MM 5-6 Flashcards
What is DNA replication and when does it occur in the cell cycle?
DNA replication occurs in during S phase of interphase. Editing of DNA happens during G2 phase. It is Semi-conservative, so each copied strand of DNA has one parent strand.
Topoisomerase
Topoisomerase unwinds the supercoil during DNA replication and transcription.
Topoisomerase bind to double-stranded DNA and cut the phosphate backbone of either one or both the DNA strands. This intermediate break allows the DNA to be untangled or unwound, and, at the end of these processes, the DNA backbone is resealed again.
Helicase
Helicases are motor proteins that move directionally along a nucleic acid backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis. Many cellular processes, such as DNA replication, transcription, recombination, and DNA repair involve the separation of nucleic acid strands that necessitates the use of helicases.
Single-Strand Binding Proteins
Single-Strand Binding Proteins attach to single strands to prevent strands from re-associating.
primase
Primase makes a small RNA primer that is 5 bases long and runs complimentary to the template. This occurs because DNA polymerase cannot extend a chain from scratch. After replication, the primer is removed and replaced by DNA Polymerase.
DNA Polymerase
DNA polymerase reads in a 3-5 direction and replicates in a 5-3 direction by adding nucleotides with Watson Crick base pairing and catalyzing the phosphodiester bonds.
Proliferating Cell nuclear antigen (PCNA)
Proliferating Cell nuclear antigen (PCNA) keeps DNA polymerase bound to the template like a sliding clamp.
DNA Polymerase alpha:
DNA Polymerase alpha: involved with initiation but lacks proofreading, later replaced by sigma or epsilon.
DNA Polymerase sigma:
DNA Polymerase sigma: Lagging strand synthesis and fills gaps
DNA Polymerase epsilon
DNA Polymerase epsilon: Leading strand synthesis and fills gaps
DNA Polymerase beta:
DNA Polymerase beta: involved in DNA repair. Performs base excision repair required for DNA maintenance, replication, recombination.
DNA Polymerase gamma:
DNA Polymerase gamma: Replicates mitochondrial DNA
Okazaki fragments
segments on the lagging strand, separated by primer.
Telomeres
Telomeres (TTAGGG): thousands of repeated sequences that are synthesized and maintained by Telomerase. Telomerase exists in rapidly dividing single cells and germ line cells. It is absent in most somatic cells, so they get shorter through time
Types of DNA editing
Mismatch repair, base excision repair, nucleotide excision repair, recombination repair.
Transcription
Transcription makes RNA. Thymine is replaced with Uracil. Single stranded. Start (promoter) and stop (terminator) signals area of transcription. Occurs in nucleus and then RNA is transported through nuclear membrane to ribosomes.
rRNA
rRNA: Ribosomal RNA. Accounts for 80-90% of RNA in cells. It is produced by transcription but not translated. It plays a structural and enzymatic role in ribosomes.
tRNA
tRNA: Transfer RNA. Transcribed but not translated. Covalently bind Amino acids and transports them to ribosome.
mRNA
mRNA: Messenger RNA is translated and contains instructions for protein synthesis.
RNA Polymerase
RNA Polymerase (RNAP): Produces primary transcript RNA. Reads DNA coding (sense) strand in 3-5 direction (only). Produces RNA template (antisense) strand in 5-3 direction. Does not need primer.
sense/antisense strands
sense = template (DNA) strand antisense = coding (RNA) strand
RNAP 2
RNAP 2: makes mRNA
RNAP 1
RNAP 1: makes rRNA
RNAP 3
RNAP 3: makes tRNA
endonuclease
Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. RNA is transcribed beyond the translated region so that endonuclease has room to cleave the RNA
post-transcriptional mRNA processing
Post-transcriptional mRNA processing: The product of RNAP2 transcription, called heterogeneous RNA (hnRNA), is unfinished and unedited. Only after 5’capping, splicing, and 3’ poly(A) tailing do we have finished mRNA.
5’ Capping
5’ Capping: the 5’ end gets capped with 7-methyl-guanosine , which attracts proteins that protect the hnRNA from nucleases.
Poly(A) polymerase
Poly(A) polymerase adds sequences of adenine to the 3’ end, to which proteins bind, protecting it from rapid destruction in the cytosol so that the mRNA may be translated many times.
Differential Splicing
Differential Splicing: introns are removed by the spliceosome in collaboration with Small Nuclear RiboNucloeProteins (snRNP). Introns removed in lariat shape and exons merged. One hnRNA can make several different mRNAs depending on how it is spliced. Splice variants normally occur in different tissues. Therefore, an intron in one primary transcript may be an exon in another. This is how 30,000 genes code for 100,000 proteins.
RNA editing
Editing events may include the insertion, deletion, and base substitution of nucleotides within an RNA molecule. RNA editing also allows for different proteins being made by the same primary transcript by adding a stop codon into the sequence of the final RNA, making the amino acid sequence shorter, the protein smaller.
