DNA Replication, Transcription, Translation, DNA Damage Response, DNA Repair Mechanisms, Recombination, & Cell Cycle

Flashcards covering DNA replication, transcription, translation, DNA damage response, DNA repair mechanisms, recombination, and the cell cycle.

Chargaff’s rule

Pyrimidines and purines always in same concentration, A-T and C-G, imparting complementarity for self-replication.

DNA polymerase

Enzyme that catalyzes polymerization from 5’ to 3’ during DNA replication.

DNA primase

Adds RNA primers, de novo synthesis, not processive, and lacks proofreading.

Processive enzyme

Enzyme that remains bound to a substrate during repetitions of a catalytic event.

DNA ligase

Catalyzes the formation of a phosphodiester bond between adjacent base pair nucleotides.

Sliding clamp (PCNA)

Slides with polymerase and clamps it to the DNA to maintain processivity.

Clamp loading (RFC)

Binds to the sliding clamp with ATP, cracks it open for DNA loading, and hydrolyzes ATP to close.

DNA helicase

Catalyzes strand separation, loads on the lagging strand.

Hairpins

Secondary structures within the same single strand of DNA.

Single-strand DNA binding proteins

Binds to the backbone to straighten the DNA, allowing the bases to stick out.

Topoisomerase I

Relieves coiled stress by cutting a single strand, unwinding, and resealing.

Topoisomerase II

Cuts both strands, passes a double strand through the cut, and reseals the strands.

Initiator proteins

Destabilize AT-rich sequences in the origin of replication.

Helicase-loading proteins

Loads DNA helicase at the starting point of replication.

Telomers

Contain a G-rich series of repeats and are recognized by telomerase.

Telomerase

Recognizes the tip of an existing repeat sequence and contains an RNA template for elongation.

Tautomers

Isomers that differ in the position of a proton, accompanied by a switch of a single and adjacent double bond.

Base selection

Before incorporation of a nucleotide, the polymerase recognizes the correct base and then hand closes.

Proof reading

After incorporation of a nucleotide, mismatch due to tautomers is recognized, and the polymerase backtracks.

Mismatch repair

After the replication fork, a protein cleaves the part where the wrong base is incorporated and resynthesizes the fragment.

Promotor

Specific sequence in a gene that defines the transcriptional start site (TTS).

Consensus sequence

Sequence that can change by a few nucleotides without affecting RNA polymerase binding.

BRE

B recognition element, found upstream of the transcription start site.

INR

Initiator element, located around the transcription start site.

DPE

Downstream promoter element, located downstream of the transcription start site.

Sigma factor (transcription factor)

Finds the promotor sequence and starts transcription, but unbinds after about 10 nucleotides.

RNA polymerase holoenzyme

RNA polymerase and sigma factor together in prokaryotes.

RNA pol II

Generates transcription factors (GTFs) in eukaryotes.

TFIID

TBP and TAFs together; recognizes the TATA box -30.

TBP (TATA binding protein)

Recognizes TATA box -30.

TAF (TATA-box binding protein-associated factor)

Part of the TFIID complex, binds DNA sequences near the transcription start point and regulates DNA binding by TBP.

TFIIB

Binds upstream promotor elements (BRE).

TFIIF

Stabilizes TBP and TFIIB interactions with RNA polymerase and helps localize TFIIE and TFIIH.

TFIIE

Attracts TFIIH.

TFIIH

Unwinds DNA at the transcription start site, releases RNA polymerase from the promoter.

CTD (C-terminal domain)

C-terminal domain of RPB1, consisting of multiple repeats of sequence YSPTSPS.

Promotor proximal pausing

The transition state is 25-50 nucleotides downstream of the transcription start site (TSS).

Transcriptional activators or repressors (gene regulatory factors)

Ensures gene-specific regulation of expression.

Mediator

Communication between gene regulatory proteins and RNA polymerase II/GTFs.

Topoisomerases

Remove supercoils in DNA.

Chromatin remodelling complex

Negotiates histone-packaged DNA.

Histone-modifying enzyme

Changes nucleosome binding properties.

Gene regulatory transcription factors

Recognize the base ‘codes’ in the major groove.

Zinc fingers

Binds to two spots on the same DNA strand, zinc helps stabilize the structure.

Helix-turn-helix

Two α-helices connected by a turn of a fixed angle; the biggest helix recognizes the DNA sequence.

Leucine zippers

Alpha helix with 7 amino acid repeats, hydrophobic amino acid every third or fourth position.

Combinatorial control

Combination of different proteins rather than identical proteins allow more variations in control of cellular processes.

Helix-loop-helix

Related to the leucine zipper, with a short alpha helix connected by a loop to a longer alpha helix.

Epigenetics

Biochemical features on top of the DNA sequence, modifications that alter the phenotype but not the DNA sequence.

Nucleosome

H2A-H2B and H3-H4 dimers x2, N-terminal histone tails stick out where modifications occur.

Acetylation

Opens up chromatin, on lysines, negative charge.

Methylation

Closes chromatin, gene silencing; methyl groups are added.

CpG islands

Short regions with a higher than usual frequency of the dinucleotide CpG, often found at promoters and are unmethylated.

Long range interactions

Enhancer-promoter loop model.

Cohesin

Composed of SMC3, SMC1, RAD21, SA1 or SA2, holds sister chromatids together.

CCCTC-binding factor (CTCF)

Highly conserved zinc finger protein that specifically binds to a DNA motif.

mRNA processing

Primary RNA/ precursor mRNA/ pre-mRNA is post- transcriptionally modified, mainly co-transcriptional. Facilitated by C-terminal domain of RNA pol II.

5-capping

During promoter proximal pausing, mRNA processing enzymes are being located and activated, the 5’-capping factor binds to Ser5-Pi-CTD and adds a cap (7-methylguanosine cap).

Spliceosome

5 different snRNPs (small nuclear ribonucleoprotein complexes), which catalyse splicing.

EJC (exon junction complex)

Exon junction complex, assembled to mark splicing as a quality control mark.

Alternative splicing

Different proteins from the same gene, increase of the proteome.

3’ processing

signal encoded in DNA. 3’ processing; cleavage and poly-adenylation

Cleavage and polyadenylation specificity factor (CPSF)

Binds to the AAUAAA sequence in the RNA.

Cleavage stimulation factor (CstF)

Binds to a GU-rich region downstream of AAUAAA.

Poly(A)polymerase (PAP)

Adds the poly-A tail after cleavage.

Poly-A-mRNA binding protein (PABP)

Binds to the poly-A tail after addition, to further elongate it and protect it.

Genetic code

Encoded by codons, translated in the 5’ to 3’ direction, protein synthesis N-to C terminus, forms a peptide bond.

Transfer RNA (tRNA)

Amino acid is coupled and matches with the codon to form aminoacyl-tRNA.

Aminoacyl-tRNA synthetase

Catalyses the covalent attachment of amino acid to tRNA, Determines specificity is anti-codon sequence, synthesized by RNA polymerase III

Small subunit 40S

Aligns mRNA and tRNA, reads mRNA codons, and correctly places tRNA.

Large subunit 60S

Catalyses the formation of peptide bonds.

A-site

Aminoacyl-tRNA.

P-site

Peptidyl-tRNA.

E-site

Exit.

Translation elongation factors (EFs)

Drive the reaction in the forward direction, so more efficient translation, increases the accuracy.

EF1 (eukaryotes)/ EF-Tu (prokaryotes)

Selects incoming tRNA, bends it, allows base-pairing but prevents peptide-bond formation therefore extending selection time

EF2/ EF-G

Important for translocating the ribosomal subunits.

Shine-Dalgarno consensus

Binds to 16S rRNA, an upstream ribosome binding site

Kozak-sequence

5’-ACCAUGG-3’ Surrounds start codon, helos identifying correct AUG, determines efficiency according to match, strong match increases translation initiation efficiency

Protein folding

Polar side chains on outside, hydrophobic core/ nonpolar side chains inside, Main folding determinant are the peptide back interactions, so water bridges

Chaperones

Proteins that facilitate protein folding, most of which are heat-shock proteins (Hsp).

Proteolysis

Actively destroy improperly folded proteins, The cellular destruction machine were abnormal hydrophobic patches are sent to

Proteasome

Functions as regulated gate, it recognizes, unfolds and pulls it into the core, consists of two 19S caps and one 20S cylinder

Recognition-tag

Ubiquitin (chain), is a small protein that is covalently linked to lysine residues of target proteins.

Spontaneous depurination

Losing a purine due to hydrolyses of N- glycosyl bond, so between the base and the deoxyribose sugar.

Spontaneous deamination

Losing a pyridine due to hydrolyses of bond between amino group bond and base. C-G converted into U-A, then T-A. when template can not provide right complementary base, an A is incorporated

Apurinic/ apyrimidinic (AP or abasic) site

lost of purine or pyridine creates this site.

Oxygen mediated

Reactive oxygen species (ROS) like superoxide radicals (O2) or hydroxyl radicals (-OH) directly attack DNA, leading to mispairing 8-oxo-dG – dA or dTg (thymine glycol) – dG

Aldehyde mediated

DNA crosslinks or DNA-protein crosslinks, N2-methyl dG creates

Alkylation

reactive molecules as byproducts of metabolism randomly alkylate DNA.

DNA replication errors

insertion of tautomers, strand slippage, hairpin formation at repeats by slippage leads to such genetic disfunction.

Vulnerable transcription bubbles

the single-strand coding strand is vulnerable to e.g. oxidation, deamination, G4 structures during these type of bubbles

Chemicals

environmental agents that Agents that slip between base pairs of DNA or chemical modifications of nucleotides.

Radiation

in aqueous environment cause OH and O2 radicals and Aberrant chromosome segregation, Causing mutation.

CPD

two adjacent pyrimidine, usually TT, formation of four- membered cyclobutene ring between bases due to UV light

Consequences of genome instability

Disturb RNA replication, Reduce fidelity or stops fork progression, disturb/reduce fidelity, block elongation of transciption

DNA damage signalling

Rapid sensing of DNA damage by damage-recognizing proteins leads activation of DNA damage signalling kinases by phosphorylation

MRN complex

senses double-strand breaks caused due to Instability

Ataxia telangiectasia mutated (ATM)

activated by ds- DNA breaks

ATM- and Rad3 -related (ATR) kinases

activated by ss- DNA, by lesion-stalled replication forks due to lesions