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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: