DNA/Nucleic Acids

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1

Deoxyribonucleic acid (DNA)

A nucleic acid, the polymer of nucleotides in which heritable genetic information of an organism is stored

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Nucleotides

The building blocks/monomers of nucleic acid polymers, there are only four types that can make up DNA -- these types are determined by the structure of their (see) nitrogenous bases
*****each nucleotide's chemical structure must contain a deoxyribose (sugar), a phosphate group and a nitrogenous base

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Deoxyribose

A ring-shaped sugar, a component of a nucleotide

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Phosphate

A phosphorus atom surrounded by four oxygen atoms, a component of a nucleotide

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Nitrogenous base

A single or double ring of carbon and nitrogen atoms with functional groups, a component of a nucleotide; four different types:
-Thymine (T) --> T+A
-Adenine (A)
-Cytosine (C) --> C+G
-Guanine (G)

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Pyrimidines

Single-ring structures of nitrogenous bases: T and C

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Purines

Larger, double-ring structures of nitrogenous bases: A and G

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Double-helix

Two strands of nucleotides wind around each other: sugar-phosphate backbones are on the outside and nitrogenous bases are on the inside, forming hydrogen bonds with their complementary base pair

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Complementary base pairs

-Pyrimidine bases pair with purine bases: A pairs with T, C pairs with G
-Though the sequence of a strand of DNA can have innumerable variations, the other strand of the double helix is dictated by the first strand and vice versa

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Plasmid

A small, circular DNA molecule of a bacterium separate from the much larger bacterial chromosome
-may carry genes that can make copies of itself (much like a chromosome), but UNLIKE chromosomes, when it replicates it can pass one copy from one bacterial cell to another --> "sharing" of genes

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Gene cloning

-Scientists can use the "sharing" quality of plasmids to make many copies of a desired gene through the reproduction of a single bacterium
**1. Remove plasmid from bacterial cell
**2. Insert desired gene (from any kind of cell) into plasmid
**3. New plasmid, with RECOMBINANT DNA (combination of old and new DNA) is put back into bacterial cell
**4. Bacterial cell reproduces as usual, but this time it is duplicating its recombinant DNA and therefore making many copies/CLONING the desired gene

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Restriction enzymes

Enzymes found in bacteria (that protect bacteria against intruding DNA from other organisms/phages) which can remove the desired gene from the much longer DNA molecule in order to clone genes:
1. these enzymes chop foreign DNA into small pieces by recognizing specific nucleotide sequences and breaking the bonds of the sugar-phosphate backbone for those particular sequences
2. make staggered cuts (not straight across double-helix), leaving single-stranded DNA hanging off the ends of the fragments... such single-stranded portions are called "sticky ends"

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Sticky end

The single-stranded portion of DNA which is the byproduct of the "staggered cutting" of double-helixes by restriction enzymes
-- it is available to bind to any sequence that is complementary to it, and is therefore useful for recombining DNA
---> complementary sticky ends of two DNA fragments can join together by base-pairing together with the help of DNA ligase... DIFFERENCE BETWEEN DNA AND POLYPEPTIDES

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DNA ligase

Another enzyme which "glues" sticky ends together in order to repair the sugar-phosphate backbone

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Polymerase chain reaction (PCR)

A technique that makes many copies of a certain segment of DNA without using living cells; can copy specific segments of DNA; DNA does not have to be purified before beginning the process; speedy; enables scientists to create copies of rare DNA

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Gel electrophoresis

A technique for sorting molecules/fragments of molecules by length in order to compare DNA samples from different sources
1. Restriction enzymes cut DNA strand (each fragment is unique because sequences are located in different places along strand)
2. A few drops of each sample are placed in small pocket/well at one end of a gel
3. Other end of gel has positive charge (all DNA molecules are negatively charged) --> they move through pores in gel toward positive pole
***shorter molecules slip more easily through pores of the gel, so after a set amount of time, shorter fragments will be closer to the positive end of the gel than the longer fragments (DNA must be treated with stain)

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Genetic markers

Particular stretches of DNA that are variable among individuals... for example, fragments can include certain alleles for diseases so by analyzing them, one can trace their family history to determine the probability of them inheriting this trait

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DNA fingerprints

A particular banding pattern produced by restriction fragments that is unique for each individual
-made by being extracted from a drop of blood or hair follicle, undergoing PCR to create multiple copies, then comparing genetic markers

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Template mechanism

Something that serves as an outline/"template" when copying genetic information/DNA

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DNA replication

The process of copying the DNA molecule:
1. Parent DNA's strands of the double helix separate
2. A complementary strand aligns to each original strand in accordance to base-pairing rules
3. Enzymes link nucleotides together
** one parent DNA molecule --> two daughter DNA molecules, each with one original strand (parent strand) and one new strand of DNA

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DNA polymerase

An enzyme that makes the covalent bonds between the nucleotides of the new DNA strand

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Origins of replication

The specific sites in which DNA replication begins