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Nucleotides

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Building blocks of DNA and RNA. Composed of bases, sugars and phosphate groups

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Nucleosides

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a base bonded to a sugar Ex. Adenosine, Guanosine, Cytidine, Thymidine (DNA), Uridine (RNA)

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Bases Types in DNA/RNA

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make up nucleotides/nucleosides, two types: Pyrimidines (CUT) Purines (AG)

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Pyrimidines

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Base type.Consists of: Cytosine (C) Uracil (U) in RNA Thymine (T) in DNA

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Purines

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Base type consisting of Adenine (A) Guanine (G)

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Sugars in Nucleotides

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Ribose and Deoxyribose Diffference is the lack or presence of oxygen on the #2 carbon always the D form of the sugar at 1 carbon and OH on is always up Beta on 1 carbon

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DNA nucleotides

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consist of a base (A,T,C,G), deoxyribose and 1-3 phosphate groups

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RNA nucleotides

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consist of a base (A,U,C,G), ribose, and 1-3 phosphate groups.

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Triphosphates

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the building blocks of DNA and RNA.

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ATP

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adenosine 5'-triphosphate nucleotide needed for RNA synthesis and also for storing metabolic energy in cells

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Glycosidic Bonds

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bonds between the sugar and base in RNA/DNA. takes place on the 1 carbon of the sugar and 1 N of pyrimidine and 9N on purine

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Nucleic acids

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linear polymers of nucleotides (polynucleotides) linked by phosphodiester bonds

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Phosphodiester Bonds

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link nucleotides together Connect the 3' carbon of one nucleotide with the 5' carbon of another

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DNA double helix

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held together by interchained hydrogen bonds involving A-T and G-C base pairs. Specific base pairing means that two DNA strands fo double helix have complementary sequences

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Base Pairing and H Bonds in RNA

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A-T base pairs have 2 H-Bonds C-G Base pairs have 3 H-Bonds

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Base Pairing in RNA

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some RNA molecules, particularly tRNA and rRNA, can have short double helical segments held together by A-U and G-C base pairing

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Prevalence of total cell RNA's

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mRNA ~2% tRNA ~16% rRNA ~82%

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Types of RNA

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messenger RNA (mRNA) ribosomal RNA (rRNA) transfer RNA (tRNA) small nuclear RNA (snRNA) and other

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Transcription

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process of RNA synthesis from a DNA template Involves, RNA polymerase enzyme which constructs RNA

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mRNA in prokaryotes vs eukaryotes

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Prokaryotes: single mRNA can code for many polypeptides,no introns.can be translated into proteins even before transcription is completed because there is no nucleus to separate all the ingredients. Eukaryotes: single mRNA encodes only 1 polypeptide. More complex. Contain exons (coding segments) and introns (non-coding) segments that must be removed. Transcription occurs in the nucleaus and translation in the cytoplasm. mature mRNA's must transport.

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Splicing

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removing introns to create mRNA that can leave nucleus and do fucntioons.

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RNA polymerase

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synthesizes RNA from DNA coding by forming the phosphodiester linkages in RNA. New nucleotides always added to the 3' end, 5' end is started.

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mRNA

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encode polypeptides, take place in transcription and translation. Encodes the protein code and transports from nucleus to cytoplasm.

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Translation

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process of protein synthesis at ribosomes in cells. Involves mRNA, ribosomes, tRNA, amino acids, and other molecules.

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Ribosomes

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composed of ribosomal RNA (rRNA) and ribosomal proteins. function is to create proteins using mRNA and tRNA

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rRNA structure

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complex secondary structure due to many short segments of A-U and G-C intrastrand hydrogen bonds

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tRNA

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transfer amino acids to the growing polypeptide chains in ribosomes. Cloverleaf structure due to short hydrogen-bonded segments.

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Acceptor stem

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3' end of of tRNA where amino acid is covalently linked

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Anticodon

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Part on the anticodon loop of the tRNA structure that binds to the codon of the mRNA that specifies the amino acid

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Nucleic Acid Primary Structure

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linear sequences of nucelotide bases along a DNA or RNA strand

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Dideoxy or Chain Termination Method

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procedure to determine the primary structure/sequence of DNA. AKA DNA sequencing uses 2',3'-dideoxynucleotides to terminate growth of DNA chains 1) denature DNA and isolate one strand 2) add primer, DNA polymerase, dNTP's (deoxynucleoside triphosphate) and ddNTP's (dideoxynucleoside triphosphates) which are fluorescently labeled. 3)DNA polymerase extends the primer by sequentially adding nucleotides that base pair with the template 4)occasional incorporation of ddNTP terminates polymerization 5) you can now read by color and size because many DNA chains differ by one nucleotide.

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2',3'-dideoxynucleotides

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aka ddNTP's lack a 3' OH group on top of a lacking 2' OH a 3'-5' phosphodiester bond cannot form therefore ending growth of DNA chain and produces a fragment

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Nucleic Acid Secondary structure

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formation of double helix by specific base pairing, A-T (or A-U) and G-C.

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B-DNA

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major form of DNA double helix of secondary structure. Right handed helix about 10 base pairs/turn. ~perpendicular Stacked .34 nm apart Repeat distance is 3.4 nm Has major/minor groove

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Major Groove/Minor Groove

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bases of a base pair are not directly across helix axis from each other creating grooves in the double helix of B-DNA

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Melting Temperature of DNA

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DNA with high G-C content (3 H-Bonds) has a higher temperature of which the strands separate/denature

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A-DNA

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formed by dehydrated DNA fibers. Similar to DNA/RNA hybrid double helices and double helical segments of RNA. Stacked at an angle to the axis due to water loss.

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Z-DNA

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synthetic DNA formed by synthetic oligonucleotides with an alternating pyrimidine purine sequence ex. GCGCGCGCGC Left Handed helix

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DNA Tertiary Structure

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Long-range, three-dimensional structure that includes supercoiling of circular DNA molecules in prokaryotes packaging of DNA into chromosomes in eukaryotes

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Supercoils

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formed in circular DNA, or linear DNA with fixed ends, if the two strands of the double helix are underwound or overwound.

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DNA Gyrase (Topoisomerase II)

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converts bacterial circular chromosomes to interwound supercoiled circles. Cuts DNA and a conformational change allows the DNA to pass through . Gyrase re-ligates the DNA and then releases it.

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Higher Order Structure of Eukaryotic DNA

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Histones interact with DNA to produce nucleosomes, Coiling of Nucleosomes into Chromatin Fibers, Folding of Chromatin Fibers into DNA loops

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Cruciform Structures

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Cruciform structure might be formed from a palindrome sequence. A inverted repeat sequence that just happens to correlate with another part of the same strand and it makes a cross.

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Palindrome Sequence

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Reads the same left to right and right to left. Causes cruciform structures

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tRNA tertiary Structure

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cloverleaf secondary structures of tRNA are folded into L-Shaped tertiary structures. helps carry out their function of protein synthesis. Acceptor stem sticks out the ]one end. Anticodon binds to mRNA also sticks but at other end.

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rRNA tertiary structure

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have many short segments of double helix which interact with numerous ribosomal proteins to form the precise 3-d structure of small and large ribosomal subunits which make up the funcitonal ribosome.

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Recombinant DNA

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refers to laboratory techniques to manipulate DNA, includes topics such as cloning vectors, cDNA's, protein expression vectors, and PCR (polymerase chain reaction)

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Cloning Vector

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DNA molecule into which foreign DNA is inserted for cloning -cloning-production of exact copy of DNA segment. Commonly used: plasmids, cosmids, bacterial artificial chromosomes (BAC's), Yeast artificial chromosomes (YAC's) 1) cut with restriction endonucleases on foreigh and using chromosome 2) heat and allow to cool slowly such that foreign DNA can base pair. 3)DNA ligase seals the gaps in DNA

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Restriction endonucleases

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useful in recombinant DNA because cut DNA at specific sequences 4-8 nucleotides. EcoRI cuts GAATTC

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DNA ligase

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puts together two pieces of DNA

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cDNA's

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DNA copies of mRNA molecules. First ADD oligonucleotide primers 1)Reverse transcriptase copies RNA into DNA used to synthesize first DNA strand 2)Ribonuclease treatment degrades mRNA strand 3)DNA polymerase synthesizes new strand

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Reverse transcriptase

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copies RNA into DNA

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Ribonuclease

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catalyzes the breaking down of RNA into smaller pieces

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Protein Expression

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vectors used to synthesize proteins including human, in E. coli bacteria and others. cDNA molecule representing the gene of interest is inserted next to a promotor and a ribosome-binding site in the vector.

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Polymerase Chain Reaction (PCR)

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an in vitro technique to greatly amplify the amount of a DNA segment. Involves multiple cycles of heating and cooling a reaction mixture that includes: 1) the DNA template, 2) oligonucleotide primers 3) deoxynucleotides 4) heat stable DNA polymerase

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oligonucleotide primers

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a synthetic, single-stranded DNA used to initiate DNA replication from a specific target sequence

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Blotting and Hybridization Methods

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allow specific DNA fragments (Southern Blotting), RNA molecules (Northern blotting), or proteins (Western Blotting) to be detected in a mixture of themselves and detected with probes (proteins-antibodies)

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Human Gene Therapy

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functional versions of defective genes are introuced into human by virus-mediated gene delivery or other techniques to correct damage caused by gene mutations 1)expression cassette-cDNA and promotor 2)Cassette incorporated into virus which can infect (DNA virus vectors, Retrovirus RNA vectors)

Biochemistry Ex1 Nucleotides, Nucleic Acids, DNA – Flashcards

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