Chapter 14-17 Flashcards
What’s the structure of a nucleotide?
-phosphate group, sugar (pentose), and nitrogenous base
What’s a nucleoside of a nucleotide?
The nitrogenous base and the sugar
How do ribonucleotides and deoxyribonucleotides differ?
-The sugar in ribonucleotides is ribose
-The sugar in deoxyribonucleotides
-Their 2’ carbon substituents are different
describe the structure of a polynucleotide? Mention phosphodiester bond and sugar-phosphate backbone. Can you describe how a polynucleotide has a 5’ to 3’ orientation?
-made up of a chain of nucleoside triphosphates (or nucleotides), held together by phosphodiester bonds: the phosphate of one nucleotide covalently bonds to the sugar of another
-each end of the polynucleotide is different: 5’ is phosphate, and 3’ is -OH and nucleic acid codes are always read from 5’ to 3’
Can you describe complementary base pairing in nucleic acids? Mention the type of bond involved and how many bonds are between each base pair.
-Complementary base pairing is the pairing between the nitrogenous bases of two polynucleotides (DNA) with the association being between a pyrimidine (C,T,U) and a purine (G,A)
-This is linked together by hydrogen bonds
-C is with G: 3 H-bonds
-A is with T: 2 H-bonds
Can you describe the levels of structure in RNA (up to quaternary structure)?
1)Primary structure: the sequence in which the bases (U, A, C, G) are aligned.
2)Secondary structure: the 2-D analysis of the [hydrogen] bonds between different parts of RNA. In other words, where RNA becomes double-stranded (tRNA, and
3)tertiary structure is defined as the three-dimensional arrangement of RNA building blocks, which include helical duplexes, triple-stranded structures
4)Quaternary structure arises from the association of multiple macromolecular chains
What are the characteristics of DNA that allows it to act as genetic material? What are the types of information that is stored in DNA?
1) Its capability for replication
2) Its semiconservative
3) It stores information, transfers it and expresses genetic information
- genetic information, nucleic acids hold the instructions for protein synthesis,
What are ribozymes? What reactions do rRNA and spliceosomes catalyze?
-specific folding of RNA allows them to have specific functions such as ribozymes
-rRNA catalyzes peptide bond formation
-certain ribozymes called spliceosomes catalyze reactions during RNA splicing
Which bases are
purines? Pyrimidines?
pyrimidine = (C,T,U)
and a purine = (G,A)
What are some of the many functions of RNA? (4 specific examples) Why is RNA capable of producing many functional classes?
-mRNA: used to make a protein (recognizes amino acid sequence)
-tRNA: facilitates translation during protein synthesis
-Spliceosomes: catalyze the reactions during RNA splicing
-rRNA: catalyzes peptide bond formation
-They’re capable of these different functions because of the 4 levels of structure
Compare coding vs. non-coding RNAs.
1) Coding RNAs generally refers to mRNA that encodes protein to act as various components including enzymes, cell structures, and signal transductors.
2) Noncoding = cellular regulators
What is Chargaff’s Rule? How did Watson, Crick and Franklin’s discovery of the double-stranded
nature of DNA explain the rule?
-A & T always have same % because they’re paired together
-G & C have the same % for the same reason
-The uniform diameter of the double helix suggests that purines must be paired with pyrimidines
What was Rosalind Franklin’s experiment and what did it show them?
-An X-ray diffraction photo of DNA was produced and it showed;
1) DNA has a helical shape
2) The width of the helix
3) the spacing of the nitrogenous bases
What is the process of replication?
-It’s the process of copying a double-stranded piece of DNA in a cell prior to cell division?
Why is DNA semi-conservative?
because one of the old strands form the original piece of DNA can be used as a template for the new strand of DNA
Can you describe the experimental design (4 steps), and results obtained for the Meselson-Stahl experiment (the bacterial experiment with N14 & N15) in 1958? Explain how the results contributed to our understanding of the mechanism of DNA replication
-Experimental design:
1) bacteria cultured in medium with N15 isotope
2) bacteria transferred to medium with N14 isotope
3) DNA sample centrifuged after first replication
4) DNA sample centrifuged after second replication
-Results: parent cell made two daughter cells that had one strand from the parent, then each of these daughter cells made two each, 2 of which were completely new and the other two contained DNA from the daughter cell
-Explains the semi-conservative properties of DNA replication
What are the steps in DNA polymerization in Prokaryotes?
1) replication begins at sites called origins of replication
2) proteins recognize the strand of origins of replication and attach to the DNA splitting the two strands which create a replication bubble
3) parent DNA copied in both directions from origin at same time until whole chromosome is replicated
What are the building blocks used in prokaryotic DNA polymerization?
1) Origin of replication (DNA sequence that starts replication)
2) Replication Fork: exists at each end of the replication bubble (2 replication forks)
3) Replication Factory: contains 12 enzymes and other proteins
4) DNA polymerase III and I
What are the enzymes used by the replication factory (in order of use)? (8)
1)Helicase
2)SSBP
3)Topoisomerase
4)Primase
5)DNA polymerase III
6)Rnase H
7)DNA polymerase I
8)DNA ligase
What are the steps of the replication factory in prokaryotes and what does it do? (6 steps)
1) Helicase unzips the strands at the origin and SSBP adheres to separated strands to prevent annealing
2) Tension is released by using Topoisomerase to break, swivel and rejoin DNA strands
3) Primase synthesizes a primer (short chain of RNA) and DNA Polymerase catalyzes the polymerization of DNA nucleotides
4) DNA polymerase III adds complementary DNA nucleotides to the free 3’ end of strand (elongated from 5’ to 3’) & a sliding clamp makes sure the polymerase stays in contact with the template strand
5) Rnase H degrades RNA primer by hydrolyzing its phosphodiester bonds & DNA pol I adds nucleotides to any exposed 3’ ends (leading and lagging)
6) DNA ligase glues fragments of DNA on the new strand to make a continuous polynucleotide strand
What are the 5 main differences between Prokaryotic and Eukaryotic DNA replication?
1) Eukaryotes have linear chromosomes (prokaryotes = circular)
2) Eukaryotes have many origins of replication per chromosome (prokaryotes have one)
3) Eukaryotes have over 11 different polymerases (prokaryotes have pol III and pol I)
4) Both have okazaki fragments but they’re present for longer in prokaryotes because they have less base pairs than eukaryotes
5) Eukaryotes require telomeres to protect the ends of their strands
What are telomeres?
short repeated DNA sequences (TTAGGG)
What happens to telomeres after each replication event?
They get shorter and shorter as we get older and more replication events occur because they act as a buffer to prevent erosion (not completely)
What are the 2 protective functions of telomeres?
1) prevent the activation of DNA damage
2) provide some protection against the organism’s genes shortening
What is the function of a telomerase enzyme in eukaryotes and where are they found?
function:
-they extend the length of telomeres
found in:
-germ cells
-cells within embryos/fetuses
-certain tumor cells
How is telomerase implicated in the difference between replication in somatic cells versus germ line cells?
normal shortening of telomeres may protect organisms from cancer by limiting the number of divisions that somatic cells can undergo
How is the copying of DNA so remarkable in its speed and accuracy? (list 3 reasons)
1) the high specificity of base pairing
2) DNA polymerases proofreading and error checking mechanisms
3) Other enzymes can fix missed errors
How can DNA pol fix “wrong” nucleotides?
It has exonuclease abilities meaning it can cleave off nucleotides and replace them with the correct nucleotide
What are 5 things that can damage DNA? (RRXUO)
1) reactive chemicals
2) radioactivity
3) x-rays
4) UV light
5) other harmful toxins (i.e. mycotoxins, asbestos, nanoparticles)
Which enzymes repair external damage and repair mismatched nucleotides? (3)
1) Nuclease enzyme
2) DNA pol
3) DNA ligase
How do we know which strand has the right sequence?
The parent strand is methylated (daughter DNA isn’t)
What are the 4 steps of DNA excision repair?
1) mismatched base pairs detected by enzymes
2) nuclease enzyme cuts damaged strand at 2 points releasing the damaged section
3) DNA pol places correct nucleotides in the gap
4) Ligase seals the nucleotides together
How does UV light damage DNA in skin cells?
UV covalently cross links two adjacent pyrimidines distorting the DNA molecule (this creates Pyrimidine dimers)
What is the disease XP and what is it caused by?
it’s an inherited disease that causes hypersensitivity to light and it’s caused by a defect in nucleotide excision repair mechanism
What are 3 forms of chromosome coils?
1) loop domain structure
2) loop anchor
3) double helix
Why is it important that chromosomes coil?
So that nothing fragments off during replication
What is the complex of DNA and proteins called?
Chromatin
What is a nucleosome?
It’s a basic unit of DNA packaging, unfolded chromatin if you will (beads on a string separated by linker DNA)
How does DNA change as it’s packaged and moved around the cell?
1) DNA double helix
2) Histones (proteins with positively charged amino acids) coil the double stranded DNA (1st level of packaging)
3) Nucleosomes (unfolded chromatin) present during interphase
4) Fibers: folding of nucleosomes that allow for interactions between histone tails and linker DNA (present during interphase)
5) Looped domains: Folding of the fibers (also fold during replication)
What diameter of chromatid (2 chromatids make a chromosome) is most appropriate for cell division?
700 nm (metaphase)
Why are even higher levels of DNA packaging are achieved in cells? and when are they achieved? (IPM - phases)
-The entire DNA strand must fit within the nucleus of a cell, so it must be very tightly packaged to fit
-Interphase: highly extended
-Prophase: chromatin coils/folds (condenses)
-Metaphase: short and thick chromosomes
