the molecules of cells chapter 3. overview introduction to organic compounds categories of reactions...
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The Molecules of Cells
Chapter 3
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Overview
• Introduction to Organic Compounds
• Categories of Reactions
• Molecules of Life– Carbohydrates
– Lipids
– Proteins
– Nucleotides
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What Are Organic Compounds?
Unique to living systems
Contain C & at least one H atom
Each has a functional group:– Specific atoms/groups of atoms covalently
bonded to C– Have specific physical & chemical properties
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Why Carbon?
Versatile bonding
Can covalently bond with up to 4 atoms
Forms stable bonds
Helps form backbone for other elements to bond with
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How Do Cells Build Organic Compounds?
Monomer:
Individual subunit of larger molecules needed to maintain cell structure & function
e.g. amino acids
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Polymer:
Combination of 3 to millions of subunits
e.g. proteins
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Hydrocarbons
H covalently bonded to C
e.g. gasoline, other fossil fuels
All 2 million+ are non-polar
Some of Earth’s most important energy sources
(electric & heat energy)
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Functional Groups
Specific atoms or groups of atoms covalently bonded to carbon atoms in organic
compounds
More reactive than hydrocarbon groups
Can affect how structurally similar molecules work
e.g. estrogens & testosterone(different positions of functional groups determines
sexual traits)
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Types of Functional Groups
Hydroxyl
– Alcohols, sugars, amino acids
– Water-soluble
Methyl
– Fatty acid chains– Insoluble in water
—OHC
H
H
H
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Types of Functional Groups continued
Carbonyl
– Sugars, amino acids, nucleotides– Water-soluble– Aldehyde if at end of carbon backbone– Ketone if within carbon backbone
—CHO
C
O
C
O
H
CO(aldehyde) (ketone)
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Types of Functional Groups continued
Carboxyl
– Amino acids, fatty acids– Water-soluble– Highly polar– Acts as acid by giving up H+
C
O
OH C
O
O-
—COOH —COO-
(ionized)(non-ionized)
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Types of Functional Groups continued
Amino
– Amino acids, some nucleotide bases– Water-soluble– Acts as weak base by accepting H+
—NH2 —NH3+
N
H
H+
H
N
H
H
(non-ionized) (ionized)
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Types of Functional Groups continued
Phosphate
– Nucleotides (e.g. ATP), DNA, RNA, some proteins, phospholipids
– Water-soluble– Acidic
P
O
O-
O-
O — P
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Sulfhydryl
– Cysteine (an amino acid)– Helps stabilize protein structure via disulfide
bridges
Types of Functional Groups continued
—SH —S—S—(disulfide bridge)
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Categories of Reactions
(1) Functional Group Transfera.k.a. exchange reaction
AB + CD → AD + BC
1 molecule gives up group to another
Making & breaking of bonds
e.g. ATP gives phosphate group to glucose in cellular respiration
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a.k.a. redox reaction
One molecule loses e-s
Another gains them
e.g. cellular respiration, where glucose is oxidized (loses e-s) to CO2 & O is reduced (gains e-s) to
H2O
(2) Electron Transfer
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(3) Rearrangement
Internal bonds reform to turn one organic compound into another
= structural isomer of original
(same molecular formula, different order of bonding)
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a.k.a. synthesis reaction
A + B → AB
2 molecules covalently bond to form a larger molecule
(1 water molecule produced for each joining)
Making of bonds (= anabolic)
e.g. Na & Cl forming NaCl, amino acids forming a protein
(4) Condensation
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a.k.a. decomposition reaction
AB → A + B
Molecule is split into 2 smaller ones
Breaking of bonds (= catabolic)
e.g. glycogen being broken down into glucose, carbs being broken down into simpler sugars
(5) Cleavage
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e.g. hydrolysis
Cleavage reaction
Molecule split by enzyme action
OH & H from H2O attached to exposed sites
e.g. hydrolysis of sucrose into glucose
& fructose
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Factors Influencing Reaction Rates
Temperature– ↑ temp, ↑ rxn rate– ↑ kinetic energy, ↑ collisions
Concentration of reactants– ↑ concentration, ↑ frequency of collisions
For reactions to occur, atoms & molecules must collide with enough force to overcome repulsion
between e-s
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Particle size– Smaller move faster so collide more
frequently
Catalyst– Substance that speeds up chemical rxns– Does not become chemically changed or part
of product
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Molecules of Life
• Carbohydrates
• Lipids
• Proteins
• Nucleotides
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(1) Carbohydrates
Sugars & starches
Make up 1-20% of cell mass
Contain C, H, O
Important source of energy
Also serve some structural purposee.g. ribose & deoxyribose in RNA &
DNA
Classified by size & solubility
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(a) Monosaccharides
“1 sugar”
Building blocks of other carbs
Most water-soluble sugars
2 or more –OH groups bonded to C backbone
1 aldehyde or ketone (carbonyl) group
Most have a 5-C or 6-C ring
—CHO CO
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Monosaccharide Structure
glucose fructose galactose
deoxyriboseribose
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(b) Disaccharides
Double sugar
Consist of 2 monosaccharides
Must be broken down to be absorbed
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(c) Oligosaccharides
“Few” or short-chain sugars
Includes disaccharides
Often found as side-chains on lipids & proteins
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(d) Polysaccharides
“Many sugars”
Chains of glucose
Least water-soluble of carbsMore complex = less soluble
Good energy storage product
Must be broken down to be absorbed
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Polysaccharide Structure: Starch
Spiral structure
OH groups stick out from coils
Storage carbohydrate of plants
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Filamentous (branched) chains
Storage carbohydrate of animal tissuesEquivalent to starch in plants
Stored in muscle & liver cells
Polysaccharide Structure: Glycogen
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Polysaccharide Structure: Cellulose
Every other sugar is “upside-down”Sheets form by H-bonding between chains
Structural carbohydrate of plantsMakes up cell walls
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Modified polysaccharideNitrogen groups attached to glucoses
Strengthens cuticle of arthropods & cell walls of fungi
=structural carbohydrate of animals & fungi
Polysaccharide Structure: Chitin
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Simple Carbohydrates
a.k.a. simple sugars
Monosaccharides & disaccharides
Taste sweet
Few essential nutrients & high in calories
e.g. candy, milk products, fruit
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Complex Carbohydrates
a.k.a. starches & fibres
Oligosaccharides & polysaccharides
Taste pleasant but not sweet
e.g. whole grains, legumes, starchy vegetables (potatoes, etc.)
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Fibre
= cellulose
↑ fibre in diet = ↓ risk of cancer, diabetes, hypertension, etc.
Processing plant foods decreases the amount of fibre & vitamins
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In excess, carbs can lead to:• Increased blood sugar
• Excess sugar being stored as fat• Increased risk of heart disease, etc.
Diet rich in whole grains, fruits, & vegetables may reduce risk of heart disease & some cancers
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(2) Lipids
Fats & oils
Contain C, H, OLess O than carbs
Some also have P
Non-polarInsoluble in water
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(a) Fatty Acids
Carboxyl group attached to backbone of up to 36 atoms
Each C is covalently bonded to 1-3 H atoms
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(i) Saturated fatty acids
C backbones completely filled with attached H atoms
Single covalent bonds only
Animal fats:Usually solid at room temperature
Associated with heart disease,
clogged arteries, etc. = bad fatse.g. palmitic acid, stearic acid
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(ii) Unsaturated fatty acids
Not all Cs have H attached
≥1 double covalent bondCauses kinks in tails
Plant fats:Usually liquid at room temperature
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Mono- vs. polyunsaturated fats
Mono-unsaturatede.g. oleic acid
– Only 1 double bond– Thought to lower cholesterol
Polyunsaturatede.g. linoleic acid
– More than 1 double bond
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Partial hydrogenation of vegetable oils
Artificial saturation
Turns liquid oils into solids (e.g. margarine)
Oil is heated; H2 gas & nickel catalyst added
Breaks C double bonds & attaches H
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Partial hydrogenation & trans-fatty acids
Partial hydrogenation = bad!Fat is now saturated
Trans-fats created by heat (e.g. deep frying) & hydrogenation
Double bonds fold in unnatural direction
Enzymes that process fat are unable to process trans-fatty acids in a normal way
Domino effect: Because trying to process trans-fatty acids, don’t
process essential fatty acids properly
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Essential fatty acids
Body can manufacture some
(palmitic acid, oleic acid, etc.)
Others must be ingested via foods
(omega-3 & omega-6 fatty acids)
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(b) Neutral Fats
3 fatty acid tails attached to glycerol backbone
= triglycerides
Large & found throughout entire body
“Body fat” used for insulation, protection, energy production
Yield > double the energy of complex carbs
e.g. butter, lard, veg. oils
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(c) Phospholipids
Glycerol backbone with phosphorus group & 2
fatty acid tails– Tails are non-polar
– Head is polar
Make up double-layered cell membranes
Help regulate what crosses boundary of cell
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(d) Waxes
Long-chained fatty acids bonded to long-chain alcohols or
carbon rings
Repel water
Protect
Lubricate
Add pliability to hair, skin, etc.
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(e) Sterols
Backbone of 4 C-rings
Differ in functional groups
In all eukaryotic cell membranes
Steroids are essential for human life(homeostasis, vitamin D, sex & metabolic hormones)
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Cholesterol
Found only in animal foods
Made in liver
Can’t dissolve in blood
Is carried to & from cells by lipoproteins (LDL & HDL)
Note: cholesterol itself is not bad
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LDL (low-density lipoprotein)
Carries cholesterol through blood to body cells
Can form fatty deposits (plaques) in artery walls
– Eventually blocks blood flow– Leads to heart attack, stroke, etc.
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HDL (high-density lipoprotein)
Carries cholesterol through blood to liver(will eventually be processed & excreted)
High levels appear to protect against heart attack
(may remove excess cholesterol from plaques, which slows build-up)
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(3) Proteins
Make up 10-30% of cell mass
Contain C, H, O, N & sometimes S & P
Form basic structural material & aid in cell function
Long chains of amino acids (from 50 to 10,000+) joined by peptide bonds
Sequence of amino acid chain dictates which protein is made
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(a) Amino Acids
Can act as bases or acids
20 amino acids– Identical except for R group
– Chemically unique
R
Amino group (NH3+), carboxyl group (COO-), H atom, & R group
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Types of R-groups: Acidic
In neutral solutions, R-group can lose proton to become negatively-charged
If interaction with basic R-group, forms salt bridge: helps stabilize a protein
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In neutral solutions, R-group can gain proton to become positively-charged
If interaction with acidic R-group, forms salt bridge: helps stabilize a protein
Types of R-groups: Basic
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R-group is an aromatic (benzene) ring
Generally hydrophobic & non-reactive
Types of R-group: Aromatic
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R-group contains S
Helps stabilize globular protein structure
Types of R-group: Sulfur
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R-groups can form H-bonds
Types of R-group: Uncharged Hydrophilic
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R-groups do not form H-bonds
Rarely reactive
Usually buried deep within a protein
Types of R-group: Inactive Hydrophobic
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R-group & amino group are directly connected
Usually located at the turn of a polypeptide chain in 3D protein structure
Types of R-groups: Special
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Essential & non-essential amino acids
Non-essential:– Can be synthesized from other substances in the body
Essential:– Can not be synthesized in the body– Must come from food– If not adequate intake, can’t make proteins
• Unable to sustain body structurally & functionally = illness & eventually death
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Histidine
Isoleucine
Leucine
Lysine
Methionine(cysteine partially meets needs because has S)
Phenylalanine(tyrosine partially meets needs)
Threonine
Tryptophan
Valine
9 essential amino acids9 essential amino acids
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Most animal sources:“Complete protein”: all of essential aas
Vegetables:
Missing or low in certain aas
If combine different vegetables, can get all essential aas
Lysine & tryptophan hard to get from plants so vegetarians need to ensure adequate intake
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From Amino Acids to Proteins
Amino acids form proteins by dehydration reactions
Peptide bonds form between amino acids
2 amino acids bonded together
= dipeptide
Many amino acids linked
= polypeptide
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Types of Proteins
Structural = hair, tendons, ligaments
Contractile = muscles
Defensive = antibodies
Signal
Transport = e.g. hemoglobin
Storage
Plus many more!
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(b) Levels of Protein Structure
1° structure
Linear polypeptide chain
(unique sequence of amino acids)
Determined by inherited genetic info
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2 ° structure
Proteins tend to twist or bend
H-bonds form between NH & CO groups
α-helix (coiled)or
β-pleated sheet
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Tertiary structure
Proteins continue to fold upon themselves
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Quaternary structure
Two or more polypeptide chains bonding & folding
together
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(c) Other Types of Protein Structure
Glycoprotein:Oligosaccharide + polypeptide
Lipoprotein:Lipid + protein
Both types important in cellular processes
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The Importance of Structure
Protein structure determines biological function
3D structure allows recognition & binding with specific molecular
targets”
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(d) Fibrous Proteins
Mostly 2° structure; some have quaternary structure
Insoluble in water
Structural functions:
chief building materials of body
e.g. collagen, elastin, keratin
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Tertiary or quaternary structure
Water-soluble
Chemically active
Used in all biological processes
e.g. antibodies, enzymes, protein-based hormones
Globular Proteins
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(e) Enzymes
Biological catalysts that keep metabolic & biochemical reactions happening
Decrease the amount of activation energy required for chemical rxn to proceed
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May be pure protein or may have cofactor (e.g. vitamin, metal ion)
Chemically specific– Named for type of reaction they catalyze
– Usually end in “ase”
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Some must be activated before use
Others are inactivated directly after use
All have an active site:Allows binding of substrate so that rxns can
proceed
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Why Is Protein Structure Important?
Structure dictates function
Proteins can only function if configured in specific way
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Denaturation of Proteins
Breaking of H-bonds that results in shape change
Caused by temperature, pH, foreign substances, etc.
Can’t perform physiological functions
Active site is destroyed when bonds are broken
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e.g. high fevers
• Denature proteins in body
• Proteins can no longer function
• Can result in serious damage/death
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Denaturation is usually irreversiblee.g. albumin in cooked egg can’t regain
original shape
Note: not all changes are bad—can sometimes result in variation in traits
one
way
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(4) Nucleotides
Contain C, H, O, N, P:N base, sugar, & phosphate
5 N bases:adenine, thymine, guanine, cytosine, uracil
Important in energy production, metabolism, cell signalling
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Nitrogen-Containing Bases
Purines (double-ringed)
Pyrimidines (single-ringed)
Adenine Guanine
UracilThymine Cytosine
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(a) DNA
Genetic material contained in cell nucleus(replicates itself before cell division so info in
cells is identical)
Contains deoxyribose sugar
Each species has unique base sequences somewhere in their DNA molecules
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The History of DNA
Pre-1920s scientists knew that:– Genes are responsible for variation in traits
among individuals of a species– Genes are located within chromosomes
– Chromosomes are made of DNA & proteins
BUT most researchers thought genes were made of proteins that held heritable traits
– Diverse traits from diverse molecules?
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Frederick Griffith (1928): – Tried to develop vaccine against Streptococcus
pneumoniae– Did not succeed BUT managed to transfer genetic
material from one bacterial strain to another
Oswald Avery (1940s): – DNA-digesting enzymes (NOT protein-digesting)
prevented bacterial cells from becoming pathogenic
Thus, genes are made of DNA
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Still …
How does DNA store genetic info?
The answer lies in the structure of DNA
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Polymer of nucleotides:
– Phosphate
– Deoxyribose sugar
– Nitrogen-containing base (A, C, G, T)
All nucleotides are identical except for base
DNA Structure
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What does DNA actually look like?
Clues in Chargaff’s ratios:
In any species
#A = #T
#G = #C
Differs between species
e.g. humans 30% A/T & 20% G/C
E.coli 26% A/T & 24% G/C
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Also clues in X-ray shadows:
X-ray diffraction of DNA crystals
No direct picture of DNA structure but could tell:
(a) long & thin
(b) helical
(c) repeating subunits
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Watson & Crick Model
DNA resembles ladder
Bases on each strand pair to make rungsG pairs with C
A pairs with T
Explains Chargaff’s ratios
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Also …
Ladder is twisted = double helix
Explains x-ray shadows
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Watson & Crick Model
DNA is a double helix of nucleotides
Sugar-phosphate backbone
Nucleotides held together at N bases by H bonds
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Sequence of bases in DNA codes for genetic info
Different sequences = different information
How does DNA store genetic info?
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(b) RNA
Carries out protein synthesis
Similar to DNA except:
– Single strand of nucleotides
– Ribose instead of deoxyribose
– Uracil replaces thymine
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(c) ATP
Stores & releases chemical energy for all life processes
Adenosine, ribose, 3 phosphate groups
Enzymes transfer terminal PO4- group from ATP to
other compounds so can use energy released from bonds breaking
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P
Brief Overview of How ATP Works
P P
PP
Energy via glucose
ADENOSINE
ADENOSINEenergyP
So essentially:
P energyATP ADP +
+
+