to ensure the cell does not burst.
• Locomotion
• For some unicellular organisms locomotion is
  achieved by the coordinated beating of cilia,
  others use flagella and Amoeba use the
  pseudopodia to move.
• Responses to External Stimuli
• Most movement is a response to changes in the
  protoplasmic contents of the organism. Some
  organisms have eyespots that detect the amount of
  visible light and trigger a phototaxic response.
• Reproduction
• This can be asexual via binary fission or, vary
  rarely, sexually through the exchange of genetic
  material

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• Bacteria have no membrane-bound organelles.
• Cellular reactions occur on the inner surface of
  the cell membrane or in the cytoplasm.
• Bacterial DNA is found in
• One, large circular chromosome.
• Several small chromosomal structures called
  plasmids.

Ribosomes
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Cell Processes
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Cell Membrane

• Surrounds the cell and keeps it separate from the
  outside medium
• Semi-permeable membrane that controls what goes
  in and out
• In animal cells, it is the outside layer but in
  plants the cell wall surrounds it
• Membrane is called a lipid bi-layer consisting of
  two hydrophillic heads on the outside and
  hydrophobic tails on the inside
• The general structure is based on the fluid
  mosaic model.

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Cell Transport

• Materials such as ions, water, molecules and
  nutrients are transported within cells and in and
  out of cells by processes which are either
  passive or active.

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Passive Transport

• This does not require energy
• It can be separated into 2 types
• Diffusion
• Osmosis

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Diffusion

• The net movement of particles from an area of
  high concentration to an area of low
  conentration.
• Difference between the two areas is the
  concentration gradient
• A large differencelarge gradientfaster
  diffusion
• The rate of diffusion varies depending on
• Size of molecules
• Temperature of substance
• State of matter
• Concentration of chemicals
• The cell membrane may contain proteins that help
  facilitate diffusion

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Osmosis

• The net movement of water from a high
  concentration to a low concentration through a
  semi-permeable membrane
• Solution with not much water hypotonic
• Solution with lots of water hypertonic
• Solution with the same water concentration
  isotonic

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Active Transport

• Movement against a concentration gradient, ie
  from a low concentration to a high concentration
• It requires energy so
• Heat is given off
• Oxygen is used up
• CO2 produced
• Glucose used up
• Two main types
• Endocytosis
• Exocytosis

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Endocytosis

• Taking particles into a cell.
• Engulfing a liquid pinocytosis
• Engulfing a solid phagocytosis

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Exocytosis

• Occurs when vacuoles expel their contents to the
  outside

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Amino Acids

• Amino acids are linked together to form proteins.
• All amino acids have the same general structure,
  but each type differs from the others by having a
  unique R group.
• The R group is the variable part of the amino
  acid.
• 20 different amino acids are commonly found in
  proteins.

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Types of Amino Acid

• Amino acids with different types of R groups
  have different chemical properties

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Polypeptide Chains

• Amino acids are liked together in long chains by
  the formation of peptide bonds.
• Long chains of such amino acids are called
  polypeptide chains.

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Protein Function

• Proteins can be classified according to their
  functional role in an organism

Hemoglobin
Function Function Examples
Structural Forming the structural components of organs Collagen, keratin
Regulatory Regulating cellular function (hormones) Insulin, glucagon, adrenalin, human growth hormone, follicle stimulating hormone
Contractile Forming the contractile elements in muscles Myosin, actin
Immunological Functioning to combat invading microbes antibodies such as Gammaglobulin
Transport Acting as carrier molecules Hemoglobin, myoglobin
Catalytic Catalyzing metabolic reactions (enzymes) amylase, lipase, lactase, trypsin
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Protein Structure

• The production of a functional protein requires
  that the polypeptide chain assumes a precise
  structure comprising several levels
• Primary structure The sequence of amino acids in
  a polypeptide chain.
• Secondary structure The shape of the polypeptide
  chain (e.g. alpha-helix).
• Tertiary structure The overall conformation
  (shape) of the polypeptide caused by folding.
• Quaternary structure In some proteins, an
  additional level of organization groups separate
  polypeptide chains together to forma functional
  protein.

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Enzymes

• Enzymes are biological catalysts, regulating cell
  metabolism.
• An enzyme acts on a molecule called the
  substrate.
• Enzymes are specific for the reactions they
  catalyze.
• Enzyme activity depends on the enzymes shape and
  its active site (the binding site for the
  substrate).
• Enzymes are often named for the substrate on
  which they work, and sometimes include the suffix
  -ase
• Lipase breaks down fats (lipids)
• Amylase breaks down starch (amylose/amylopectin)
• Lactase breaks down milk sugar (lactose)
• Cholinesterase breaks down the neurotransmitter
  acetylcholine in the nervous system

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Enzyme Structure

• Ribonuclease S (right) is an enzyme that breaks
  up RNA molecules.
• The red areas designate the active site and
  comprise certain amino acid 'R' groups.
• The substrate (in this case, RNA) is drawn into
  the active site, putting the substrate molecule
  under stress, thereby causing the reaction to
  proceed more readily.

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Functional Enzyme

• Ribonuclease S (right) is an enzyme that breaks
  up RNA molecules.
• The red areas designate the active site and
  comprise certain amino acid 'R' groups.
• The substrate (in this case, RNA) is drawn into
  the active site, putting the substrate molecule
  under stress, thereby causing the reaction to
  proceed more readily.
• Nearly all enzymes are made of protein, although
  RNA can also have enzymic properties.
• Some enzymes contain only protein.
• Others, called conjugated protein enzymes,
  require additional components to complete their
  catalytic properties.
• These may be permanently attached parts called
  prosthetic groups, or temporarily attached
  non-protein coenzymes, which detach after a
  reaction and may then participate with another
  enzyme in other reactions.

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Conjugated Protein Enzymes
Coenzyme required Contains the apoenzyme
(protein) plus a coenzyme (non-protein) e.g.
Dehydrogenases NAD
Prosthetic group required Contains the apoenzyme
(protein) plus a prosthetic group e.g.
Flavoprotein FAD
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Mechanism of Enzyme Action
Steps in Enzyme Activity In the induced fit model
of enzyme function, the enzyme fits to its
substrate somewhat like a lock and key, with the
shape of the enzyme changing when the substrate
fits into the cleft of the active site.

• The specificity of the substrate is determined by
  the complexity of the binding sites.
• The wrong substrates will not fit into the active
  site.
• Some enzymes have specificity to a bond type
  (e.g. lipases break up any chain length of lipid).

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Enzymes are Catalysts

• Catalysts are substances that increase the rate
  of chemical reactions. All catalysts speed up
  reactions by
• Influencing the stability of bonds in the
  reactants.
• Providing an alternative reaction pathway the
  binding of reactants and enzyme can weaken bonds
  in the reactants and allow the reaction to
  proceed more easily.
• Enzymes are biologicalcatalysts they alter the
  chemical equilibrium between the reactant and
  the product.
• When the substrate attains the required energy
  it is able to change into the product or
  products.

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Enzymes are Catalysts

• Catalysts provide an alternative pathway of
  lower activation energy.

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Effects of pH on Enzymes

• Like all proteins, enzymes are denatured (made
  non-functional) by extremes of pH
  (acid/alkaline).
• Within these extremes most enzymes are still
  influenced by pH.
• There is a particular pH for optimum activity for
  each enzyme. This is because the active sites of
  the enzyme can be disabled by the wrong pH.

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Temperature and Enzyme Activity

• Reactions occur faster at higher temperatures,
  but the rate of denaturation of enzymes also
  increases at higher temperatures.
• High temperatures break the disulfide bonds
  important for the tertiary structure of the
  enzyme.
• This destroys the active sites and therefore
  makes the enzyme non-functional.

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Enzyme Concentration And Enzyme Activity

• Assuming that the amount of substrate is not
  limiting, an increase in enzyme concentration
  causes an increase in the reaction rate.
• Cells may increase the amount of enzyme present
  by increasing the rate of its synthesis to meet
  demand.

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Substrate Concentration Effect on Enzyme Activity

• Assuming that the amount of enzyme is constant
  and non-limiting, an increase in substrate
  concentration causes a diminishing increase in
  the reaction rate.
• A maximum rate is obtained at a certain substrate
  concentration where all enzymes are occupied by
  substrate. The reaction rate cannot increase
  further.

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Effect of Cofactors on Enzymes

• Cofactors are substances that are essential to
  the catalytic activity of some enzymes.
• Cofactors may alter the shape of enzymes slightly
  to make the active sites functional or to
  complete the reactive site.
• Enzyme cofactors can be inorganic, e.g. metal
  ions and iron-sulfur clusters, or organic
  compounds, which are known as coenzymes.
• Many vitamins are coenzymes. Vitamins are organic
  molecules not synthesized by the body, e.g.
  vitamin K, B1, B6, and folate.

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Enzyme Inhibition

• Enzyme inhibitors are substances that prevent the
  normal action of an enzyme and thereby slow the
  rate of enzyme controlled reactions.
• Enzyme inhibitors may or may not act reversibly.
• In reversible inhibition, the inhibitor is
  temporarily bound to the enzyme, thereby
  preventing its function.
• Reversible inhibition is often a means by which
  enzyme activity is regulated in the functioning
  cell.
• In irreversible inhibition, the inhibitor
  (poison) may bind permanently to the enzyme and
  cause it to be permanently deactivated.

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Reversible Inhibition

• Reversible inhibitors are used to control the
  activity of enzymes.
• There is often an interaction between the
  substrate or end product and the enzyme
  controlling the reaction.
• Buildup of the end product or a lack of substrate
  may deactivate the enzyme. This deactivation can
  occur via competitive or noncompetitive
  inhibition.
• Competitive inhibitors compete with the substrate
  for the active site.
• Noncompetitive inhibitors bind to the enzyme, but
  not at the active site. The substrate can bind
  but enzyme function is impaired.
• Allosteric inhibitors are non competitive
  inhibitorsthat prevent the substrate from
  binding.

Model of elastase and its inhibitor
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Competitive Inhibition

• Competitive inhibitors compete with the substrate
  for the active site, thereby blocking it and
  preventing its attachment to the substrate.
• The inhibition is reversible.
• Example Malonate is a powerful inhibitor of
  cellular respiration because it is a competitive
  inhibitor of the enzyme succinate dehydrogenase
  in the Krebs cycle, which catalyzes the oxidation
  of succinate to fumarate.

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Non-Competitive Inhibition

• Non-competitive inhibitors bind to the enzyme,
  but not at the active site, and alter its shape.
  The substrate is still able to bind, but the
  reaction rate is slowed because the enzyme is
  less able to perform its function.
• Allosteric enzyme inhibitors are non competitive
  inhibitors that induce a shape change that alters
  the active site and prevents the substrate from
  binding.
• In this case, the enzyme ceases to function.

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Irreversible Inhibition

• Irreversible enzyme inhibitors are poisons that
  prevent enzyme function.
• Heavy metals Certain heavy metals bind tightly
  and permanently to the active sites of enzymes,
  destroying their catalytic properties.
• Example mercury (Hg), cadmium (Cd), lead (Pb),
  and arsenic (As).
• They are generally non-competitive inhibitors,
  although an exception is mercury which
  deactivates the enzyme papain.
• Heavy metals are retained in the body, and lost
  slowly.
• Insecticides
• These can prevent the breakdown of acetylcholine
  (ACh), a neurotransmitter in the nervous system.
• They bind to the enzyme that normally breaks down
  the ACh, causing over stimulation of the nerves.

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Energy in Cells

• Every living cell needs a regular supply of
  energy to power chemical processes
• Sources of energy are large complex molecules
  which make up food supply
• Energy is released when the bonds holding atoms
  together are released, usually as heat
• Energy is used to form adenosine-tri-phosphate
  (ATP) from adenosine-di-phosphate (ADP)
• ADP
• ATP
• Photosynthesis captures light energy and stores
  is in food glucose
• Respiration releases energy from glucose
• Energy is stored at ATP until it is needed

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Respiration

• Respiration is a process which makes ATP using
  energy in organic molecules such as glucose
  glycolysis, Krebs cycle and oxidative
  phosphorylation (electron transport chain).
• If glucose is placed in oxygen and set alight, it
  burns and releases a lot of heat energy as the
  glucose molecules combine with oxygen to form
  carbon dioxide and water and the energy from
  glucose is rapidly transferred to heat energy.
  This is an oxidation reaction.
• In a living cell, a similar process takes place,
  but in a more controlled way. You will recognise
  the equation
• Glucose oxygen ? energy carbon
  dioxide water
• C6H12O6 O2 ? energy
  CO2 H2O
• This actually happens in a series of reactions
  controlled by enzymes and the energy in glucose
  is released in small stages. A sequence of
  reactions (like in the process of respiration) is
  called a metabolic pathway.

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Glycolysis glucose converted to pyruvate

• Occurs in the cytoplasm of the cell
• Glucose (a 6 carbon compound) is converted into
  two pyruvate (pyruvic acid) molecules (a 3 carbon
  compound)
• Small amount of ATP (adenosine triphosphate) is
  made in this process (2 ATP)

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Kreb Cycle pyruvate fed into cycle of reactions

• Occurs in the matrix of the mitochondria
• If oxygen is available, pyruvate (pyruvic acid)
  formed in glycolysis passes into a mitochondrion
  through the outer and inner membranes
• Link step to convert the pyruvate into a
  different molecule which then undergoes a cycle
  of reactions
• Carbon dioxide removed (called decarboxylation)
  and diffuses out of the mitochondrion, out of the
  cell and out of organism
• 2 ATP molecules produced
• Hydrogen ions (H ions) and electrons are also
  produced in Krebs cycle to be fed into the
  electron transport chain to make more ATP

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Oxidative Phosphorylation (electron transport
chain) - electrons produced passed along an
electron transport chain to produce ATP

• This happens in the inner membrane of the
  mitochondrion
• ATP is made by the addition of inorganic
  phosphate Pi to ADP. This is called a
  phosphorylation reaction. In respiration, this
  process needs oxygen so it is known as oxidative
  phosphorylation. The enzyme ATP synthase makes
  the ATP from ADP Pi
• H ions and electrons pass through a series of
  reactions and energy is released as ATP. At the
  end of this electron transport chain, oxygen is
  needed.
• Oxygen at the end of the electron transport chain
  combines with electrons and hydrogen ions to form
  water.
• A lot of ATP is made in this part of respiration
  (34ATP molecules)

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Anaerobic Respiration

• When oxygen is not available, only glycolysis can
  occur. Therefore, a small amount of ATP is made
  (2 ATP) along with pyruvate
• Pyruvate will inhibit glycolysis so it is
  converted to something else.
• SOLUTIONS to remove the pyruvate
• ALCOHOLIC FERMENTATION LACTIC FERMENTATION
• Used by fungi plants Used by animals
• Yeast converts pyruvate to ethanol Pyruvate is
  converted to lactic acid
• Glucose ? pyruvate ? ethanol CO2 2 ATP
  Glucose ? pyruvate ? lactic acid 2 ATP
• If yeast is supplied with a supply of Lactic
  acid build up in muscles causes the pain in
• carbohydrate, it will carry out
  glycolysis exhausted muscles. The lactic acid is
• and alcoholic fermentation. transported in the
  blood to the liver and here
• it is converted back to pyruvic acid and
  then
• to glucose during recovery.
• The ethanol is used to make alcoholic
  drinks.
• In baking, the CO 2 is used to make bread, This
  requires oxygen, which is why you

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Summary of Respiration
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Photosynthesis

• Inputs CO2, H2O, light
• CO2 is absorbed from air as gas
• Water absorbed from environment
• Light red and green light most
  photosynthetically active
• Outputs C6H12O6, O2
• C6H12O6 glucose temporarily stored as starch in
  leaves to be used in respiration
• O2 is essentially a waste product that diffuses
  out
• 6CO2 6H2O ? C6H12O6 6O2
• Occurs in all green plants
• Requires sunlight so leaves broad, thin and flat
  but also prone to water loss
• Water loss decreased by waterproof cuticle which
  is a waxy layer on leaf
• Stomata present to allow CO2 in and stop water
  loss

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Photosynthesis

• Transfer of light energy into chemical potential
  energy
• Occurs in the grana of chloroplasts
• Relied on by all organisms
• Occurs in 2 stages
• The light phase
• Dark phase/Light independent phase (Calvin cycle)
• Chlorophyll plays vital role in trapping light
  energy

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Light Phase
Carries Energy
Light Independent Phase
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Chromosomes

• A Light microscope view of a chromosomefrom the
  salivary glands of the fly Simulium.
• Banding groups of genes stained light and dark.
• Puffing areas of transcription (mRNA
  production).
• B Scanning electron microscope (SEM) view of sex
  chromosomes in the condensed state during acell
  division. Individual chromatin fibers are
  visible.
• The smaller chromosome is the Y while
  thelarger one is the X.
• C Transmission electron microscope (TEM) view of
  chromosomes lined up at the equator of a cell
  during the process of cell division. These
  chromosomes are also in the condensed state.

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Chromosome States

• Interphase Chromosomes are single-armed
  structures during their unwound state during
  interphase.
• Dividing cells Chromosomes are double-armed
  structures, having replicated their DNA to form
  two chromatids in preparation for cell division.

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Chromosome Structure

• Histone proteins organize the DNA into tightly
  coiled structures (visible chromosomes) during
  cell division.
• Coiling into compact structures allows the
  chromatids to separate without tangling during
  cell division.

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Chromosome Features

• Chromosomes can be identified by noting
• Banding patterns
• Position of the centromere
• Presence of satellites
• Length of the chromatids
• These features enable homologous pairs to be
  matched and therefore accurate karyotypes to be
  made.

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Chromosomes Contain Genes

• A single chromosome may contain hundreds of
  genes.
• Below are the locations of some known genes on
  human chromosomes

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Nucleotides

• The building blocks of nucleic acids (DNA and
  RNA) comprise the following components
• a sugar (ribose or deoxyribose)
• a phosphate group
• a base (four types for each of DNA and RNA)

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Structure of Nucleotides

• The chemical structure of nucleotides

Symbolic form
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Nucleotide Bases
Purines Adenine
Double-ringed structures Adenine
Double-ringed structures Guanine
Always pair up with pyrimidines Guanine

• The base component of nucleotides which comprise
  the genetic code

Pyrimidines Cytosine
Single-ringed structures Cytosine
Single-ringed structures Thymine
Always pair up with purines Thymine
Thymine
Uracil
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DNA Structure

• Phosphates link neighboring nucleotides together
  to form one half of a double-stranded DNA
  molecule

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DNA Molecule

• Purines join with pyrimidines in the DNA molecule
  by way of relatively weak hydrogen bonds with the
  bases forming cross-linkages.
• This leads to the formation of a double-stranded
  molecule of two opposing chains of nucleotides
• The symbolic diagram shows DNA as a flat
  structure.
• The space-filling model shows how, in reality,
  the DNA molecule twists into a spiral structure

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DNA Replication 1

• DNA is replicated to produce an exact copy of a
  chromosome in preparation for cell division.
• The first step requires that the coiled DNA is
  allowed to uncoil by creating a swivel point.

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DNA Replication 2

• New pieces of DNA are formed from free nucleotide
  units joined together by enzymes.
• The free nucleotides (yellow) are matched up to
  complementary nucleotides in the original strand.

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DNA Replication 3

• The two new strands of DNA coil up into a helix.
• Each of the two newly formed DNA strands will go
  into forming a chromatid

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DNA Replication 4

• Free nucleotides with their corresponding bases
  are matched up against the template strand
  following the base pairing rule

A pairs with T
T pairs with A
G pairs with C
C pairs with G
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Control of DNA Replication

• DNA replication is controlled by enzymes at key
  stages

3'
5'
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The Leading Strand

• Enzymes can build strandsonly in the 5 to 3
  direction
• This means that only one strand, called the
  leading strand, can be synthesized as a
  continuous strand.

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The Lagging Strand

• The other complementary strand, called the
  lagging strand, must be constructed in fragments,
  which are later joined together

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Enzyme Control of Replication 4
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The Cell Cycle

• The process of mitosis is only part of a
  continuous cell cycle where most of the cell's
  'lifetime' is spent carrying out its prescribed
  role a phase in the cycle called interphase.
• Interphase is itself divided up into three
  stages
• G1 First Gap
• S Synthesis
• G2 Second Gap
• Mitosis is the process bywhich the cell
  producestwo new daughter cellsfrom the original
  parent cell

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Mitosis
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Mitosis Micrographs

• Cell division for somatic growth and repair

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Meiosis

• The purpose of meiosis is to produce haploid sex
  cells.
• Haploid sex cells have only one copy of each
  homologous pair of autosomes plus one sex
  chromosome

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Meiosis I

• The first division of meiosis is called a
  reduction division because it reduces (halves)
  the number of chromosomes.
• One chromosome from each homologous pair is
  donated to each intermediate cell

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Meiosis II

• The second division of meiosis is called a
  mitotic division, because it is similar to
  mitosis.
• Sister chomatids of each chromosome are pulled
  apart and are donated to each gamete cell

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Meiosis Mitosis Compared
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Prokaryotes

• Single-celled bacteria and cyanobacteria
• The chromatin materia (DNA) is not held in a
  membrane
• The chromosome is a simple DNA chain with the
  ends joined to form a circle
• The cells do not have membrane-bound organelles

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Eukaryotes

• Higher cells that have a true nucleus
• The chromatin material (DNA) is enclosed within a
  nuclear membrane
• The chromosome is a length of DNA folded like a
  concerta. It is wound around proteins called
  histones, with other proteins present
• Cells have membrane bound organelles and form
  spindles during mitosis and meiosis