Topic 1B Flashcards
nucleotide
a constituent of nucleic acids, consisting of a 5-carbon sugar, a nitrogen-containing base, and one or more phosphate groups
explain the purposes and components of a nucleotide:
the 5-carbon sugars and phosphate forms the backbone of the molecule, the nitrogen base sticks out and gives each nucleotide its chemical identity
deoxyribose
the sugar in DNA
what happens to the hydroxyl group at cellular pH (7)?
the free hydroxyl groups become negatively charged by losing a proton (the two oxygen atoms have a negative charge)
purines
double-ring structures
pyrimidines
single-ring structures
what are the purines?
adenine (A) and guanine (G)
what are the pyrimidines?
thymine (T) and cytosine (C)
nucleoside
a molecule consisting of a 5-carbon sugar and a base
what are the nitrogen containing bases?
A, G, (purines) and T, C, (pyrimidines)
what molecule is used to form nucleotide polymers (DNA, RNA)?
nucleoside triphosphate (nucleosides-sugar+base and three phosphate groups)
phosphodiester bond
a bond that forms when a phosphate group in one nucleotide is covalently joined to the sugar unit in another nucleotide. Phosphodiester bonds are relatively stable and form the backbone of a DNA strand
polarity
an asymmetry such that one end of a structure differs from the other- caused in a strand of DNA by the phosphodiester linkages
5’ end
the end of a nucleic acid strand containing a free 5’ phosphate group (top)
3’ end
the end of a nucleic acid strand that carries a free 3’ hydroxyl (bottom)
in the double helix model, where are the components of the nucleotides located?
the sugar-phosphate backbones point wind outwards with the bases pointing inward
major groove
the larger of two uneven grooves on the outside of a DNA duplex
minor groove
the smaller of two unequal grooves to the outside of a DNA duplex
why are the grooves important?
proteins that interact with DNA often recognize a particular sequence of bases by making contact with the bases via either/both the major/minor grooves
antiparallel
oriented in opposite directions; the strands in a DNA duplex are antiparallel
complementary
describes the relationship of purine and pyrimidine bases, in which the base A pairs only with T and G pairs only with C
what explains the specificity of complementary base pairs?
hydrogen bonds (A-T has 2) and (G-C has 3)
what contributes to the stability of the DNA double helix
the total number of hydrogen bonds between base pairs and base stacking
base stacking
stabilizing hydrophobic interactions between bases in the same strand of DNA
brief explanation for how replication of DNA occurs:
strands unwind and each strand serves as a “parent” or template to create daughter strands
supercoil
a coil of coils; a circular molecule of DNA can coil upon itself to form a supercoil-seen in prokaryotes
topoisomerase
any one of a class of enzymes that regulates the supercoiling of DNA by cleaving one or both strands of the DNA double helix, and later repairing the break
how are DNA molecules shaped in eukaryotic cells?
linearly
chromosome
in eukaryotes, the physical structure in which DNA in the nucleus is packaged
chromatin
a complex of DNA, RNA, and proteins (histones) that gives chromosomes their structure; chromatin fibres are either 30 nm in diameter or, in a relaxed state, 10 nm
evolutionarily conserved
characteristics that persist relatively unchanged through diversification of a group of organisms and therefore remain similar in related species
why do histone proteins (found in all eukaryotes) interact with double-stranded DNA without regard to sequence?
because the proteins are evolutionarily conserved
the more distantly related two organisms that share conserved sequences…
the more highly conserved the sequence is
the genomes of ALL organisms are ______ relative to the size of the cell
large
describe bacterial genomes:
circular, the DNA double helix is under-wound (fewer turns in going around the circle)-caused by topoisomerase II
topoisomerase II
an enzyme that breaks a DNA double helix, rotates the ends, and seals the break
what does under-winding create on the DNA molecule
strain (relieved by formation of supercoils)
what are supercoils that result from under-winding called?
negative supercoils
what are supercoils that result from over-winding called?
positive supercoils
what kind of supercoils form in DNA in most organisms?
negative supercoils
nucleoid
in prokaryotes, a cell structure with multiple loops formed from supercoils of DNA
how is DNA packaged in eukaryotes?
the linear DNA forms a single chromosome which is packaged with histone proteins into a complex called chromatin
nucleosome
a beadlike repeating unit of histone proteins wrapped with DNA making up the 10-nm chromatin fibre
how many histone proteins are in a nucleosome
8 (2 of each-H2A, H2B, H3, and H4)
describe the components of a histone protein:
amino acids:lysine and arginine, with positive charges
10-nm fibre
a relaxed 30-nm chromatin fibre, the state of the chromatin fibre in regions of the nucleus where transcription is currently taking place
30-nm fibre
a chromosomal conformation created by the folding of the nucleosome fibre of DNA and histones
chromosome condensation
the progressive coiling of the chromatin fibre, an active, energy-consuming process requiring the participation of several types of proteins
scaffold
a supporting protein structure in a metaphase chromosome-how DNA spreads out without histones
homologous chromosomes
pairs of chromosomes, matching in size and appearance, that carry the same set of genes; one of each pair was received from the mother, the other from the father
at what stage are chromosomes in chromosome paintings?
metaphase of mitosis
karyotype
a standard arrangement of chromosomes, showing the number and shapes of the chromosomes representative of a species
Since the DNA in each pair of homologous chromosomes is different from that in any other pair of homologous chromosomes….
a particular labeled DNA fragment hybridizes (marks) only with the two homologs of one chromosomes
what is the relationship between chromosome number and genome size?
there is no relationship
because each type of organelle has its own DNA, this means that…
eukaryotic cells will have multiple genomes
nuclear genome
in eukaryotic cells, the DNA in the chromosomes
mitochondrial genome
in eukaryotic cells, the DNA in the mitochondria
chloroplast genome
in photosynthetic eukaryotes, the genome of the chloroplast
how is organelle DNA packaged?
as a nucleoid rather than a chromosome (similar to bacterial ancestors)-difference between structures of mitochondria/chloroplast nucleoid
