• West Windsor-Plainsboro High School South

• BIOLOGY 56

DNA[Types[A[Right handed; shorter form]B[Right handed form; predominant in cells]Z[Left handed; phosphate groups zigzag; lack of major and minor grooves]]Supercoiling[Positive[Formed

during replication and transcription]Negative[When DNA is least stranded]Plectonemes[Figure 8; shape taken by plasmids]Toroidal[Sequenced twists]Solendial[Occurs due to histones; most

common in eukaryotes]DNA Binding Motifs /domain: independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA. A DBD can

recognize a specific DNA sequence (a recognition sequence) or have a general affinity to DNA]Helix-turn helix[commonly found in repressor proteins and is about 20 amino acids long. In

eukaryotes, the homeodomain comprises 2 helices, one of which recognizes the DNA (aka recognition helix). They are common in proteins that regulate developmental processes]Zinc

finger[mostly found in eukaryotes, but some examples have been found in bacteria- between 23-28 amino acids long- In transcription factors these domains are often found in arrays (usually

separated by short linker sequences) and adjacent fingers are spaced at 3 basepair intervals when bound to DNA; Leucine ZipperThe basic leucine zipper (bZIP) domain is found mainly in

eukaryotes and to a limited extent in bacteria. The bZIP domain contains an alpha helix with a leucine at every 7th amino acid. If two such helices find one another, the leucines can interact as

the teeth in a zipper, allowing dimerization of two proteins. When binding to the DNA, basic amino acid residues bind to the sugar-phosphate backbone while the helices sit in the major grooves.

It regulates gene expression; Winged HelixConsisting of about 110 amino acids, the winged helix (WH) domain has four helices and a two-strand beta-sheet.; Winged Helix-turn- HelixThe winged

helix-turn-helix (wHTH) domain SCOP 46785 is typically 85-90 amino acids long. It is formed by a 3-helical bundle and a 4-strand beta-sheet (wing).; Helix loop helixThe basic helix-loop-helix

(bHLH) domain is found in some transcription factors and is characterized by two alpha helices (α-helixes) connected by a loop. One helix is typically smaller and due to the flexibility of the loop,

allows dimerization by folding and packing against another helix. The larger helix typically contains the DNA-binding regions.; HMG-boxHMG-box domains are found in high mobility group

proteins which are involved in a variety of DNA-dependent processes like replication and transcription. They also alter the flexibility of the DNA by inducing bends.The domain consists of three

alpha helices separated by loops.; Wor3 Domain Wor3 domains, named after the White–Opaque Regulator 3 (Wor3) in Candida albicans arose more recently in evolutionary time than most

previously described DNA-binding domains and are restricted to a small number of fungi; OB-fold domain The OB-fold is a small structural motif originally named for its

oligonucleotide/oligosaccharide binding properties. OB-fold domains range between 70 and 150 amino acids in length. OB-folds bind single-stranded DNA, and hence are single-stranded binding

proteins.OB-fold proteins have been identified as critical for DNA replication, DNA recombination, DNA repair, transcription, translation, cold shock response, and telomere

maintenance]Replication[Types of DNA polymerase[I[Most common form; has both 3’-5’ exonuclease activity; Processing of okazaki fragments; 95% of activity in E. coli]II[DNA repair]III[Leading

and lagging strand]alpha[primer creation]delta[lagging strand]epsilon[leading strand replication]Structure[DNA clamp consists of the beta subunit which moves along the DNA strand; alpha

subunit possesses DNA polymerase activity and the epsilon subunit possesses 3’-5’ exonuclease activity]]Prokaryotes[Initiation[DNA A loader interacts with DNAC helicase loader which recruits

DNAB helicase to unwind the strand of DNA]Elongation[DNA G primase binds to helicase to form primosome to place primer; DNA pol III does leading strand replication; DNA pol I does lagging

strand replication and some excision repair and starts at the primer and replaces RNA nucleotides with DNA nucleotides; DNA ligase links okazaki fragments together]Termination[Use of tus

protein]All 3 DNA polymerases have 3’-5’ exonuclease activity]Eukaryotes[Initiation[Cyclin dependent kinases and other proteins for the pre-replication complex; Replication initiation factors and

others combine to form the initiation complex]Elongation[Other proteins combine to form the replisome; DNA pol ε does leading strand replication and DNA pol δ does lagging strand; DNA pol α

creates primers]Termination[Formation of Ter-tus barriers]]]Transcription[Structure of gene[CAAT box[Consensus sequence for a transcription factor for RNA polymerase binding]TATA box[Start

located 25-35 before transcription start site]Pribnow box[prokaryotes; TATAAT; located 10 bases from transcription start site]] transcription factors[TFIIA[Second protein to be

recruited]TFIIF[Assembles with RNA polymerase to form the Polymerase II complex]TFIIB[Third transcription factor to be recruited]TFIID[AKA TATA binding protein; only one that leaves aft