GENE3200 - DNA and Chromosomes (class 1)

DNA and RNA…

are macromolecules (very long molecules)

primary structure

the chain of many nucleotide units linked together (polymer)

repeating units of DNA and RNA

-pentose sugar

-phosphate group

-nitrogenous base

pentose sugars and phosphate groups of DNA and RNA

make up the phosphodiester backbone of polynucleotide chains

phosphate

-carries a negative charge

-always bonded to the 5’ carbon atom of the sugar

RNA vs DNA

RNA is less stable compared to DNA

nucleotide

base + deoxyribose (dN, dG, dA, dT, dC) + phosphate group

purines

adenine, guanine

pyrimidines

cytosine, thymine, uracil

one purine…

pairs with one pyrimidine to maintain the same width of dsDNA

AGTC ratios

-A to T ratio = 1

-G to C ratio = 1

-A+G = T+C

polynucleotide strands of DNA

-the two strands are antiparallel (5’ → 3’ and 3’ → 5’)

-phosphodiester bonds

-hydrogen bonds

phosphodiester bonds

between 5’-PO₄ and 3’-OH groups of adjoining nucleotides on each strand

hydrogen bonds

between complementary bases of opposite strands (intermolecular)

hydrogen bonding between complemntary nucleotides

-hydrogen bond is a weak electrostatic interaction between a hydrogen atom covalently bound to an electronegative atom (e.g, N and O) and another electronegative atom

-A-T base-pairs have 2 H-bonds

-G-C base-pairs have 3 H-bonds

H-bonds in DNA can…

separate and reform

H-bonds in DNA can separate and reform

-complementary base pairing is crucial for every process that DNA takes part in (DNA replication, chromosome pairing and recombination, repair, and transcription)

-many procedures in molecular biology and genomics are based on complementary base-pairing (hybridization)

denaturation and renaturation (reannealing)

-double-strand DNA → single-strand DNA → double-strand DNA

-melting temperature - temperature at which DNA becomes denatured

-more energy required to denature G-C base pairs than A-T base pairs

physical units of DNA

-single stranded DNA - ssDNA

-double stranded DNA - dsDNA

-1bp = 1 pair of H-bonded bases in dsDNA

-1Kbp or Kb = 1,000 bases

-1Mbp or Mb = 1,000Kb

secondary structures in ssDNA and RNA

-intramolecular hydrogen bonding - complementary base-pairing within a molecule of DNA or RNA

-know difference between a hairpin (stem-loop) and a stem

DNA double helix

-secondary structure of DNA

-two strands are antiparallel and held together by h-bonds between complementary bases

-sugar-phosphate backbone is on the outside

-base pairs are in the middle

tertiary structure of bacterial DNA

-supercoiling

-supercoiled DNA is additional winding/twisting of double-helix DNA

-topoisomerases

topoisomerase

add or remove rotations in DNA by breaking and then rejoining DNA strands

tertiary structure of eukaryotic DNA

-linear chromosomes

eukaryotic chromosomes (tertiary structure)

-consist of a double-stranded DNA helix and a diverse array of proteins (histones)

-organized as chromatin (DNA and associated proteins of a chromosome)

-protein components of chromosomes are essential for condensation, segregation, and organization of chromosomes during mitosis and meiosis

-each chromosome contains 100s-to-1000s of genes

eukaryotic chromosomes organized as chromatin

-each chromosome is approximately ½ DNA and ½ protein

-about half of the proteins are positively-charged histone proteins

-the remaining proteins, the nonhistone proteins, are very diverse and perform a variety of functions in the nucleus