Structure, Function and Replication of DNA Flashcards
3´–OH terminus
End of a polynucleotide that terminates with an -OH.
Attached to 3´-carbon of the sugar
5´–P terminus
End of polynucleotide that terminates w/ a mono-, di- or
triphosphate attached to 5´-carbon of the sugar
β-N-glycosidic bond
Linkage between base and sugar of a nucleotide.
adenine
Purine base found in DNA and RNA.
A-form DNA
Not common in cellular DNA, only found in dehydrating conditions
antiparallel
Refers to opposite directional arrangement of 2 polynucleotide strands in double helix (5’ to 3’ & 3’ to 5’)
Base pairing
Attachment of one polynucleotide to another, or one part of one to another part of the same polynucleotide, by base pairs.
B-form DNA
Commonest structural conformation of the DNA double helix in living cells
Complementary
Refers to two nucleotides or nucleotide sequences that are able to base-pair with one another.
Cytosine
One of the pyrimidine bases found in DNA and RNA
Deoxyribonucleic acid (DNA)
One of two forms of nucleic acid in living cells;
genetic material for all cellular life & many viruses
Guanine
Purine nucleotide found in DNA and RNA.
Hydrogen bond
Weak electrostatic attraction between an electronegative atom (e.g. Oxygen/nitrogen) and a hydrogen atom attached to a second electronegative atom
Major groove
Larger of two grooves that spiral around the surface of the Bform of DNA.
Minor groove
Smaller of two grooves that spiral around the surface of the Bform of DNA
Monomer
One of the structural units that are joined together to form a polymer
Nucleoside
Purine/pyrimidine base attached to 5-C sugar
Nucleotide
Purine/pyrimidine base attached to 5-C sugar, to which a mono-, di-, or triphosphate is also attached. The monomeric unit of DNA and RNA.
Pentose
Sugar comprising five carbon atoms.
Phosphodiester bond
Chemical link between adjacent nucleotides in a
polynucleotide.
Polymer
Compound made up of a long chain of identical or similar units.
Polynucleotide
Single-stranded DNA or RNA molecule.
Purine/pyramidine
One of two types of nitrogenous base found in nucleotides.
Thymine
One of the pyrimidine bases found in DNA
Z-form DNA
Conformation of DNA in which the 2 polynucleotides are wound into a left-handed helix. Found naturally w/ B-DNA but only in certain regions. Unclear function.
Complex multigene family
Type of multigene family where genes have
similar nucleotide sequences, but are different enough to code for proteins w/ distinctive properties
Discontinuous gene
Gene split into exons and introns
Exon
Coding region within a discontinuous gene
Intergenic DNA
Region of genome not containing genes
Intron
Non-protein coding region within a discontinuous gene
Kilobase pair (kb)
1000 base pairs
Megabase pair (Mb)
1000kb or 1,000,000 bp
Molecular clock
Device based on inferred mutation rate enabling measure of rate at which gene sequence changes
Multigene family
Group of genes, clustered or dispersed, w/ related nucleotide sequences
Pseudogene
Inactivated and non-functional copy of a gene
Simple multigene family
Multigene family in which all genes are the same
Tandem array
Set of identical or very similar genes arranged one after the other in a group
Buoyant density
Density possessed by a molecule/particle when suspended in an aqueous salt or sugar solution
Conservative replication
Hypothetical mode of DNA replication in which one
daughter double helix is made up of the two parental polynucleotides and the other is
made up of two newly synthesized polynucleotides
Dispersive replication
Hypothetical mode of DNA replication in which both polynucleotides of each daughter double helix are made up partly of parental DNA and partly of newly synthesized DNA.
DNA topoisomerase
Enzyme that adds.takes turns from the double helix by breakage & reunion of one or both polynucleotides
Plectonemic
Helix whose strands can only be separated by unwinding
Semiconservative replication
Mode of DNA replication in which each daughter
double helix is made up of one polynucleotide from the parent and one newly synthesized polynucleotide
Type I topoisomerase
Topoisomerase that makes a single-stranded break in a double-stranded DNA molecule
Type II topoisomerase
Topoisomerase that makes a double-stranded break in a double-stranded DNA molecule.
3´→5´ exonuclease
Enzyme that sequentially removes nucleotides in 3´→5´direction from end of a nucleic acid molecule
5´→3´ exonuclease
Enzyme that sequentially removes nucleotides in 5´→3´direction from the end of a nucleic acid molecule
DNA polymerase III
Main prokaryotic DNA replicating enzyme
DNA polymerase α
Enzyme that primes DNA replication in eukaryotes
DNA polymerase δ
Main eukaryotic DNA replicating enzyme
DNA-dependent DNA polymerase
Enzyme that makes a DNA copy of a DNA
template.
Leading strand
Strand of double helix which is copied in a continuous fashion during genome replication.
Primase
RNA polymerase enzyme that synthesizes RNA primers during bacterial DNA replication.
Replication fork
Region of a double-stranded DNA molecule that is being opened up for DNA replication to occur
Single-strand binding protein (SSB)
One of the proteins that attach to single-stranded
DNA in region of replication fork, preventing base pairs forming between the two parent strands before they have been copied.
Adenine full name
2’ -deoxyadenosine 5’ -triphosphate dATP
Guanine full name
2´-deoxyguanosine 5´-triphosphate dGTP
Cytosine full name
2’ -deoxycytidine 5’ -triphosphate dCTP
Thymine full name
2’ - deoxythymidine 5’ -triphosphate dTTP
Example of structural proteins
Collagen
Keratin
Motor proteins
Myosin, dynenin
Catalytic proteins
Hexokinase
DNA polymerase
Transport proteins
Hemoglobin
Serum albumin
Storage proteins
Ovalbumin
Ferritin
Protective proteins
Immunoglobulins
Thrombin
Regulatory proteins
Insulin
Somatostatin
Somatotrophin
Primer for DNA synthesis in prokaryotes
- Made of RNA by primase enzyme
- Is 4-15 nucleotides in length
- DNA pol III makes strand once primer is made
Primer for DNA synthesis in eukaryotes
- Made of RNA by primase but first extended by DNA pol alpha
- DNA pol alpha adds about 20 nucleotides
- DNA pol delta then makes the rest of the strand
DNA ligase
Enzyme that synthesizes phosphodiester bonds in DNA replication, repair & recombination processes.
DNA polymerase I
Bacterial enzyme which completes synthesis of okazaki fragments during genome replication of the lagging strand
Lagging strand
Strand of the double helix which is copied in a discontinuous fashion during genome replication
FEN1
The ‘flap endonuclease’ involved in replication of the lagging strand in eukaryotes
Telomerase
Enzyme that maintains ends of eukaryote chromosomes by synthesizing telomeric repeats
What are the 5 types of histones associated with DNA?
H1 H2A H2B H3 H4
Gamma-complex
Multisubunit bacterial protein that attaches and detaches DNA
pol. III during copying of the lagging strand
Helicase
Enzyme that breaks base pairs in double-stranded DNA.
Origin of replication
Site on DNA where replication initiates
Prepriming complex
Protein compex including the DnaB helicase which triggers construction of a replication fork on bacterial DNA.
Primosome
Protein complex including DnaB helicase and primase involved initiation of DNA replication in bacteria.
Proliferating cell nuclear antigen (PCNA)
Accessory protein involved in DNA replication in eukaryotes, whose function is to hold DNA polymerase delta tightly to DNA.
Terminator sequence
One of several sequences on a bacterial genome involved in termination of genome replication.
Tus
Protein that binds to a bacterial terminator sequence and mediates termination of genome replication.
30nm chromatin fibre
Relatively unpacked form of chromatin made of a possibly helical array of nucleosomes in a fibre approximately 30nm in diameter, beads on a string.
Beads-on-a-string
Unpacked form of chromatin consisting of nucleosome beads on a string of DNA
Centromere
Constricted region of chromosome that is the position at which the pair of chromatids are held together.
Chromatid
Arm of chromosome
Chromatin
Complex of DNA and histone proteins found in chromosomes
Chromatosome
Subcomponent of chromatin made up of a nucleosome core octamer with associated DNA and a linker histone.
Constitutive heterochromatin
Chromatin that is permanently in a compact organisation
Core octamer
Central component of a nucleosome, made up of two subunits each of histones H2A, H2B, H3 and H4, around which DNA is wound.
Euchromatin
Regions of a eukaryotic chromosome that are sparse and likely to contain active genes.
Facultative heterochromatin
Chromatin that has a dense, compact organization in some cells,, thought to contain genes that are inactive in some cells or at some periods of the cell cycle.
Heterochromatin
Chromatin that is relatively condensed and is thought to contain DNA that is not being transcribed.
Histone
Basic protein found in nucleosomes
Interphase
Period between cell divisions
Karyogram
Entire chromosome complement of a cell, with each chromosome described in terms of its appearance at metaphase.
Linker DNA
DNA that links nucleosomes: ‘string’ in ‘beads-on-a-string’ model for chromatin structure
Linker histone
Histone (like H1) that is located outside of the nucleosome core octamer
Metaphase chromosome
Chromosome during metaphase, when chromatin takes on most condensed structure and features (like banding pattern) can be visualized
Nuclear matrix
Proteinaceous scaffold-like network that permeates the cell
Nuclease protection experiment
Technique that uses nuclease digestion to determine the positions of proteins on DNA or RNA molecules
Nucleosome
Complex of histones and DNA that is the basic structural unit in chromatin
Telomere
End of a eukaryotic chromosome
Joining okazaki fragments in prokaryotes
DNA pol III stops at RNA primer of fragment and is replaced by DNA pol I. DNA ligase joins fragments with phosphodiester bond.
Joining okazaki fragments in eukaryotes
DNA pol delta stops at RNA primer. Helicase and DNA pol delta lift up primer as flap. FEN1 cuts it off. Ligase joins fragments.
DnaA
Protein involved in genome replication. DNA winds around it, base pair at origin of replication break as a result
DnaB
Helicase, whose addition to origin of replication forms prepriming complex
Primosome
Formed when two primase enzymes are added to prepriming complex
Enhancer
Sequence of DNA containing regulatory information
What accessory factor recruits RNA pol II to the promoter?
TTIID
TATA
Promoter sequence in RNA polymerase II initiation complex
TBP
Binding protein in RNA polymerase II initiation complex.
Interacts with minor groove of DNA.
Attracts TFIIA and TFIIB.
Similar sequence to sigma factor in prokaryotes.
TAFs
TBP-associated factors.
Interact with TBP and DNA
TFIIA
Helps TFIID bind
TFIIB
Sets distance from TATA element to start site
What makes up TFIID
TATA
TBP
TAFs
