Unit 6 Flashcards
Generally speaking, what is the structure and function of DNA?
A long thin organic polymer in which the linear sequence of covalently linked nucleotide subunits encodes the genetic message
Given the structures of the four common bases, identify each as a purine or pyrimidine (or describe their general structures)
Heterocyclic compounds, aromatic character:Purines - BIG. two nitro-carbon rings, one with 6C and the other 5C. Connected to pentose by nitrogen at “bottom” of 5C ring.Pyrimidines - SMALL. one n-c 6C ring, connected to the pentose by the nitrogen at the bottom of the ring.
What are the characteristic components of a nucleotide?
1) Nitrogenous base (purine or pyrimidine)2) pentose3) one or more phosphate groups
What are the components of a nucleoside?
A molecule consisting of a nitrogenous base and a pentose. NO PHOSPHATE.
Convention: How are carbons numbered in the pentose ring of nucleotides?
Carbons are designated with ‘ or “# prime” carbon to distinguish them from the base carbons.
Nucleotide structure: Which atom in the sugar is the base attached to?
1’ C
Nucleotide structure: What bond connects the sugar and base?
N-beta-glycosyl bond.Formed from removal of H2O. Connects 1’ C to N-1 or N-9 in pyrimidines and purines, respectively.
What is general deoxyribonucleotide structure?
Nucleotide (pentose, Pi, & N base). -H group at 2’ C of pentose. Still have 5’ and 3’ -OH available to bind phosphates and other groups.
What is general ribonucleotide structure?
Nucleotide (pentose, Pi, & N base). Have -OH groups at 2’, 3’ and 5’ C.
Draw structures representing:1) a 2’-deoxynucleoside2) a 2’-deoxynucleotide3) a 2’-deoxynucleoside 5’-di- or triphosphate
1) 2’-Deoxy = no -OH at 2’ C. NucleoSIDE = pentose and base.2) 2’-Deoxy = no -OH at 2’ C. NucleoTIDE = pentose, base, and one or more Pi groups, unspecified location.3) 2’-Deoxy = n -OH at 2’ C. NucleoSIDE + 5’-di or triphosphate = 2 or 3 phosphate groups connected at 5’ C.
What characteristic defines DNA vs. RNA?
The pentose used in the nucleic bases:RNA has ribonucleotides.DNA has deoxyribonucleotides.
What are the purine bases?
Guanine and Adenine (GA, big state that makes PURE orange juice).
What are the pyrimidine bases?
Cytosine, Thymine, and Uracil. (CT is a small state with a lot of $$$).
What functional group is at the 3’ position in ribo- and deoxyribonucleotides?
- OH
Identify the atom that is found at the 2’ position in deoxyribonucleotides?
- H
In DNA and RNA nucleotides, to which atom in the sugar is the phosphate bound?
5’ C
Discuss the nucleotides found in DNA.
A, C, T, G. Never U.
Draw a section of DNA (use the letters A, C, G, and T to represent the structure of the base). Point out:a. phosphodiester linkageb. sugar-phosphate backbonec. 5’ and 3’ endsd. overall charge
DO IT.
What bond connects successive nucleotides?
Phosphodiester linkages. R-O-(PO2-)-O-R
What is the overall charge of nucleic acid polymers?
Negative, because of the negative sugar phosphate backbone.
What gives nucleic ACIDS (RNA, DNA) their acidic character?
The negatively charged backbone. The phosphate group acts as an acid much more so than the nitrogenous bases contribute basic character. They are protected on the interior of the duplex, usually.
Convention: What direction are nucleic acid sequences written in?
ALWAYS 5’ to 3’.
Distinguish between an oligonucleotide and a polynucleotide.
Oligonucleotide is short, or < 50 bases.Polynucleotides are longer than that.
Discuss the hydrogen bonds that stabilize the DNA double helix.
Aromatic and relatively hydrophobic bases line the interior of the duplex. dBs give them slightly polar character and causes them to hydrogen bond to each other’s polar groups when complementary base pairs are aligned linearly as “wrungs” in the duplex ladder.A and T bond through 2 H bonds.G and C bond through 3.Bonding pairs are always purine/pyrimidine.
Describe how Hershey and Chase showed DNA to be the genetic material.
Expt. by Hershey and Chase:- Viruses were radioactively labelled so either proteins or DNA were detectable- Cells were infected and lysed.- Lysate was centrifuged and contents of pellet (the cells) were scanned for radioactive contentOutcome:- Only the virus with radioactive label in the DNA gave a radioactive cell pellet. ** The DNA was what the virus incorporated into the host and produced the genetically mediated viral infection. Radioactive caspids were in the supernatant (not what conferred the effect in cells).
How was DNA shown to be the genetic material?
The results of experiments by Avery, MacLeod, and McCarty: a non-infectious bacterium population was injected with the DNA of an infectious strain. The non virulent strain became infectious.
Why was the base composition (Chargaff’s rules) important in suggesting a model for the structure of DNA?
Chargaff & co found that bases occurred in DNA in different proportions and that the proportions of certain bases were related. (%G = %C, %A = %T)This is supportive of the WC base pairing paradigm, where two certain bases occur jointly and therefore should compose equal proportions of the whole bp population.
What other information was crucial in the structure determination of DNA?
Franklin and Wilkins - x-ray crystallography and diffraction = helical with two periodicities (2 groove sizes)
Discuss the structure of B-form double-stranded DNA. (Point out the major and minor grooves, the sugar-phosphate backbones, and the stacked base pairs.)
Double helix formed by coiling complementary, anti parallel strands. Bases paired on interior (maintained by h-bonds and hydrophobic forces). 10.5 bp per turn = 36 Angstroms per turn and 3.4 Angstroms between bps.
Discuss the strand polarity in doublestranded DNA. What word is used to describe the polarity of the two strands?
Antiparallel.
5’ to 3’ is matched with a complementary, antiparallel strand going from 3’ to 5’.
What base pairs are found in DNA? Discuss the key difference between these two base pairs.
Always purine paired with a pyrimidine.
C-G and A-T.
CG bases interact through 3 hydrogen bonds. AT interacts through 2.
What is the position of the sugar-phosphate backbone relative to the bases in B-form DNA?
Backbone forms the outer most layer of the helix and insulates the interacting base pairs in the core of the spiraling duplex.
Do Worked Example 8-1 on base pairing in DNA:
You are given the relative Adenine base composition of two gene sequences - 0.17 and 0.32 for bacteria Y and X. What are the relative other proportions of bases in these DNA samples? What assumptions have you made? Which species is likely thermophilic?
1) Y : 0.17 A = 0.17 T = 1 - (20.17) C = 1 - (20.17) G.
X: 0.32 A = 0.32 T = 1 - (20.32) C = 1 - (20.32) G.
2) Assumed that the DNA follows normal WC base pairing rules.
3) Y, bc a larger proportion of the bps are GC, which have more hydrogen bonds and stronger annealing (more resistant to high temperatures).
Discuss the types of bonds broken during denaturation.
Breakdown of duplex structure occurs because of hydrogen bond breakdown and base stacking interactions between base pairs. No covalent bond (phosphodiester) breakage involved.
What is the melting point (tm) of a given DNA segment? What is the relationship between tm and the base composition?
Tm = temperature at which 1/2 of the DNA in the sample has been denatured. Directly proportional to proportion of the DNA that is GC base pairs.
Define annealing.
The “re-zippping” of a denatured or partially denatured piece of DNA. When unwound segments of DNA spontaneous re-wind to give the intact duplex.
Define and distinguish between DNA replication, transcription, and translation.
Replication: DNA dependent synthesis of DNA (by DNAp)
Transcription: DNA dependent synthesis of mRNA (by RNAp)
Translation: RNA dependent synthesis of a polypeptide (by ribosome + tRNA)
What is a gene? How are genes named?
Gene is any segment of DNA that codes for some biosynthetic endproduct - INCLUDES INTRONS.
Bacteria gene naming convention: three letters, lowercase and italicized that reflect gene’s apparent function.
What distinguishes a plasmid from a chromosome?
Plasmid is a small, extrachromosomal, self replicating element that is circularized. May be laterally passed and endow advantages or no change at all (common to prokaryotes).
Chromosome is a tertiary structure of DNA containing genetic information for the whole organism packed into nuclear, condensed arrangements in eukaryotes.
Is all eukaryotic DNA stored in the nucleus?
No: mitochondrial and chloroplast DNA is separate and replicates separately. Contributes to symbiotic theory for development of these energy metabolizing organelles.
