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249 Cards in this Set
- Front
- Back
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Biology |
Science of life Observation/ evidence based |
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Scientific method |
Observe to generate a hypothesis Make a prediction and test by experiments Observations and experiments should be reproduceable |
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Null hypothesis |
No affect |
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Alternative hypothesis |
There is an effect |
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If null hypothesis is true |
Accept null hypothesis and reject alternative |
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Test group |
Conditions where test variable is changed |
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Control group |
Know the result Point of comparison |
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P value |
0.05 error rate |
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The cell |
Most basic unit of life |
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Prokaryotes structure |
Nucleoid Flagella Cell wall Capsule Ribosomes |
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Eukaryotic cell |
Mitochondria Nucleus Nucleolus Cell membrane Ribosomes |
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All cells |
Have a cytoplasm Cell membrane Harness energy Ribosomes Store and transmit information for growth, function and reproduction (DNA) |
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DNA |
Double stranded helix Sequence of molecules that code cells information Information can be copied from cell to cell or organism and progeny |
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Evolution |
Change over time Unity and diversity Unity-common ancestor Diversity- natural selection or artificial selection |
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Evolution example of moths |
Light peppered moth easily seen on black bark Dark pepper moth blends in so dark moth reproduces and survives |
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Artificial selection |
Breed individuals with desired traits |
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a 99.9% bacterial cleaner does not always have the same effective amount |
More resistant bacteria Bacteria reproduce resistant bacteria |
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Phylogenic tree |
Show relationship with ancestor and descendant Closely related have more common traits |
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Atom |
Makes up an element, this cannot be broken down further |
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118 elements known ? Natural? Artificial |
94 natural 24 artificial |
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Elements essential to life |
25 |
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These atoms make up 94-96%of living matter |
Carbon, hydrogen, oxygen and nitrogen |
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We have more oxygen because |
It's heavier than hydrogen We are made of 70% water |
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Trace elements |
Required in minute quantities |
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Atoms structure and location |
Protons positive Electrons negative Neutrons no charge Protons and neutrons in nucleus Electrons around nucleus |
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Atomic number |
Number of protons A specific element |
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Atomic mass |
Protons + neutrons |
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Isotopes |
Different neutrons for same element |
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Ion example sodium chloride |
Sodium loses electron to be positive Chloride gains electron to be negative |
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Horizontal row on periodic table |
Same number of shells |
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Vertical column |
Same number of electrons in outermost shell |
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Molecules |
Atoms combine by chemical bonds |
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Ability of atoms to combine with other atoms |
Determined by distribution of electrons in outermost shell |
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Chemical reaction |
Reactants are transformed into products Number of each atom remains the same Arrangements differ |
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Covalent bond |
Two atoms share valence electrons |
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How many covalent bonds can you have |
Depends on amount of unpaired valence electrons |
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Double bonds |
Atoms share two valence electrons |
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Molecule stability |
Electrons fill the outermost shell (more stable) |
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Electronegativity |
Atoms ability to attract electrons O and n can attract electrons better than c and h |
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Non polar covalent bond |
Atoms are shared equally |
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Polar covalent bond |
One atom is more electronegative the atoms do not share electrons equally resulting in partial charges |
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Polar covalent bonds in water |
Oxygen pulls electrons closer to itself |
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Hydrogen bonds |
Hydrogen is attracted to oxygen on the other water bond |
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Formaldehyde |
is a polar molecule one end is partial positive, the other is partial negative CH2O |
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Carbon dioxide |
Non polar Both ends are partial negative due to symmetry Individual bond polarities cancel each other out CO2 |
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Nacl in water |
oxygen is more electronegative than hydrogen so oxygen is partial negative and hydrogen is partial positive Oxygen pulls na+ away and hydrogen pulls cl- away Nacl is charged due to ionic bonds (see ionic bond) |
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Hydrogen bonds |
Interactions between hydrogen. And more electronegative atom on another molecule Hydrogen bonds are weaker than covalent bonds |
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DNA hydrogen bonds |
In between the nitrogenous bases |
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Hydrophilic |
Water loving Ionic or polar |
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Hydrophobic |
Afraid of water (non polar) |
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Cohesive behavior |
Water molecules stick together with other polar molecules |
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Expansion upon freezing |
Water is less dense solid |
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Ability to moderate temperature |
Water resists temperature changes In order to increase temperature hydrogen bonds must break |
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Versatility as a solvent |
Water can dissolve more materials than any other liquid |
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Cohesion in plants |
Adhesion to cell walls resists downward pull Cohesion is Evaporation of water leaves pull water upwards from roots through water conducting cells |
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When water freezes |
Forms a crystallin lattice structure with 4 other water molecules |
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Heat is released |
Hydrogen bonds form |
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Heat is absorbed |
Hydrogen bonds break |
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Sweating |
Water molecules absorb heat and evaporate cooling us of |
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pH |
Water exists as hydronium ion or hydrogen is. And hydroxide ion |
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pH formula |
pH= -log(H+) |
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Basic |
pH is above 7 |
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Acidic |
pH less than 7 |
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Neutral |
pH 7 |
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Acid |
Releases a H+ |
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Base |
Accepts H+ or releases OH- |
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pH scale is logarithmic |
1 pH is a tenfold difference in H+ Concentration |
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Buffers |
Minimizes changes in concentration of H+ and OH- Weak acid base pairing that donates or accepts H+ |
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Carbon |
Organic molecules |
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Structure is associated with |
Function |
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Carbon |
Has four unpaired valence electrons Methan four hydrogen connect producing a tetrahedron which rotates freely |
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Carbon atoms link to form |
Branched or ring structure |
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Carbon double bonds |
Share two pairs of electrons Not free to rotate Flat shape |
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Isomers |
Spatial arrangement of atoms Two molecules can have same chemical formula with different structure and function |
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Structural isomers |
Differ in covalent bond arrangements |
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Cis trans isomers |
Same covalent bond arrangements but differ in spatial arrangement due to double bonds 2 different groups |
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Enantiomers |
Mirror image Differs in shape due to chiral carbon Chiral carbon is attached to four different atoms |
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Thalomide enantiomers |
Mirror images R effective against morning sickness S causes birth and limb defect |
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Functional groups |
Group of atoms attached to carbon skeleton Involved in chemical reactions Number and arrangement gives unique properties |
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Hydroxyl |
-OH |
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Carbonyl |
C double bonded to O |
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Carboxyl |
Carbon bonded to hydroxyl and double bonded to O Acidic when h leaves |
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Amino |
NH2 accepts H becomes basic |
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Sulfhydrl |
SH |
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Phosphate |
Two double bonds to O and single bonds Negative charge H leaves making it basic |
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Methyl |
CH3 |
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Organic molecules |
Proteins, nucleic acid, carbohydrates and lipids Polymers consisting of monomers connected by covalent bonds |
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Proteins |
Polymer of amino acids |
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Nucleic acids |
Polymers of nucleotides |
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Polysaccharides |
Polymers of monosaccharides |
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Lipids |
Not a monomer |
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Limitless chemical diversity |
Macromolecules from monomers |
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Proteins |
Provide structural support and act as catalysts that facilitate chemical reactions Diverse with tens of thousands of proteins 20 amino acid monomers |
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Structure of amino acid |
Central carbon atoms Carboxyl Amino Hydrogen r group |
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Peptide bond |
Amino acids joined together Carbon to nitrogen through dehydration synthesis Carbon loses OH and nitrogen loses H |
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Nucleic acids |
DNA - genetic material RNA- for protein synthesis |
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Nucleotide structure |
Five carbon sugar Nitrogenous base One or more phosphate group |
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Bases |
Adenine and guanine are purines Thymine, cytosine and uracil are pyrimidines |
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Phosphodiester bonds |
Phosphate is joined with sugar Dehydration synthesis |
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Structure of DNA |
Two strands of nucleotides twisted in a double helix sugar and phosphate form a backbone |
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Carbohydrates |
One carbon two hydrogen one oxygen Monosaccharide is one sugar Disaccharide is two sugars Polysaccharide is many sugars |
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Monosaccharides |
Major energy source for cells Raw material for building molecules 6 carbon sugar |
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Glycosidic bonds |
Join monosaccharides |
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Starch |
Storage polysaccharide by plants for energy Made of alpha glucose below the plane of the ring |
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Cellulose |
Structural polysaccharide and major component of wall of plant cells Beta glucose above plane of the ring |
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Lactose intolerance |
People stop producing lactase |
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Lipids |
Hydrophobic Not from monomers E.g. fats phospholipids and steroids |
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Steroids |
Testosterone and estrogen |
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Fats |
Glycerol- three carbon alcohol with hydroxyl group attached to each carbon Fatty acid long chain of carbons attached to carboxyl |
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Triacylglycerol |
In Animal fat and plant oil Structure- three fatty acids and glycerol Attached by ester linkages Mostly for storage |
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Saturated fatty acids |
Max hydrogen atoms and no double bonds
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Unsaturated fatty acids |
Less than max hydrogen atoms and one or more double bonds |
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Van der waals forces |
Constant movement of electrons lead to regions of slight charge Charges attract or repel neighbouring molecules |
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DNA |
Stores genetic information for protein Plays role in transmission of information from parents to offspring to maintain identity overtime |
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Griffith experiment on genetic material step one |
Two strains of bacteria one pathogenic and one harmless He mixed killed virulent bacteria and living harmless of streptococcus pneumonia bacteria |
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Griffith experiment part two |
Some living became pathogenic Concluded that type of molecule in the debris contained genetic information for virulence |
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Transformation |
Change in genotype and phenotype due to assimilation of foreign DNA |
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Griffith experiment part three |
DNA transformed non virulent to virulent Enzyme to kill DNA was unable to transform non virulent bacteria |
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Genome |
Complete set of DNA |
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Genes |
Specific stretch of DNA that codes for protein or RNA |
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Chromosome |
In Prokaryotic is circular In eukaryotic it is called chromatin It consists of linear strands of DNA wrapped around histones forming a nucleosome |
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Histones |
Protein |
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Replication |
DNA copies itself almost exactly |
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Mutations |
Most are harmful Some are beneficial making organism better able to adapt |
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Nucleoside |
Consists of sugar and base |
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DNA |
Found by James Watson and Francis crick Five carbon sugar, base and one or more phosphate groups |
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Phosphodiester bonds |
Nucleotide sugar is linked with phosphate of neighbouring nucleotide C-O-P-O-C linkages is a phosphodiester bond |
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Polarity of DNA |
One end differs from the other phosphate negative so sugar is positive |
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DNA is read from |
Five prime to three prime |
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Base pairing rules |
Erwin chargraff %A=%T %C=%G |
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Rosalind franklin |
Helical structure of DNA |
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DNA double helix structure |
Two strands of DNA run in opposite directions Sugar and phosphate outside Bases inward Purine binds with pyrimidine |
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Purine binds with pyrimidine |
Through Hydrogen bonds |
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DNA is semi- conservative |
Two strands of DNA unwind Parental strand provides template for daughter strand |
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DNA copying |
Quick and accurate A dozen enzymes and proteins participate in DNA replication |
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Origin of replication |
Two strands of DNA are separated Opening up replication bubble Replication proceeds in both directions until entire molecule is copies |
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DNA polymerase |
Catalyzes DNA synthesis Adds to three prime Cannot make new strand |
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RNA primase |
Synthesizes RNA primer |
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Lagging strand |
Synthesizes away from replication fork |
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Leading strand |
Synthesizes toward replication fork |
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Okazaki fragments |
Discontinuous pieces of lagging strand |
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DNA polymerase |
Removes RNA primer and replaces it with DNA Proofreads it corrects an error by removing an incorrect nucleotide and inserts the correct one |
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DNA ligase |
Joins DNA fragments together |
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Helicase |
Unwinds DNA duplex at replication fork |
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Topoisomerase |
Relieves stress from unwinding by breaking, partially unwinding and reattaching DNA strand |
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Single stranded binding proteins |
Stabilize single strands of DNA |
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Lagging strand becomes shorter |
RNA primer is removed and DNA remains unreplicated Shortened template results in shorter chromosome Pattern were to persist it would be severely shortened |
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Telomere |
Consists of sequence TTAGGG repeated 1500 to 3000 times Postpone erosion of genes |
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Adult somatic cells divide 50 times |
Telomeres are shortened so cell stops dividing |
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Telomerase |
Germ and stem cells have this It prevents the chromosome ends from being shortened Contains RNA template that restores original length of telomeres |
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Somatic cancer cells |
Reactivate telomerase activity So it keeps growing |
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Scientists can |
Isolate identify and sequence DNA fragments This can help determine risk factors, identify DNA at crime scene and produce genetically engineered organisms |
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Insulin |
1. Human Gene insulin is amplified, cut and combined with bacterial DNA with a plasmid 2. Plasmid introduced into bacteria for protein production 3. Human insulin is isolated and purified from bacteria |
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Polymerase chain reaction |
Amplifies specific DNA region It needs a DNA template, DNA polymerase, primer and nucleotides |
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PCR |
1.Template is longer than amplified region 2. 20 to 30 base primers used 3. Each round doubles number of molecules 4. 2n copies 2^30= 10^9 |
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Gel electrophoresis |
Electric current passed through DNA moves to positive end Smaller moves quicker |
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Restriction enzymes |
Recognize and cleave specific sequences of DNA |
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Recombinant DNA |
Recombines DNA from two or more different sources into a single molecule uses DNA ligase |
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Transformation |
recombinant DNA introduced to bacterial cell Bacteria are chemically induced to take DNA from outside cell Bacterial cell divides and replicates Replicating recombinant DNA |
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GMOs example |
1. Sheep product human protein in milk for emphysema 2. Salmon increased hormone for rapid growth |
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DNA editing |
1.CRISPR 2. Genomic DNA can be targeted specifically for cleavage by Cas9 3. Cut DNA is altered |
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RNA and transcription RNA and transcription |
RNA is used for DNA replication, transcription and translation RNA evolves and acts as a catalyst |
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DNA |
DNA- double stranded Hydrogen on sugar A,T,C,G Deoxyribonucleic sugar Large in size Monophosphate |
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RNA |
Single stranded A,U,C,G Ribose sugar Triphosphate Smaller |
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Central dogma |
1. Transcription rewrites DNA into RNA using same nucleotide language 2. Translation switches nucleotide language to amino acid language |
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% of human genome codes for protein |
2% |
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Transcription |
1. DNA unwinds one strand as template for RNA transcript 2. T is replaced with U 3. RNA polymerase changes it It grows in five prime to three prime |
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Initiation and termination of transcription |
Eukaryotic promoters contain sequence TATAAA First nucleotide transcribed is 25 base pairs from TATA box |
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Eukaryotic promoter |
Initiation requires general transcription factors binding to promoter Transcription activator proteins bind to enhancer |
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Eukaryotic promoter |
1.RNA polymerase binds to template DNA and unwinds it 2. Looping of transcriptional activator proteins, mediator complex, RNA Polymerase and general transcription factors are brought into close proximity for transcription to proceed |
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RNA polymerase two adds nucleotides to three prime end |
1.Transcription occurs in RNA Polymerase complex 2.Two DNA strands separate and growing RNA strand forms duplex with DNA template |
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Polymerization reaction |
1. Incoming nucleotides connect if they correctly pair 2. Three prime hydroxyl of growing strand attacks high energy phosphate bond of incoming riboucleotide providing energy to drive reaction 3. Two phosphates of incoming riboucleotide released as pyrophosphate |
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RNA primary transcript |
RNA comes off DNA strand as primary transcript |
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Primary transcript |
Contains information of gene transcribed and information needed to produce protein |
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mRNA |
RNA molecule that combines with ribosome to direct protein synthesis |
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RNA processing |
Primary transcript undergoes complex process of chemical modifications |
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Poly adenylation |
The addition of 250 consecutive adenines to three prime end of mRNA This helps export mRNA into cytoplasm Protect end of transcript and stabilize RNA transcript |
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RNA processing |
The addition of five prime cap consisting of seven methylguanosince |
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RNA processing |
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RNA splicing |
Excision of introns Leaves exons 90% of human genes contain at least one intron Catalyzed by complex RNA and protein known as spliceosome |
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Alternative RNA splicing |
One primary transcript codes for multiple genes Gene formed depends on how transcript is spliced |
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Noncoding RNA |
Ribosomal RNA found in ribosomes, the site of protein synthesis Transfer RNA transports amino acids to site of protein synthesis |
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Amino acid |
consists of an alpha carbon connected by covalent bonds to amino group, carboxyl group, hydrogen and R group |
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Bonds R groups of hydrophilic amino acids form |
Hydrogen bonds |
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Basic and acidic amino acids |
Hydrophilic |
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R groups Inside? Outside? |
Hydrophobic inside Hydrophilic outside |
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Primary structure (protein) |
Amino acid sequence listed from amino end to carboxyl end This structure determines secondary and tertiary structure 20^n is number of protein sequences |
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Secondary structure |
Result of hydrogen bonding to backbone of polypeptide Two types Beta sheet Alpha helix |
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Beta sheet |
Pleated sheet that is stabilized by hydrogen bonds between carbonyl and amino group from one chain to the other |
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Alpha helix |
A coil stabilized by hydrogen bonds between amino acid's carbonyl and amino group four residuals away |
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Tertiary structure |
3D shape made of several secondary structures Determined by spatial distribution of hydrophobic and hydrophilic groups along molecule and chemical bonds and interactions between R groups |
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Tertiary structure models |
1.Ball and stick model- atoms in amino acid chain 2.Ribbon model emphasized alpha helices(twisted ribbon) and beta sheets (broad arrows) 3. Space filling model shows shape and contour of folded protein |
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Function of tertiary structure |
Contours and distribution of charge outside molecule Presence of cavities that might bind with smaller molecules inside |
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Function |
Enzymatic proteins Catalyze chemical reactions Defensive proteins Protect against disease E.g. antibodies Storage proteins Storage of amino acids E.g. ovalbumin Transport proteins Transport molecules from one place to another E.g. channel proteins and hemoglobin |
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Functions two |
Hormonal proteins Messengers that regulate bodies activities Receptor proteins Helps cells communicate with external environment through use of signaling molecules Contractile and motor proteins Responsible for movement E.g. actin and myosin Structural proteins Are fibrous and provide support |
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Denaturation of proteins |
Alterations in pH, temperature and salt concentration causes protein to unfold and lose its shape and function If optimal conditions return some proteins refold and regain functions |
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Quaternary structure |
Many tertiary structures which influences shape and function of proteins Subunits of quarternary structure can be identical or different |
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Collagen |
Composed of three identical polypeptides coiled like a rope |
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Hemoglobin |
Composed of four polypeptides, two copies of one type and two copies of a second type |
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Components of translation |
mRNA, initiation factors, elongation factors, release factors, aminoacyl trna syntases, transfer RNA, ribosomal RNA and ribosomal proteins |
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Translation |
Sequence of bases in mRNA specifies the order in which amino acids are added to synthesize a polypeptide |
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Ribosomes |
Translation takes place Coordinate functioning of mRNA and tRNA and synthesis of polypeptide |
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Ribosomes have two subunits |
Small and large Each subunit is composed of RNA and proteins Large subunit contains three binding sites for tRNAs |
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Three binding sites on large ribosome subunit |
Exit site Peptidyl site Aminoacyl site |
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Ribosome sequence |
Continuous and non overlapping groups of three nucleotides Constitute a codon Reading frame is where ribosome begins reading sequence of nucleotides |
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tRNAs |
Transfer RNA consists of a single RNA strand about 80 nucleotides long |
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tRNA |
Picks up amino acid at three prime Uses an anticodon to recognize codons in mRNA |
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Aminoacyl tRNA syntases |
Connect amino acids to tRNA molecule They are very accurate |
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tRNA |
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Base pairing |
Specifies DNA, RNA and codon anticodon interactions |
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Codon and anticodon |
Codon circled in black, anticodon circled in orange |
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Genetic code |
20 amino acids specified by 64 codons |
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Redundant |
Many amino acids specified by more than one codon |
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Unambiguous |
One codon codes for one amino acid |
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Redundant |
Wobble effect mRNA can be translated with fewer than 64 tRNAs that would be required without wobble |
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Genetic code is nearly universal |
Genes from humans can be cloned into other species and will identify the same polypeptide Useful in biotechnology and genetic engineering |
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Process of translation |
Step one Initiation Initiator AUG codon is recognized and Met is established as first amino acid in new polypeptide chain Elongation successive amino acids added to carboxyl end Termination the addition of amino acids stops and polypeptide chain is released from the ribosome |
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Initiation |
1. Initiation factors bind to five prime cap of mRNA 2.Initiation factors bring up tRNA met 3. Small subunit of ribosome is recruited 4. Complex scans for AUG codon |
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Initiation |
Large ribosomal subunit joins complex Initiation factors are released Next tRNA is ready to join ribosome |
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Initiation |
New tRNA is in place, Met detaches from tRNA and attaches by a peptide bond to the next amino acid |
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Initiation |
Ribosome shifts one codon to the right removing uncharged tRNA to E site and the other tRNA to P site freeing the A site for next charged tRNA in line to come in |
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Elongation |
Process continues in which successive amino acids are added one by one to the growing chain |
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Termination |
Process occurs until stop codon A release factors binds to A site causing the bond connecting to the polypeptide of tRNA to break this terminating translation |
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Mutations |
Change in sequence of genetic material |
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Mutagens |
Chemical increases probability of mutations |
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Mistake in transcription/translation that is not critical |
Change of one protein |
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RNA is not heritable |
Only heritable in viruses |
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Mutation rates |
Mutation is rare for individual nucleotides |
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Highest rate of mutations |
RNA viruses and retroviruses |
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Mutations in DNA replication occur in humans |
One nucleotide in every ten billion |
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Mutations affect proteins |
Affect level and timing of expression |
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Mismatch repair enzymes |
Fix any error missed by DNA polymerases |
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Mismatch repair enzymes recognize parental strand from daughter strand |
DNA methylation New DNA is not modified yet |
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Types of Mutations |
Nucleotide substitution Frameshift mutation Large scale (chromosomal mutations) |
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Nucleotide substitution is the most frequent |
DNA is mismatched e.g. T is matched with G In the next replication the nucleotide is correctly matched in the daughter strand e.g. G is matched with C |
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Point mutations |
Depends on part of genome where mutation occurs Coming or no coding region |
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Synonymous mutation |
Does not change amino acid |
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Non synonymous mutation |
Changes amino acid |
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Nonsense mutation |
Changes amino acid to stop codon that terminates translation early resulting in incomplete polypeptide |
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Sickle cell disease |
Inherited blood disorder from single nucleotide substitution in protein hemoglobin subunit beta globin Non synonymous mutation Oxygen carrying capacity is reduced Molecules crystallize into a fiber |
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Frameshift mutation |
Insertion or deletion of one or two based results in shifting of reading frame |
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Deletion of three bases |
Protein CFTR (cystic fibrosis transmembrane) caused protein to not told properly and result in cystic fibrosis |
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Transposable elements |
DNA sequences that move from one position to another in the genome Transposons insert into genes and disrupt function |
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Chromosomal level insertion/ deletions |
Duplication- region is present twice Deletion- region is missing |
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Cri-du-chat syndrome |
Deletion in chromosome Effects one out of fifty thousand |
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Inversion |
Normal order of block of genes is reversed Two breaks in chromosome is flipped before breaks are repaired |
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Reciprocal translocation |
Joins segments from different chromosomes E.g. Chronic myelogenous leukemia results from part of chromosome 22 switching with small fragment from tip of chromosome 9 |
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Lynch syndrome |
One genes of mismatch repair is inactivated through mutations More than 50% of people with Lynch syndrome develop colorectal cancer in their lifetime |
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BRCA1 BRCA2 |
Inherited Increased probability of breast and ovarian cancer in women Up to 50% of women with these gene mutations can develop breast and ovarian cancer in their lives Products of BRCA genes involved in repair of DNA damaged by xray or UV Ray |
