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Conferences Courses Physics 982-003-50(Conted) Br n’s B o ia i
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BIOLOGY 003Part 1:
The Cell and DNAThe Cell and DNA
What is Biology?
The Scientific Study of Life
Very Broad
topic
Living vs. Non-living
Properties of Life
So…
Order: living things are made up of cells
Bacterial cells
Plant cells
Human bone cells
Cells are the basic unit of lifeSingle celled protist
OrderEach cell has internal order & the cells within the body have specific arrangements & functions
Cell theory: fundamental principle in biology
1. a cell is the smallest unit of life
2. cells make up all living things
3. new cells arise from pre-existing cells
The Cell:
as fundamental to biology as the atom is to chemistry
atoms
molecules
cells
tissues
organ
system
http://aimediaserver4.com/studiodaily/videoplayer/?src=ai4/harvard/harvard.swf&width=640&height=520
Cell Size
Most neurons in µm range
Eukaryotes
Prokaryotes
Limitations to Cell sizeLimitations to Cell size
Cell size – variable
small : 8 to 100 um
1 meter = 1000 mm
= 1 000 000 um
Why so small?
Larger organisms do not generally have larger cells than smaller organisms—simply more cells.
Limitations to cell Size:Limitations to cell Size: homeostasishomeostasis
• Oxygen required
• Waste products are released – must be removed from cell
• Exchanges food, gases, nutrients takes place through cell surface
cell size metabolic needs
• As a cell becomes larger, its volume increases at a greater rate than its surface area (plasma membrane)
Cell Size limited by :• Cell surface area (plasma membrane)
• Surface area-to-volume ratio
Volume increases faster
than surface area
• Metabolic demands: determined by volume
• But the transport of materials into or out of the cell is determined by surface area
Surface area / Volume RatioSurface area / Volume Ratio
• Small objects have large surface area to volume ratio
• Cells – small lots of surface area
Ex:
Things all Cells have in Common
• surrounded by a membrane
• internal mass (cytoplasm)
• contain genetic information (DNA)
• have ribosomes (protein synthesis)
Two Major Types of Cells
• Prokaryotic cells– Domain: Bacteria and Archaea– No nucleus – Lack most organelles
• Eukaryotic cells
– Domain: Eukarya
– Nucleus present in each cell
– Organelles present
1 µm
OrganellesNucleus (contains DNA)
Cytoplasm
Membrane
DNA(no nucleus)
Membrane
Eukaryotic cell Prokaryotic cellvs.
Virus
• DNA – free in cytoplasm
• ribosomes
• outer capsule (sugar or protein)
• cell wall
Cytosol (fluid)
Prokaryotic cells
Comparison Between Eukaryotic and Prokaryotic Cells
Table 3.1
Eukaryotic Cell
ex: plant and animals
-Typically larger- Contain internal membranes that form organelles (more complex)- DNA in membrane bound nucleus
Plasma MembraneA cell is surrounded by Plasma Membrane
- boundary between cell contents and surroundings
- everything that enters/leaves cell passes through cell membrane
- divides cells into compartments
Why would me want to separate internal and external environments?
Structure of Plasma Membranes
Two components:
1. Phospholipid molecules
2. Protein molecules
HEAD
TAIL
Phospholipid Molecules
Amphipathic molecules
Phospholipid Molecules• One end attracted to water (Head)
• One end repelled by water (Tail)
When placed in water:
- they self assemble into a bi-layer (double layer)
- shield hydrophobic portions
Cell organization & Size
plasma membrane
- to maintain homeostasis: cell contents separated from external environment
Phospholipid bi-layer(Proteins not shown)
Cell Membrane:- Selectively permeable: it allows some substances to cross it more easily than others
Cytoplasm & Cytosol• Cytoplasm: region between the nucleus and the plasma membrane
• Cytosol: semifluid substance within the membrane – contains the organelles (makes up most of the cell mass)
- Therefore; the cytoplasm is filled with cytosol
Nucleus
• contains Genes• wrapped in double
membrane
= nuclear envelope
Nucleus:
Contains DNA + Protein • Chromatin: loosely arranged DNA and Protein • Chromosomes: tightly packed
Contains Nucleolus: Not membrane bound
makes ribosomes
The Cell’s Heritable Information
- All cells contain deoxyribonucleic acid (DNA) = heritable material that directs the cell’s activities.
Inherited DNA Directs development of an organism
Information Transfer
- Living things must have a set of instructions that allow them to grow, develop, respond to stimuli, reproduce…
- those “instructions” are found in DNA
- blueprint for all cellular activities
- DNA made up of genes
- Genes are the units of inheritance that transmit information from parents to offspring.
Four main classes of biological molecules
1.Carbohydrates2. Lipids3. Proteins4. Nucleic acids
Organic Compounds
• Contain carbon (C backbone)
• Most contain H and O
• May contain other elements
N = Nitrogen
P = Phosphorus
S = Sulfur
Why is Carbon Special?
Carbon can form 4 covalent bonds– bonds with up to 4 separate atoms– can bond with other C atoms
long chains of carbon atoms
can combine with many other kinds of atoms
• Straight chains– short or long
• Branched chains– Single or multiple
• Rings
Carbon Skeleton:Carbon Skeleton:
Distinctive properties of an organic molecule depends on:
1) Arrangement of carbon skeleton
2) Functional groups = molecular components attached to that carbon skeleton)
• Give molecule distinctive chemical properties
Functional groups:
Biological molecules are composed of subunits that are linked to each other
• Single unit = monomer
• Chain or ring of of monomers = polymer
(pearl necklace)
(pearl)
Synthesis and Breakdown of Polymers
• SynthesisSynthesis–Addition of subunits chain grows
• BreakdownBreakdown –Removal of subunits chain
shortens
Dehydration synthesis:
Building Chains (polymers)
Condensation or Dehydration synthesis is the chemical reaction that links repeating subunits together. When dehydration synthesis occurs, a bond forms and WATER is released.
Result:
• Increase in “chain”
• molecule of water released
Breakdown of polymers
Hydrolysis:
Splitting a polymer by the addition of water
Nucleic acids
(DNA and RNA)
Nucleic acids Purpose:- Store and transmit hereditary information
in Genes = units of inheritance
- Program amino acid sequence of Proteins
Made of nucleotides
Types
1. Deoxyribonucleic acid (DNA):
Stores information for protein synthesis
2. Ribonucleic acid (RNA):
Directs protein synthesis
Structure
– Consists of building blocks called nucleotides
Nitrogenousbase
O
O
O
O P CH2
5’C
3’CPhosphate
group Pentosesugar
Nucleotide
O
i) phosphate molecule (P)
ii) 5-carbon sugar (S)
iii) nitrogenous base (B)
Structure
Nucleotides form chains called polynucleotides
Fig. 5-27ab
5'C
3'C
3' end
(a) Polynucleotide, or nucleic acid
Nucleoside
Nitrogenousbase
3'C
5'C
Phosphategroup Sugar
(pentose)
Nitrogenousbase
O
O
O
O P CH2
5’C
3’CPhosphate
group Pentosesugar
(b) Nucleotide
O
Structure
Nucleotide = building block
Nucleic acid = chain
DNA vs. RNADNA RNA
Phosphate
Sugar Deoxyribose Ribose
Bases Adenine (A)
Guanine (G)
Cytosine (C)
_____________
Thymine (T)
____________Double stranded
Uracil (U) ___________
Single-stranded
DNA and RNA – 4 POSSIBLE NUCLEOTIDES FOR EACH
DNA RNARNA
DNA• Needed for cell replication• Contains genes• Genes tell cells which
proteins to make• Complementary base
pairing Hydrogen bond
J Watson & F Crick Cambridge University; 1953
The sequence of bases along a nucleotide polymer is unique for each gene
DNA AssemblyDNA Assembly
P P S – B -- B - S P P S - B -- B - S P P S - B -- B - S P P S - B -- B - S
Bases:
Adenine (A)
Guanine (G) Cytosine (C) Thymine (T)Thymine (T)
2 strands held together by hydrogen bonds between the paired bases
Complementary Base Pairing
In DNA: A and T C and G – always line up together!
Referred to as complementary complementary base pairingbase pairing
P P S – A -- T -- S P P S -- G -- C C --S P P S -- CC -- G -- S P P S -- T -- A -- S
DNA Assembly
Summary: DNA
• DNA contains the genetic code
• DNA contains “blueprint” for making different proteins
DNA over 2m long!
The way DNA encodes a cell’s information is analogous to the way
we arrange the letters of the alphabet
RAT =
ART=
Sequence in letters = changes in meaningSequence of nucleotides = different proteins
Genetic Information• Each gene carries information needed to make a
specific PROTEIN
• Genes carry information that determines the primary sequence of the protein
Protein synthesis
Proteins
aka polypeptides
Proteins
Proteins account for 50% of the organic matter in a typical animal body, and they play a critical role in almost all life processes
Proteins
• Proteins are made of amino acids.
• There are 20 common a.a.
• Polypeptide: chain of a.a.
• Protein: 1 or more polypeptides folded/coiled into a specific shape
Amino Acids - building blocks of proteins
• All amino acids have same basic skeleton:
R group - variable
Carboxyl group
• Animal cells can make some, but not all amino acids
• Essential a.a.: those that we can’t make or make enough of to meet our needs.– Required from diet
Essential Amino Acids
Asparagusic Acid Methylmercaptan
Asparagine Ammonia (pee) and Oxaloacetate
Harmful Amino Acids;
Aspartame?
Protein = chain of amino acids
Synthesis reaction
As the chain grows you create a polypeptide
Structure
• very complex
– large variety of amino acids– very large– different protein molecules have
their own distinct shape
4 levels of structure
• Primary
• Secondary
• Tertiary
• Quaternary
• Polypeptide can spontaneously organize into complex shapes (change)
• Protein shape essential to function– Ex receptor, antibody, enzyme
i) PRIMARY STRUCTURE:
- Number and Sequence
Each sphere = 1 amino acid
Ex. insulin
ii) SECONDARY STRUCTURE: 2 types
a) alpha helix (coiled)
Hydrogen bondshold helix cellsin shape
b) Beta Pleated sheet (folded)
ii) SECONDARY STRUCTURE
Hydrogen bondshold neighboringstrands of sheettogether
iii) TERTIARY STRUCTURE:
Protein alreadycoiled or folded
Examples:
Hydrogen bonds
Ionic Bonds
Disulfide bridges
Hydrophobic interactions
iv) QUATERNARY STRUCTURE
The fusion of two or more proteins
Examples:
A very important protein: Ribosome
• Uses RNA to make other proteins
• Made in the nucleolus
Conformation: determines function
- single amino aid substitution
Denaturation- when a protein unravels and loses its
native conformation
Denaturation
Renaturation
Denatured proteinNormal protein
• For cell to reliably make proteins, it must be able to control the placement of animo acids
Proteins are complex
–made up of building blocks called amino acids
–20 different kinds
–number and sequence of the aa’s = primary sequence controls shape function
• Each protein has its own unique primary sequence!
Recall… Protein Structure
How does the Information on the DNA Molecule get
Converted into a Protein?
• DNA not used directly
• Involves various forms of RNA (the other nucleic acid)
• Accomplished by a process called: PROTEIN SYNTHESIS
mRNA
Synthesis ofmRNA in thenucleus
DNA
NUCLEUS
mRNA
CYTOPLASM
Movement ofmRNA into cytoplasmvia nuclear pore
Ribosome
AminoacidsPolypeptide
Synthesisof protein
1
2
3
Protein
Synthesis
Transcription
Translation
1) Transcription1) Transcription DNA RNA
2) Translation2) Translation RNA Protein
2 major steps in protein synthesis
(information storage)
(information carrier)
(product)
Step 1: Transcription
Transcription = transfer of genetic = transfer of genetic information from DNA to messenger RNA information from DNA to messenger RNA (mRNA)(mRNA)
Transcription a) Separation of DNA
Gene = DNA Sequence that codes for a protein:
Transcription of a Hypothetical Gene: a) Separation of DNA
ATG GGA TTT AAC CCT GGA GGG TAA* TAC CCT AAA TTG GGA CCT CCC ATT**
- Two strands separate in region of gene
ATG GGA TTT AAC CCT GGA GGG TAAXXXX XXXXXXXXXX XXXXXX **TAC CCT AAA TTG GGA CCT CCC ATT **
**coding strand
Transcription: b) Synthesis of mRNA
Synthesis of an RNA molecule that is complementary complementary to to
the DNA (following the base pair rule)the DNA (following the base pair rule)
DNA mRNA = This molecule is called messenger RNA
Transcription: b) Synthesis of mRNA
(DNA) XXXX ATG GGA TTT AAC CCT GGA GGG TAA XXXXXX
(mRNA) AUG GGA UUU AAC CCU GGA GGG UAA
(DNA)XXXX TAC CCT AAA TTG GGA CCT CCC ATT ** XXXX
DNA: A T C GRNA: U A G C
Summary of Transcription and Release of completed mRNA molecule
enzyme
Once the mRNA molecule is complete the transcription process is over
• Transfer of information from DNA to mRNA completes first phase of protein synthesis (Transcription)
Next question:
How is the information in mRNA used How is the information in mRNA used to make a protein?to make a protein?
What information do we have?
mRNA: AUG GGA UUU AAC CCU GGA GGG UAA
Need to:
convert nucleic acid language (in the mRNA) into amino acid language (protein)
Step 2: Translation
Polypeptide
Ribosome
Aminoacids
tRNA withamino acidattached
tRNA
Anticodon
Trp
Phe Gly
Codons 35
mRNA
Translation = Assembly of the protein primary structure according to instructions (codon sequence) on the mRNA
• information on mRNA is contained in groups of 3 nucleotides called CODONSCODONS
mRNA: AUG GGA UUU AAC CCU GGA GGG UAA
Translation
• Codons on mRNA provide the sequence or order in which the amino acids must be arranged to create the primary structure of the protein
• mRNA has the information but doesn’t do the work
mRNA Protein
In example: 8 codons
AUG GGA UUU AAC CCU GGA GGG UAA
translation requires a second type of RNA called transfer RNAtransfer RNA (tRNA)
Amino Acids are not nucleic acids – so they have nothing to do with the base pair rules
The cell needs a way to match up amino acids with the 3 letter codons on the mRNA….
Translation
aa
transfer RNA transfer RNA (tRNA)“decoder”
Amino Acid
Anticodons
Translation
Transfer RNA (tRNA): Anticodon
ANTICODON = group of 3 Nucleotides complementarycomplementary to CODONS on mRNA
In example anticodon is AAG
- AAG (ANTICODON) would pair with CODON UUC on a mRNA molecule
Translation
aa
Transfer RNA (tRNA): Amino Acids
At other end Attachment site for 1 AMINO ACID molecule
Recall… there are 20 aa
How many codons are there?
aa
Translation
Many Kinds of tRNA
Each kind is unique in that:
1. it has a unique ANTICODON
2. Each can attach 1 (and only 1 kind) of
AMINO ACID (aa)
Translation
Each codon site on mRNA:- has only 1 ANTICODON that can bind to it
- the tRNA with the appropriate anticodon can only transport 1 kind of amino acid
- Therefore only one kind of amino acid can be placed at a particular codon site
aa aa aa aaaa
Codons on mRNA
Translation
Example
• Suppose a mRNA: – UUU UUU UUU UUU UUU
• What tRNA can be used?
• How many amino acids are in the protein?
• What amino acids are they?
Translation
Codons for Amino Acids (on the mRNA)
• MANY amino acids have several CODONS
64 possible anticodons:• 1 start (met), 3 stop• 61 anticodons code for
amino acids
Translation
AUG (on the mRNA) =
START CODON
- Met is inserted!
Translation
codon on mRNA: AUC therefore anticodon on tRNA UAG….
Translation
Role of tRNA
• Positions each amino acid in its proper proper orderorder in the amino acid chain as determined by the sequence of codons in the mRNA molecule
• Each tRNA has a unique anticodon and it carries only 1 kind of amino acid
Translation
Ribosomes (= Protein + rRNA)
• Attach to start end of mRNA
• As tRNAs attach to mRNA the ribosome begins to move along mRNA molecule
• As it does, it aligns first 2 aas which are then joined together by an enzyme
• Repeats by aligning & joining aa# 3 to aa#1+2 so they can be joined and so on
• When it reaches the end of mRNA molecule the aa chain is released into cytoplasm
Translation
ribosome
Translation
Transcription
Translation
Videos:
- http://www.youtube.com/watch?v=D3fOXt4MrOM&feature=related
- http://jacusers.johnabbott.qc.ca/~biology/index.asp
Genetic Code- Same in almost all organisms!
Mutation & Sexual Recombination Produce Genetic Variation
• New genes and new alleles originate only by mutation • A mutation is a change in the nucleotide sequence of an
organism’s DNA.• Most mutations occur in somatic cells and are lost when the
individual dies.• Only mutations in gametes can be passed on to offspring,
and only a small fraction of these spread through populations and become fixed.
Mutations = changes in the nucleotide sequence of DNA Cause new genes and alleles to arise
Mutation rates– Tend to be low in animals and plants– Average about one mutation in every
100,000 genes per generation– Are more rapid in microorganisms
RNA: CGAUGCGAGUUACCCAGCUCGGAUAA
DNADNA: GCTACGCTCAATGGGTCGAGCCTATT
Step 1. Coding strand:
- what is this step called?
- what kind of RNA did you make?
REVIEW:
(Start) Arg- Val- Thr- Gln - Leu – Gly (stop)
- steps involved?
-Types of RNA?
mRNA: CG AUG CGA GUU ACC CAG CUC GGA UAA
Codon on mRNA
aa on tRNATrp
REVIEW:
ribosomes (rRNA) help in aa assembly to make the protein
codons on mRNA decoded by tRNA
base pair rule mRNA
Translation
Transcription
REVIEW:
DNAmolecule
Gene 1
Gene 2
Gene 3
DNAtemplatestrand
TRANSCRIPTION
TRANSLATION
mRNA
Protein
Codon
Amino acid
REVIEW: