Molecules, Cells and Genes Notes

8/9/2019 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

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

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

o

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

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

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

o

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

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 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:

o

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

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 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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