Mkgrady8 Nucleic Acid Structure And Properties

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5 functions of nucleotides

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energetics, intracellular signaling, metabolism/co-enzymes, oligosaccharide structure, and genetics

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energetics

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ATP --> AMP for energy (muscular contraction etc.)

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intracellular signaling

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cyclic AMP; GDP and G-protein-coupled receptors; other functions

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metabolism/co-enzymes

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metabolism- uric acid, NADPH, coenzyme A, flavin adenine dinucleotide (FAD), pentose phosphate pathway, and others; diseases- gout, adenosine deaminase (ADA) definiciency, and Lesch0Nyhan syndrome

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genetics

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DNA structure and RNA structure

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RNA and DNA differ by

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a single oxygen but chemically this is a big difference

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RNA and DNA are called nucleic acids because

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they are most prevalent in the cellular nucleus, and they stain with basic (as in acid/base) chemical stains

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nucleic acids are polymers of

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nucleotides

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2 types of nucleic acids are

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ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)

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nucleotides are composed of

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a pentose sugar backbone, and a purine or pyrimidine base; nucleotides have 1-3 phosphate groups (PO4) attached to their 5' ends

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nucleosides are

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nucleotides that lack the phosphate groups (which are replaced with a 5' hydroxyl)

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the 5 common nucleotides

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adenosine, guanosine, cytosine, uridine, and thymidine

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adenosine

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ATP or dATP; a purine; ATP- adenosine (or deoxyadenosine) triphosphate (3 phosphates); ADP- adenosine (or deoxyadenosine) diphosphate (2 phosphates); AMP- adenosine (or deosyadenosine) monophosphate (1 phosphate)

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guanosine

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GTP of dGTP; this is a purine; guanosine (or deoxyguanosine) triphosphate; GDP, GMP, etc.

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sytosine

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CTP or dCTP; this is pyrimidine; guanosine (or deoxyguanosine) triphosphate; CDP, CMP, etc.

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uridine

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UTP; this is a pyrimidine; RNA only; UTP- uridine triphosphate; UDP, UMP, etc.

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thymidine

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dTTP; this is a pyrimidine; DNA only; dTTP- deoxythymidine (usually thymidine) triphosphate; dTDP, dTMP, etc

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DNA bases

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G, A, T, C

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RNA bases

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G, A, U, C

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common abbreviation N

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aNy nucleotide

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common abbreviation R

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puRine (A or G)

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common abbreviation Y

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pYrimidine (C, T, or U)

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RNA sometimes contains

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modified nucleotide bases- iosine, pseudouridine, and others, certain bases in transfer RNA (tRNA) are always modified, the 2' position in the ribose sugar is modified in eukaryotic mRNA capping

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DNA bases are sometimes modified by

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methylation in chromatin

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2 classes of nucleotide bases

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purines and pyrimidines

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purines

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have a double condensed ring structure; A and G; fat georgans

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pyrimidines

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have a single 6 membered ring; C, U, T

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nucleic acids are

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both RNA and DNA; long linear polymers

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directionality of nucleic acids

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5'-->3'

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standedness of DNA and RNA

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DNA is usually double stranded and RNA is usually single stranded

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the way RNA is created

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RNA is usually a copy of a DNA template

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what is the genetic material

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DNA which is found in the cell nucleus and in mitochondria

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when what is RNA

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structural (rRNA), informational (mRNA), adaptational (tRNA), or regulatory (microRNA); is found throughout the cell

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in what direction is DNA and RNA written

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most of the time they are written 5'-->3' but not always

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shorthand notations for nucleic acids- p

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stands for 5' phosphate group emphasizing phosphate backbone

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shorthand notations for nucleic acids- OH

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OH stands for 3' hydroxyl group

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shorthand notations for nucleic acids- ppp

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triphosphate remaining at 5' end, normal monophosphate backbone; 5' triphosphate is a hallmark of the 1st nucleotide of a newly synthesized RNA (or DNA) chain

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shorthand notations for nucleic acids- pG

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a guanosine mononucleotide, synonymous with "GMP"; a common product of enzymatic digestion of nucleic acids

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shorthand notations for nucleic acids- Gp

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guanine 3' phosphate; usually a product of enzymatic "nuclease" digestion; phosphate was originally on the next 3' nucleotide

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what binds with what

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G with C (triple bond) and A with T or U (double bond); so a purine always bonds with a pyrimidine

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DNA is parallel or antiparallel

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antiparallel so the strands like up like this:

5'--3'

3'--5'

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DNA structure forms what kinds of grooves

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major and minor grooves

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a single stranded RNA can form internal basepairs called

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secondary structure

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secondary structure

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regions of an RNA molecule can be complementary to other regions and these complementary regions will form intramolecular (within the same molecule) bps called secondary structure which can be critically important to an RNA molecule's function (such as tRNAs or rRNAs)

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DNA structure can be

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supercoiled or relaxed

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supercoils can be

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either negative (right handed supercoils that tend to unwind the double helix) or positive (left handed supercoils that tend to tighten the double helix); any net increase in the positive or negative supercoiling requires the input of energy in the form of ATP hydrolysis

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relaxed DNA

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has no net negative or positive supercoils; DNA that is nicked (one strand is missing a phosphodiester bond) or cut (both strands have missing phosphodiester bonds) till tend to unravel to a relaxed state

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topoisomerases are

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enzymes that wind and unwind DNA; also called gyrase (which is different from helices); bacterial topoisomerase is called gyrase; eukaryotic cells have 2 types of topoisomerases= type I and type II

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type I topoisomerase

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nicks and reseals one DNA strand at a time

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type II topoisomerase

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cuts and reseals both DNA strands at the same time

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topoisomerases require what to increase supercoiling

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ATP hydrolysis; in the absence of ATP topoisomerase will relax DNA

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another way to twist DNA is to

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wind it around a central core- this is how eukaryotic histones work

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2 drugs that affect bacterial gyrases but not eukaryotic topoisomerase are

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nalidic acid and ciprofloxacin; used in treatment of urinary tract and other bacterial infections

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DNA denaturation

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melting 2 strands apart; need high temps (body temp is too low); temp at which 50% of a particular DNA is denatured is known as Tm; or need low salt concentrations (body salt concentration is too high to allow most DNA to melt); or need low GC content (less than 25% of bps) because then there are less bonds to break- we can calculate the Tm from the GC content; this can happen relatively quickly

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DNA renaturation

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zipping 2 stands together; also called hybridization; can happen in low temps (below the Tm- at temps too much below the Tm the individual strands of DNA will often snap back on themselves and form bps within the same strand so it is no longer able to hybridize to its proper complementary strand; or higher salt concentrations (body salt); or higher GC content; need increases time for this to happen (sequences that are more frequent will renature faster than those that are less frequent

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renaturation calculation

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C0t or [initial DNA concentration] x time

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another action of RNA (what can it do)

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act as an enzyme