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BSCI Exam review 4
Terms in this set (48)
Describe the features of the Watson-Crick Model of DNA
- Double helix with sugar-phosphate backbone outside
• Antiparallel strands
• Strict base-pairing of nucleotides (A:T; C:G)
• Two strands held together by hydrogen bonding between bases
Cells make two kinds of polynucleotides or nucleic acids
RNA and DNA
is a polymer of the four nucleotides A, C, G and T and uses the sugar deoxyribose.
DNA is a double helix of two polynucleotides with sugar-phosphate backbones on the outside and bases on the inside.
is a polymer of the four nucleotides A, C, G and U and uses the sugar ribose.
be either purines (A and G) , which have a double ring base or pyrimidines (C,T and U), which have a single ring base.
are oriented as anti-parallel strands meaning the polynucleotides run in opposite directions.
The bases in DNA follow
strict base pairing, meaning the bases on opposite strands interact in a very precise way: A is always paired with T, and C is always paired with G.
The double helix is held together by
hydrogen bonding between complementary bases - A:T pairs form two hydrogen bonds, while C:G pairs have three hydrogen bonds between them. These pairs can only interact in this way if one base is oriented "upside down" relative to the other - that means polynucleotide strands have to be anti-parallel, making that feature an emergent property of hydrogen bonding between base pairs!
in chromosomes in combination with proteins (chromatin). Chromosomes carry heritable information making up the genotype of an organism.
by semi-conservative replication, such that each parental strand from a double helix is used as a template to make a daughter strand along its entire length. This results in two double helices, each one having an "old" DNA strand paired with a "new" DNA strand.
involves a number of proteins that are required to unwind the double helix and make new, complementary strands.
breaks hydrogen bonds between bases
relieves torsional strain caused by helicase
makes an RNA primer
DNA polymerase III
extends the 3' end of the primer to make a new DNA strand
DNA pol I
removes the RNA primer and replaces it with DNA nucleotides
links two DNA fragments together with a covalent bond
When does DNA replication start?
at an origin of replication, where origin recognition proteins bind and begin to separate the DNA strands. A replication bubble forms, consisting of two replication forks that move away from each other in opposite directions as helicase and topoisomerase work together to unwind the parental DNA. As the replication bubble expands the new daughter strands are replicated inside the bubble using the parental strands as templates.
The fact that hydrogen bonding between polynucleotides results in antiparallel strands is the underlying cause of the difference between leading and lagging strand daughter DNA during replication.
Because DNA polymerases can only add to a 3' end, DNA pol III is always moving toward helicase and following the replication fork on the leading strand, but moving the wrong way (away from fork) on the lagging strand. Each time new template DNA is exposed along the lagging strand a new primer is made, starting a new daughter strand, resulting in a series of Okazaki fragments.
Describe the molecular composition of nucleic acids
A nucleotide has three components: a phosphate group, a sugar (ribose or in the case of DNA, deoxyribose), and a base. It is the bases that will encode information in the DNA.
The Central Dogma states
DNA is used to make RNA is used to make Protein.
The information encoding proteins is organized as genes on DNA, and all genes have the same basic structure:
A transcription start site denoted as "+1" corresponding to the first nucleotide at the 5' end of the RNA product.
A transcribed region that acts as the template for the transcribed RNA, located "downstream" of the transcription start site (base positions denoted by positive numbers).
A regulatory domain called a promoter located "upstream" of the transcription start site (base positions denoted by negative numbers).
'Directionality' in a gene is described using the terms
"upstream" and "downstream" which are relative to the direction of transcription starting at +1. Directionality is relative, depending on which strand is used as the template for a particular gene because the RNA product will be anti-parallel to the template strand.
Gene expression is
regulated by transcription factors acting as activators or repressors of RNA polymerase activity.
Basal transcription factors
bind to the promoter to recruit RNA polymerase, with their presence or absence acting as an on/off switch for transcription.
Regulatory transcription factors including both activators (positive regulation) and repressors (negative regulation)
can bind to proximal control elements upstream of the promoter, modifying transcription at different times, or in different cells.
called enhancers greatly increase transcription when bound by transcriptional activators.
For transcription, one strand of DNA
acts as a template for the production of an RNA strand by the enzyme RNA polymerase.
RNA polymerase unwinds
DNA locally and assembles complementary RNA nucleotides along the DNA template strand, linking them with phosphodiester bonds into a polynucleotide.
Like DNA polymerases,
RNA polymerases can only add to the 3'-end of the growing polymer.
Unlike DNA polymerases
RNA polymerases do not need a primer.
Process of transcription stages
Initiation, Elongation, Termination
RNA polymerase interacts with the promoter at the TATA box to establish transcription complex. RNA polymerase can directly interact with the promoter in prokaryotes, but requires basal transcription factors in eukaryotes.
the RNA polymerase extends the new RNA by adding to the 3' end.
a sequence in the DNA that halts transcription.
Transcription in eukaryotes makes
"pre-mRNA" that must be processed to mature mRNA. A 5' cap, a 3'poly A tail, and splicing are all required for maturation, and once these processes are complete the mRNA can be exported to the cytoplasm.
a protein coding sequence using codons which are translated using tRNA.
There is a different tRNA and associated enzyme for each of the 20 amino acids.
A tRNA hydrogen bonds with the proper codon on mRNA through its anti-codon using strict base pairing.
Codons represent a degenerate code, with more than one codon representing the same amino acid. By reading codons in order, a polypeptide sequence can be determined.
in the ribosome, a large multi-protein complex that interacts with mRNA and enzymatically assembles polypeptides.
Initiation of translation occurs
when the small ribosomal subunit binds to mRNA near the 5' cap and recruits the large subunit at the first 5' AUG, or start codon, positioning the first Met tRNA in the ribosomal P-site.
a charged tRNA enters the A-site. Ribosomal enzymes cut the growing polypeptide free from the P-site tRNA, and attach it to the new amino acid on the tRNA in the A-site with a peptide bond. As this happens the ribosome slides down the mRNA one codon, shifting the tRNAs over (P to E, and A to P).
The used tRNA
exits at the E site and the process repeats until a stop codon lines up with the A-site and binds to a release factor, halting translation.
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