Biochem 3-1 Nucleic Acid And Chromosome Structure

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nucleic acids

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nucleotides polymerized by phosphodiester bonds (RNA and DNA)

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DNA

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(A chemical) - double stranded polymers of deoxyribonucleotides

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RNA

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single stranded polymers of unmodified nucleotides

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chromosome

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(A Structure) - single molecule of DNA, often millions of base pairs long. Chromosomes contain most of a cell’s genes

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gene

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(A functional unit) - the entire DNA sequence controlling a specific trait, usually by encoding a polypeptide or functional RNA

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ribose

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a five carbon sugar that constitutes the central moiety of nucleotides; The carbons at the 3’ and 5’ positions are important for polymerization.

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bases (5)

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side groups of nucleotides. They are attached to the 1' carbon of ribose; pyrimidines and purines

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pyrimidines

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nucleotides with a base that has1 ring:
-cytosine
-uracil
-thymine

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purines

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nucleotides with a base that has 2 rings:
-adenine
-guanine

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nucleoside

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nucleotide precursor, with a base attached to the 1' carbon of ribose, without a phosphorylated 5' end.

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nucleotide (NTP)

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nucleic acid subunit, consisting of ribose with a 5' phosphorylated carbon, and a base bound to the 1' carbon. If one phosphate is added it’s called a monophosphate, two makes a diphosphate, three is a triphosphate.

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Nucleotides with _____ bonds are used as the energy currency of the cell.

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triphosphate; The form used most often for this purpose is ATP, but all four nucleotides are used by different enzymes.

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deoxynucleotide

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modified nucleotide that lacks the 2' hydroxyl group of its ribose moiety. Deoxynucleotides are used to produce DNA, while RNA consists of unmodified nucleotides
-Note, the term nucleotide refers to both the unmodified and deoxy-forms. Deoxynucleotides are simply a subclass of nucleotides

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Nucleic acids are produced by polymerizing _____ into long chains.

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nucleotides; These subunits are linked together by phosphodiester bonds between 3' hydroxyl group of one nucleotide and the 5' phosphate of an incoming nucleotide

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Free nucleotides are always added to the ___ OH of the growing chain.

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3'

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cytosine, uracil, guanine & adenine are _____

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bases

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cytidine, uridine, guanosine, & adenosine are _____

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nucleosides

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uridine monophosphate (UMP) is a _____

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nucleotide

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guanosine diphosphate (GDP) is a _____

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nucleotide

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thymidine monophosphate (TMP), is a _____

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deoxynucleotide; so are thymidine di- and triphosphate... the rest of the deoxynucleotides are named according to the scheme:
-dCDP: deoxycytadine diphosphate
-aATP: deoxyadenosine triphosphate

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A consequence of polymerization is that there is one free __ phosphate at one end and a free __ OH at the other end.

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5', 3'; all other 3' OHs and 5' phosphates are bound together.

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Polymerization requires the cleavage of the high enegy _____ bond to provide energy for the reaction.

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triphosphate

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Distinctions between RNA & DNA (4)

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1. DNA is composed of deoxynucleotides which lack 2’ hydroxyl groups. RNA is made of unmodified nucleotides, so it has 2' hydoxyls.
2. DNA has thymidine, RNA uses uridine. The only difference between the two nucleotides is thymine has a methyl group. Note, in natural cells there is no deoxyuridine, and thymidine is always in the deoxy form.
3. DNA (millions of base pairs long) is much larger than RNA ( ~50 -40,000 nucleotides long).
4. DNA forms double stranded helices, RNA exists as single strands (almost always).

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In the double helix, two nucleotides are held together by _____ bonds.

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hydrogen

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DNA length is counted in _____. RNA length is counted in _____.

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base pairs, nucleotides; RNA doesn't have nucleotides

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complimentary base pairing

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A-T, G-C`

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antiparallel conformation

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the two strands of the double helix are in opposite, 5'-3' orientations

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Denaturation, Deannealing or Melting DNA

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for double helices to dissociate into single strands due to adverse conditions such as elevated temperature

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Annealing or reannealing

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to allow denatured DNA strands to reform double helices. This is most commonly accomplished by allowing a heated solution to cool slowly.

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hybridization

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for two strands from different sources to anneal.
Examples include complimentary DNAs from different species, and RNA/DNA hybrids.

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antisense RNA

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RNA with a sequence complimentary to a DNA or RNA. Antisense RNA will form a double helix. In fact, a RNA/DNA helix is stronger than a DNA/DNA helix, and a RNA/RNA is stronger yet. The reason RNA does not normally form double helices is simply that only one strand of RNA is normally synthesized. Antisense RNA is usually made in the laboratory as a synthetic probe. However, there are rare examples in nature of antisense RNA used as a specific repressor of gene expression.

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What determines base pair specificity?

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-2 H bonds btw A-T
-3 H bonds btw C-G

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How many rings span the double helix?

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3, because purines always pair with pyrimidines

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Why are DNA and RNA negatively charged acids?

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Oxygen is negatively charged; 4 oxygens in phosphate groups of phosphodiester bonds are positioned around the outer perimeter of the double helix.

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DNA double helix B conformation

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Most common form; right handed double helix w/ 10 bp per turn. Bases are held together in core while sugar-phosphate backbones wrap around the periphery.

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major and minor grooves

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Sugar-phosphate backbones are staggered so that the space between the backbones on one side of the double helix is wide, on the other side it is narrow. The wide space is known as the major groove; the narrow span is the minor groove. This characteristic is important because factors that bind DNA such as regulatory proteins and various enzymes, usually bind in the major groove where they have greater access to the bases.

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DNA double helix A conformation

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more compact that B DNA (11 bp / turn), with more tilt to the base pairs, and a central hole between the strands. A DNA forms with DNA/RNA and RNA/RNA hybrids. It is actually more stable than B DNA.

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DNA double helix Z conformation

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left handed double helix, characteristic of regions with alternating purine, pyrimidines. Regions of Z DNA may be involved in repression of gene expression.

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Triple-helical DNA

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this forms between one polypurine and two polypyrimidine strands.

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Fnx of supercoiling

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store potential energy of double helix

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chromatin

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DNA + protein; note, all DNA is bound by protein

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heterochromatin

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Highly condensed, darkly staining chromatin.Not only are these regions more condensed, they often contain few genes and the genes they do have tend to be transcriptionally inactive, which means they are not expressed.

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euchromatin

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Less dense, lightly staining, transcriptionally active, chromatin

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histones

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proteins that form octameric complexes, which eukaryotic DNA wraps around.
Histones are the most abundant protein of chromatin. The mass of histones equals the mass of DNA.

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Histones are rich in _____ and _____, which are basic (positively charged) amino acids. This allows them to bind the negatively charged DNA.

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lysine & arginine

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T/F: histones are found in both prokaryotes and eukaryotes.

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False; eukaryotes only

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nucleosomes

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histone octamers and associated DNA, not including the linker regions.

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The DNA wraps around the surface of the octamers _____ times, in a _____ handed superhelix.

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1.75, left

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solenoids

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nucleosomes coiled around each other, forming hollow tubes.

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During interphase most of the condensed, transcriptionally inactive, _____ is believed to exist as solenoids. Much of the transcriptionally active _____ exists as uncoiled nucleosomes (beads on strings).

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heterochromatin, euchromatin

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solenoid tangling

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Chromosomal condensation during prophase also involves solenoids tangling in complex patterns to form the mitotic (or meiotic) chromosomes.

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scaffold proteins

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The second most abundant class of chromatin protein; tie solenoids together to form condensed, mitotic chromosomes and maintain supercoiling
-Topoisomerase II

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mitotic (meiotic) chromosome structure

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centromere

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- The region of a chromosome that is bound to the mitotic spindle. Centromeres are recognized as highly constricted regions of mitotic chromosomes. These are known as primary constrictions to distinguish them from the more shallow secondary constrictions of the other bands.

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metacentric

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central centromeres

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submetacentric

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off center

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acrocentric

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towards the end

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telocentric

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at the ends (don't occur in humans

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Centromeres consist of _____ sequences repeated thousands of times, end to end.

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short; centromeres have no functional genes

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arms

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divide centromeres into two regions:
-p arm: short (petite) arm
-q arm: long arm

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telomeres

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ends of chromosomes; tend to be constricted in mitotic chromosomes, and contain repetitive (GT rich) sequences with few genes (the repeat sequence for humans is AGGGTT)

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karyotypes

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number, size and banding patterns of all mitotic chromosomes

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genome

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All DNA controlling the genetics of a cellular unit. Genomic DNA of a eukaryote refers to the DNA of the nucleus. This distinguishes it from mitochondrial DNA