Revision Notes, Molecules, Cells And Genes

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University of New South Wales | Molecules, Cells and Genes

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Cells The Building Blocks of Life

The cell is an organisms 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 cells 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 cells 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
o 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)
o Includes three multicellular kingdoms: plantae, fungi, animalia

Bacteria, Archaea and Eukarya

Similarities

Differences

Structure and
Features

Bacteria & Archaea

Eukarya

- Plasma membrane
- Semifluid substance cytosol (fills the
cytoplasm, contains salts, minerals, organix
compounds)
- Chromosomes
- Ribosomes (make proteins)
- Simpler and smaller
- No nucleus
- No membrane-bound organelles
- DNA in unbound region nucleoid
- Cytoplasm bound by plasma membrane
- Unicellular
- Cell wall
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 the
cytoplasm
Cell wall: rigid structure outside the plasma
membrane
Capsule: jellylike outer coating of many
prokaryotes
Flagella: locomotion organelles on some
bacteria

- Plasma membrane
- Semifluid substance cytosol
- Chromosomes
- Ribosomes (make proteins)

- Eukaryotic cell has membrane-enclosed

organelles (the largest being the nucleus)
- Multicellular

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 total
collection of DNA molecules and associated
proteins, make up eukaryotic chromosome;
nucleolus within nucleus, non-membrane bound,
composed of protein and nucleic acid,
manufactures ribosomes (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 of
interconnected membranes, ribosomes cluster on
the ER.
Two types of endoplasmic reticulum:
1. Rough ER mRNA travels to ribosomes 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 the
organelle
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 cells 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)

Reproduction

Bacteria Vs.
Archaea

Nuclear envelope is
connected to rough ER,
which is also
continuous with
smooth ER

Membranes and
proteins produced by
ER flow in the form of
transport vesicles to the
Golgi

Golgi pinches of
transport vesicles and
other vesicles that give
rise to lysosomes, other
specialised vesicles and
vacuoles

Plasma membrane
expands by fusion of
vesicles and proteins
are secreted from the
cell

Transport vesicle
carries proteins to
plasma membrane for
secretion

Lysosome is available
for fusion with another
vesicle for digestion

- 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
- Cell membrane contains ester bonds
- Cell wall made of peptidogylcan
- One RNA polymerase
- Ribosomes sensitive to antibiotics (archaeal
are not)
- Ubiquitous

The Endomembrane System:

The eukaryotic cells endomembrane system is a
manufacturing and material transport network that
enables the cell to make, move and break down
cellular products.

Archaea
- 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
o Joining of these small molecules into macromolecules
o Packaging of molecules into probionts
o Origin of self-replicating molecules
Fossil records show macroevolutionary changes over large time scales
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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 Darwins four postulates.

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

Macromolecules
Elements 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
Carbohydrate
Lipid
Protein
Nucleic acids

Monomer (Subunit)
Monosaccharides (simple sugars)
Fatty acids (not all classified as polymers)
Amino 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 structural
o 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), dont 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
o Secondary
o Tertiary
o Quarternary (arises when protein consists of 2 or more polypeptide chains)

Protein function
Structural
Storage
Transport
Hormones
Defence
Movement
Growth factors
Enzymes

Protein Example
Collagen, keratin
Casein, ovalbumin
Haemoglobin, albumin
Insulin
Antibodies
Actin and myosin
Human growth factor
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
o 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 and
flagella 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:
o Maintain cell shape
o 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
o 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 concentration
gradient
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 Metabolism
Parts of Chapter 8&9

Extracting Energy from Food

Parts of Chapter 9

Photosynthesis

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