Biochem Chap 4 Flashcards
What is a nucleoside?
only have nitrogenous base and pentose sugar - no phosphate.
What are the purines? Pyrimidines?
A and G - two rings. C, T, U - one ring.
Describe the sugar phosphate backbone
repeating pattern of sugar and phosphate groups. The phosphate group of one nucleotides creates phosphodiester bond with 3’ carbon of the pentose sugar on adjacent nucleotide. Backbone is negatively charged - attractive force between aqueous environment and DNA
5’ end - where phosphate group is bound to 5’ carbon of pentose sugar. 3’ end is where the 3’ carbon creates phosphodiester bond with adjacent nucleotide.
Describe G-C content
percentage of nucleotide bases. Determines melting point of DNA
Describe DNA replication
DNA replication starts at the origin of replication - rich in A + T. Chromosomes of eukaryotic organisms may have multiple sites.
Helicase and DNA topoisomerase begin to unzip the DNA and relax the coiling DNA. Topoisomerases help unwind the tangled cords that form by making cuts in the backbone and repairing them.
DNA polymerase adds nucleotides to new daughter strand while ligase seals the nucleotides together. DNA polymerase creates a complementary translated strand. It only works 5’-3’ DNA primase adds new primers along lagging strand and DNA polymerase uses these to create short sequences called Okazaki fragments - DNA ligase seals gaps.
DNA is replicated in a semiconservative manner.
DNA polymerase proofreads the new daughter strand. Many mistakes are resolved via proofreading. For mistakes that aren’t caught - mismatch repair occurs in G2 phase to correct any leftover errors. Uses enzymes ie. MSH2 and MLH1.
Describe Telomeres and Hayflick limit
protect and stabilize the coding regions of DNA. As they shorten, they reach the shortest length and that cell stops replication. The Hayflick limit is number of cell divisions that this point is reached.
Describe transcription
DNA → RNA. RNA polymerase creates new RNA transcript. Single-copy DNA - DNA regions that encode proteins are transcribed by RNA polymerase - in contrast to repetitive DNA - long regions of repetitive sequences that act as introns or protective sequences that do not encode any proteins. Transcription may be affected by transcription factors - proteins that bind to segment of DNA to promote or repress its transcription. RNA polymerase stops when encounters a stop sequence. If all goes well, new strand of RNA complementary to the template strand of the DNA and identical to the coding strand.
Describe translation
RNA → protein. RNA transcripts undergo posttranscriptional processing and sent out of nucleus. Translation occurs in ribosomes - binds start codon AUG.
What is degeneracy and the wobble effect?
Multiple codons code for same amino acid - degeneracy. The third nucleotide is not as important - wobble effect - non-Watson Crick base pairing that allows for weak binding between third nucleotide and anticodon.
What are retroviruses and what do they use?
Retroviruses are RNA viruses that use the enzyme reverse transcriptase to create double-stranded DNA out of the RNA they have. ie. HIV creates DNA from its RNA and splices it into host cell’s genome.
What is epigenetics? Describe the example of imprinting
Epigenetics - physical changes on DNA that amplify or silence expression of certain genes. Passed on from parent to offspring. Example: Imprinting - inherited copy of gene is silenced due to epigenetic modifications passed from parent to offspring. The silencing of one parental copy means expression relies on the other - typically occurs in gamete maturation.
What is a nucleosome?
Nucleosome - two parts - protein octamer - histone and DNA. two H2A, two H2B two H3 and 2H4. 150-200 bp wrap around each. H1 helps anchor DNA around histone. This is chromatin.
Describe acetylation
Acetylation - adding acetyl group to histones. Histone acetyltransferases (HATS) perform this. The negative DNA backbone is attracted to positive lysine residues on histones - when lysines are acetylated, they lose their positive charge - reducing interaction between DNA and histone. Their attraction is decreased, allowing enough space for RNA polymerase to access and transcribe. When histones are acetylated - gene expression increases.
Describe deacetylation
Deacetylation - performed by histone deacetylases (HDACs) - remove acetyl groups from lysine. They regain charge and interact with DNA - RNA polymerase cant access DNA. It is gene silencing.
How does cell regulate gene expression?
Targeting histones.
