Biochem Genome, Nuc Acids, DNA Replication (1)

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Biochem Genome, Nuc Acids, DNA Replication (1)
2013-06-15 23:16:47
MED UNC Biochemistry Genome Nucleic Acids DNA Replication

MED UNC Biochemistry Genome, Nucleic Acids, DNA Replication june 11
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  1. 5' and 3'
    1)The 5′-end (pronounced "five prime end") designates the end of the DNA or RNA strand that has the fifth carbon in the sugar-ring of the deoxyribose or ribose at its terminus. A phosphate group attached to the 5′-end permits ligation of two nucleotides, i.e., the covalent binding of a 5′-phosphate to the 3′-hydroxyl group of another nucleotide, to form a phosphodiester bond. 2)The 3′-end of a strand is so named due to it terminating at the hydroxyl group of the third carbon in the sugar-ring, and is known as the tail end. The 3′-hydroxyl is necessary in the synthesis of new nucleic acid molecules as it is ligated (joined) to the 5′-phosphate of a separate nucleotide, allowing the formation of strands of linked nucleotides.
  2. anti-parallel
    To form the base pairs, the DNA strands must be oriented with respect to each other (one goes 5’ to 3’ and the other 3’ to 5’)
  3. base pair
    adenine (A)-thymine (T) and the amount of guanine (G)-(C).These base-pairs have identical geometries, thus they “stack” over one another on the inside of the double-stranded DNA structure.
  4. chromatin
    The combination of proteins and DNA that make up a chromosome
  5. chromosome
    one molecule of double-stranded DNA associated with a variety of proteins.Bacteria-one circular.Euk-multiple
  6. complementarity
    enables DNA replication without altering info. A always pairs with T; G always pairs with C, the sequence of one strand of DNA immediately yields the sequence of the other strand
  7. diploid
    most eukaryotic organisms chromosomes exist as (nearly identical) pairs. exception: sex chromosomes- females contain two (nearly identical) X chromosomes but males contain only one X and one, quite dissimilar, Y chromosome.
  8. DNA ligase
    Okazaki fragments are joined when the intervening RNA primers are removed, replaced with DNA, and the two fragments are joined together by
  9. DNA polymerase
    enzyme that adds nucleosides to the new DNA chain. Importantly, it can add a nucleotide only to an existing 3’ OH of another polynucleotide
  10. euchromatin/heterochromatin
    1)After cell division is completed, regions with actively transcribed genes are once again partly unpacked into more loosely organized chromatin. The looser packing (still very tight) facilitates access by enzymes and other proteins that act on the DNA to carry out gene expression. 2)Regions in which genes are not being transcribed- largely retain the highly condensed structure throughout the life of the cell
  11. gene
    a segment of genome copied into an RNA molecule. Some RNA molecules direct synthesis of proteins; other RNA molecules function as RNA.
  12. genome
    total DNA of a cell. the entire set of instructions that govern the development and functioning of that individual. in multicellular, the genome is the same in every cell (w/ exceptions); however, diff cell types express diff sets of genes
  13. glycosidic bond
    The bases are attached to the (deoxy)ribose through a C1’-N bond
  14. haploid
    The germ cells (eggs and sperm) contain a single copy of each chromosome
  15. helicase
    protein uses the energy of ATP hydrolysis to break base pairs. moves along a DNA duplex, leaving two single stranded template strands behind it.
  16. histone
    compact, globular proteins with extended non-globular tails containing many positively charged amino acid side chains (Lys and Arg). The positive charge of the histones interacts with the negative charge of the DNA phosphate backbone. DNA is wrapped around the octamer twice for a total of about 150 bp.
  17. hydrogen bond
    between the bases are crucial for holding the DNA chains together. G-C pair with 3 H-bonds more stable than A-T with 2 H-bonds. DNA with total GC > AT is held together more tightly than DNA with AT > GC. Hydrogen bonds can be disrupted by high temperature or pH, or by low cation (e.g., Na+) concentration.
  18. leading/lagging strand
    1-After priming, synthesis can occur on one strand continuously in the same direction as the fork is being advanced. 2-other parental strand is oriented in the opposite sense, so the direction of synthesis must be opposite to the direction the fork is moving. It is synthesized in a discontinuous fashion.
  19. melting
    a process when high temperature separates a double helix into two single strands; also "denaturation". primarily a function of the relative frequency of A-T vs G-C base pairs (the more G-C, the higher the Tm) and the total number of uninterrupted base pairs (longer paired segment = higher Tm)
  20. nucleoside
    sugar-base molecule. exist in cells with one or more phosphates attached to the 5’ carbon to give a nucleotide (mono-phosphates, di-phosphates or tri-phosphates)
  21. nucleosome
    basic unit of chromatin structure. protein octamer containing two copies each of the H2A, H2B, H3 and H4 histone proteins. positive charge of the histones interacts with the negative charge of the DNA phosphate backbone. "beads on a string"
  22. nucleotide
    an aromatic base, a 5-carbon sugar, and a phosphate group. Two types of nucleic acids, defined by the sugar: deoxyribonucleic acid (DNA) contains deoxyribose; ribonucleic acid (RNA) contains ribose.
  23. Okazaki fragment
    A primer is laid down and initiates synthesis that continues until it meets up with the 5’ end of a primer from a previous round of synthesis. The periodic priming and discontinuous synthesis___. Are found only on the lagging strand template. Okazaki fragments are joined when the intervening RNA primers are removed, replaced with DNA, and the two fragments are joined together by DNA ligase.
  24. phosphpdiester bond
    between the 5’-OH of one (deoxy)ribose and the 3’-OH of another (deoxy)ribose
  25. primase
    uses ribose triphosphates to synthesize a short RNA chain, a primer, complementary to the template strand
  26. purine
    bases are composed of a fused five and six-member ring
  27. pyrimidine
    bases are composed of a 6-member ring
  28. replication
    Single-celled organisms must duplicate their genomes before cell division. so progeny inherit the same genetic information. Multicellular organisms must duplicate their genomes before cell division. during development, even though different cell types will express only subsets of the total genetic information. Genome replication must be exceedingly accurate (near perfect fidelity). Large genomes require insanely rapid replication rates. Biochemically, high accuracy and high speed are incompatible. Thus, replication doesn’t begin at one/few sites, proceeding through billions of base pairs. Replication begins at thousands of sites, so accurate and fast replication occur simultaneously.
  29. replication fork/ origin primer
    The point of transition between the duplex parent molecule and the two single stranded template strands is the replication fork. As progresses, the fork advances by continually unwinding the duplex DNA.
  30. replicative senescence
    A process where after many generations the chromosomes are recognized as being defective and no more cell divisions occur. prevents uncontrolled cell proliferation, the hallmark of cancer.
  31. reverse transcriptase
    The protein that carries out DNA synthesis within telomerase because it uses RNA instead of DNA as a template to synthesize DNA.
  32. ribose, deoxyribose
    RNA- a OH instead of a H in the ribose 2´ position. usually exists in single-stranded form
  33. semi-conservative replication
    The two strands of the parental DNA duplex unwind and each unwound strand serves as a template for synthesis of a new daughter strand by base pairing specificity. Thus, in each of the two resulting duplex product molecules, one strand is derived from the original parent duplex while the other is newly synthesized, i.e., 1/2 (semi) of each of the two product DNA duplexes is derived from the parental duplex (conserved).
  34. single stranded binding protein (SSB)
    Single-stranded DNA must not re-pair. DNA is coated with a protein.
  35. telomere/telomerase
    1)a short sequence repeated many times in tandem. 2)synthesizes DNA at the ends of chromosomes to prevent shortening. contains an RNA molecule that is partly complementary to the chromosome end and serves as a template for DNA synthesis.
  36. template
    sequence of DNA that is copied during the synthesis of mRNA