DNA Flashcards
DNA is a polymer of ________ and stands for __________?
Nucleotides, deoxyribonucleic acid
List the three components of DNA and what they are responsible for
phosphate backbone - acidity, stabilization
deoxyribose sugar (5 carbons = pentose monosaccharide) (carbohydrate) - stability, as the sugar can’t undergo alkaline hydrolysis
nitrogenous base - purine or pyrimidine containing nitrogen. The sequence of the bases determines genetic code.
Nucleoside?
Pentose sugar + nitrogenous base
Nucleotide?
Phosphate + pentose sugar + nitrogenous base
State the structural difference between DNA and RNA’s ribose sugars
DNA will NOT have a hydroxyl group on the 2nd carbon hence deoxy, will also have thymine as a base.
RNA will have this hydroxyl, will have uracil as a base.
Purines
2 ringed structure of a nitrogenous base. Adenine and guanine.
Pyrimidines
1 ring structure of a nitrogenous base. Cytosine and thymine.
DNA helix properties
Double stranded, hydrophobic bases in center, hydrophilic phosphate heads on outside. Hydrophobic bases interact with hydrogen bonds.
DNA: ______ (base) always pairs with ________ (base) via 2 hydrogen bonds
Adenine + thymine
DNA: ______ (base) always pairs with ________ (base) via 3 hydrogen bonds
cytosine + guanine
RNA: ______ (base) always pairs with ________ (base) via 2 hydrogen bonds
Adenine + uracil
Chargaff’s Rules
Purines : Pyrimidines = 1:1 (A+G = C+T)
Percent composition w/in purines and pyrimidines should be same: (purines: %A = %G and pyrimidines: %T = %C)
When attached to a ribose sugar, what happens to the base names?
Add suffix “-osine” (purine) or suffix “-idine”
When attached to a deoxyribose sugar, what happens to the base names?
The prefix “deoxy-“ is added to the nucleoside
DNA replication is semi-conservative, explain.
Each strand unzips and acts as a template for a new strand. For each strand unzipped a new strand will be synthesized.
Define the terms bidirectional and anti-parallel
Bidirectional: DNA replication originates at a specific site within the DNA (origin) and creates a replication bubble (the DNA is replicated in both directions) of two replication forks
Anti-parallel: 5’ phosphate is always opposite the 3’ hydroxyl
Helicase
Enzyme that breaks the hydrogen bonds between nitrogenous bases of the template DNA. Unwinds the DNA.
Topoisomerase
Works ahead of the replication fork to combat torsional forces by hacking and cleaving the DNA preventing supercoiling. If topoisomerase did not do this, the coiling would be too tight for polymerase to act.
Single-stranded binding proteins!
After helicase breaks the hydrogen bonds the SSBPs bind to the strands to prevent annealing, to stabilize and maintain the single-stranded DNA template.
Primase
Lays down complementary RNA primers which are used in the process of extending the DNA. DNA cannot be created from nothing so primers are needed.
What bond links the phosphates of the 5th carbon of the deoxyribose sugar to the following nucleotide? (think, building up!)
Phosphodiester bond links the phosphate backbone together. Phosphates on the 5th carbon are linked to where the 3’ hydroxyl used to be. Phosphodiester bonds are created by the addition of the 5’ phosphate of a dNTP molecule to the 3’ hydroxyl group.
Replication occurs in what direction?`
5’ to 3’.
Replication from the RNA primer can occur as the helicase unwinds the DNA CONTINUOUSLY on which strand? Which enzyme replicates this strand?
Leading strand is replicated by DNA Polymerase 3 in E. coli
On which strand are multiple primers necessary for replication? What are the fragments of replicated DNA called and which enzyme synthesizes them?
Lagging strand is replicated by DNA Polymerase 1 in E coli. The fragments of synthesized DNA are called Okazaki fragments
In a replication bubble, the leading and lagging strands are switched for the two opposite replication forks. Why is this possible?
Helicase travels in opposite directions.
How are RNA primers degraded?
Enzymatically degraded by RNases, endonucleases, or the proofreading function of DNA Pol 1.
What are RNA primers replaced with and how are the replaced?
Replaced with new complementary DNA BASES by extending the Okazaki fragments using DNA Pol.
DNA ligase
Repairs the phosphate backbone through the use of a phosphodiester bond at the nick
Why does a lack of an Okazaki fragment for extension at the end of the chromosome create issues? What is this term known as?
Creates an overhang of single-stranded DNA which will be lost in one of the daughter cells because the other template strand will miss this information during further replication. Known as chromosome shortening.
What are the functions of telomeres?
Prevent chromosome shortening. A repetitive nucleotide sequence is added in tandem (called a telomere) and provides a disposable buffer at the ends of chromosomes.
What process causes telomere shortening? Which enzyme can replenish telomeres and how does it accomplish this?
Cell division. Telomerase can replenish telomeres using it’s own RNA template for the replication and extension of telomeres.
Telomere shortening is thought to be the cause of what?
Senescence (cellular ageing) where cells have a limit to the number of times they can divide.
