BIOMG 3300: Principles of Biochemistry -Unit 6 Flashcards
Given the structure of the four common bases, identify each as a purine or pyrimidine and give it’s common name. ( you will no be asked to draw it’s structure.
-Purines Contain have two cyclic rings, Pyrimidines have one. -Guanine is the only purine with a double bonded oxygen -Thymine is the only pyrimidine with a methyl group attached -Uracil is used in RNA, it is distinguishable from the other pyrimidines via the presence of two double bonded oxygens -Purines are Adenine,Guanine. (Remember that pure gold is AU) -Pyrimidines are Cytosine and Thymine (Remember Pyramids in CT)
What is a Nucleoside? Given the base, you must be able to draw the structure.
A Nucleoside consists of a Sugar ( Deoxyribose, or Ribose) and a Nucleic Base. There is no bound phosphate. -Remember : S in Nucleoside.. stop drawing the molecule at the phosphate.
What is a Nucleotide? Given the base, you must be able to draw the structure.
A nucleotide consists of the sugar, nucleotide base, and at least one phosphate. - A name denoted with 5’ d- or triphosphate indicates a nucleotide with multiple phosphates.
Use Fig. 8-1 (p. 281) to discuss the numbering convention for the pentose ring. Which atom in the sugar is the base attached to? What kind of bond joins the sugar to the base (p. 282)? Using Fig. 8-4 (p. 283), identify the atom that is found at the 2’ position in deoxyribonucleotides? - in ribonucleotides? What functional group is at the 3’ position in ribo- and deoxy-ribonucleotides? To which atom in the sugar is the phosphate bound?
-The carbons are numbered in a clockwise fashion starting from the carbon next to the oxygen in the pentose ring. -The atom in the sugar that the base is attached to is the 1’ carbon. -N-B-Glycosyl bond -In Deoxyribonucleotides, the 2’ consists of just a hydrogen ( hence de-oxygenated). In ribonucleotides, the 2’ consists of an Oxygen and hydrogen ( hydroxyl group) -The 3’ group of both nucleotides consist of a hydroxyl group. -The phosphate is bound to the 5’ carbon of the pentose ring
Use Fig. 8-4 (p. 283) to discuss the nucleotides found in DNA. Compare and contrast these nucleotides to those found in RNA.
The DNA Nucleotides have a hydrogen at the 2’ carbon. They also consist of the four common bases Adenine, Cytosine, Guanine, and Thymine. The RNA Nucleotides possess a hydroxyl group at the 2’ carbon. Instead of a nucleotide possessing thymine like in DNA, these nucleotides have a Uracil based nucleotide denoted as uradine.
Draw a section of DNA (use the letters A, C, G, and T to represent the structure of the base). Point out the following (Fig. 8-7, p. 285): a. phosphodiester linkage b. sugar-phosphate backbone c. 5’ and 3’ ends d. overall charge
Distinguish between an oligonucleotide and a polynucleotide (p. 286).
- A short nucleic acid is referred to as an Oligionucleotide. Generally referring to polymers containing less than 50 or fewer nucleotides. -A longer Nucleic acid is called a polynucleotide
Use Fig. 8-11 (p. 287) to discuss the hydrogen bonds that stabilize the DNA double helix.
-The functional groups of purines and pyrimidines are ring nitrogens, carbonyl carbons, and exocylcic amino groups. Hydrogen bonds involving the amino and carbonyl groups are the most important interaction between two complementary strands of nucleic acid. -Adenine and Thymine form two hydrogen bonds. -Cytosine and Guanine for three hydrogen bonds.
How was DNA shown to be the genetic material (p. 288)? Why was the base composition (Chargaff’s rules) important in suggesting a model for the structure of DNA (p. 288)? What other information was crucial in the structure determination (p. 288)?
-Avery, MacLeod, and McCarty found that DNA extracted from a virulent bacterium could transform a non- virulent strain into a virulent strain of bacterium. - Later Alfred Hershey performed experiments involving radioactively labeled proteins and nucleic acids, and their transmission from bacteriophages to bacteria cells. - Chargoff Concluded that different species varied in base composition. Regardless the relative composition of complementary bases remained the same. A+G=C+T -Rosalinda Franklin’s X-Ray Diffraction Patterns provided evidence of DNA’s Helical Structure.
Use Fig. 8-13 (p. 289) to discuss the structure of double-stranded DNA. Point out the major and minor grooves, the sugar-phosphate backbones, and the stacked base pairs.
- The DNA structure consists of two helical DNA Chains wound around the same axis to form a right handed double helix. The hydrophilic backbones consisting of deoxyribose and phosphate are on the outside of the double helix facing the water. The offset pairing of the two strands creates a major and minor groove. The stacked base pairs enable a greater increase in stability
Use Fig. 8-14 (p. 289) to discuss the strand polarity in double- stranded DNA. What word is used to describe the polarity of the two strands? What base pairs are found in DNA? Discuss the key difference between these two base pairs. What is the position of the sugar-phosphate backbone relative to the bases?
-The two DNA strands run in opposite directions. ( whether the 3’ and 5’ phosphodiester bonds should run in the same direction) -The word used is Anti-parallel. - The base pairs found in DNA : A=T,G=C - Adenine and Thymine form twi hydrogen bonds, while Cytosine and Guanine form three hydrogen bonds. - The sugar phosphate bonds run perpendicular to the base pairing in the double helical model.
What two forces stabilize the DNA Double helix? p.289
- The hydrogen bonds between complementary bases - The Base stacking interactions make the major contribution to the stabilization to the stability of the helix.
Double-stranded DNA can be reversibly denatured and renatured (pp. 297 - 298). a. Discuss the types of bonds broken during denaturation (p. 297). b. Use Fig. 8-27 (p. 298) to discuss the following: 1) What is the melting point (tm)? 2) What is the relationship between tm and the base composition? c. Define what is meant by “annealing” (p. 297).
a.- Hydrogen bonds between paired bases and of base stacking causes unwinding of the the double helix to form two separated or partially separated single strands. No covalent bonds in DNA are Broken . b1.- tm is the melting point at which half the DNA is present as separated single strands. b2.- The higher the concentration of Guanine and cytosine, the higher the temperature of tm. this is because cytosine and Guanine form three hydrogen bonds between the bases, thus raising the melting point. c.- The term Annealing refers to the process in which DNA reforms the double helix.
Define and distinguish between DNA replication, transcription, and translation (p. 977).
DNA replication - the copying of parental DNA to form daughter DNA molecules with identical nucleotide sequences. Transcription - the process by which parts of the genetic message encoded in DNA are copied precisely into RNA Translation - the genetic message encoded in messenger RNA is translated onto the ribosomes into a polypeptide with a particular sequence of amino acids.
What is a gene (p. 980)? How are genes named (p. 1010)? Later you will learn about sequences that control expression of genes. These and introns are part of the modern definition of a gene.
-A gene is all the DNA that encodes the primary sequence of some final gene product ( such as polypeptide or RNA) - bacterial genes are generally named using three lowercase, italicized letters, often reflecting their apparent function
What distinguishes a plasmid from a chromosome (p. 981)?
Many bacteria contain one or more small circular DNA molecules that are free in the cytosol. Chromosomes are the repositories of genetic information.
DNA Supercoiling (pp. 985 - 993): a. What is meant by “linking number” (p. 988; do not worry about the equations)? What is a “topoisomer” (p. 989)? b. Discuss how over-winding or underwinding the DNA double helix leads to the formation of positive or negative supercoils respectively (Figs. 24-13 and 24-16; pp. 987, 989). c. List two reasons why it is advantageous for cells to maintain their DNA in the underwound state (pp. 987 - 988). d. What is a topoisomerase (pp. 989 - 990)? 1) Differentiate between type I and type II topoisomerases in E. coli (p. 990). 2) Describe how E. coli topoisomerase I removes negative supercoils, thereby increasing the linking number (Fig. 24-20, p. 991).
DNA is coiled in in the form of a double helix. The coiling about itself is termed supercoiling. a. Linking Number- the Number of times closed cirular DNA intersect each other b. Overwinding of DNA leads to positive supercoiling or the formation of a right handed helix. Underwinding of DNA leads to negative supercoiling or the formation of a left handed helix. c. Cells keep DNA in the underwound state to facilitate it’s compaction via coiling. Underwound DNA is also easier to access the genetic information. d1.type I topoisomerase break 1 strand of DNA, pass the unbroken strand through the break and rejoin the ends, they increase the linking number by 1. Type II break both strands of DNA, they increase the linking number in increments of 2. d2. Tyr residue cleaves the phosphodiester bondds.
Use Figs. 24-29 (p. 1000), 24-30 (p. 1000), and 24-31 (p. 1001) to discuss higher order organization of eukaryotic DNA.
First there is double stranded helical DNA. Then H1 stimulates the formation of the 30 nm fiber. Further coiling and looping occurs into the form of rosettes which eventually coil into thicker structures and eventually the mitotic chromosome.
What is a replication fork (p. 1012)? Use Fig. 25-3 (p. 1012) to discuss bi-directional replication.
Inside the loop of Ecoli, One or both ends of the loop are dynamic points, where parent DNA is being unwound and the separated strands are quickly replicated.
Using Fig. 25-4 (p. 1013), discuss leading and lagging strand synthesis. What is the direction of DNA synthesis? In what direction is the template strand read? Which strand is replicated continuously, and which discontinuously? What are Okazaki fragments?
-A new strand of DNA is always synthesized in a 5’->3’ direction. ( the 3’ OH is the point of Elongation) -Because the to DNA Strands are antiparallel, the strand serving as the template is read from it’s 3’ end toward it’s 5’ end. - The leading strand is replicated continuously. It is the strand in which the 5’-> 3’ synthesis proceeds in the same direction as the replication fork movement. -The lagging strand is replicated discontinuously, it is the strand where 5’->3’ synthesis occurs opposite to the replication fork - The lagging strand is synthesized in short fragments called Okazaki fragments.
DNA Polymerases a. What are the two “central requirements” of DNA polymerase for DNA polymerization (pp. 1013 - 1014)? b. Use Fig. 25-5 (p. 1014) to discuss the reaction catalyzed by DNA polymerases. 1) Which type of nucleotide (dNMP, dNDP, or dNTP) are used as substrates? 2) What process drives the reaction toward the formation of products (p. 1013)? Discuss in terms of Le Chatelier’s principle. c. Define processivity (p. 1014).
a All DNA polymerases require a template.Polymerases also require a primer ( a strand segment with a free 3’ OH group o which a nucleotide can be added) b.The catalytic mechanism involves two Mg^(2+), coordinated to the phosphate groups of incoming nucleotide triphosphate. the 3’ hydroxyl group of the primer will act as aaanucleophile. The Mg(2+) ion depicted at the top facilitates the attack of the 3’ hydroxyl group of the primer on the alpha phosphate of the nucleotide triphosphate. The other Mg(2+) facilitates the displacement of pyrophosphate. b1. dNTP b2. Non-covalent base stacking and base pairing interactions provide extra stabilization to lengthened DNA. The formation of products is helped by energy generated in the hydrolysis oh the pyrophosphate product by the enzyme pyrophosphates. c. average number of nucleotides before a polymerase dissociates.
Use Table 25-1 (p. 1016) to compare DNA pol I and DNA pol III. Pay particular attention to the following: 1) 3’ to 5’ exonuclease activity (proofreading) 2) 5’ to 3’ exonuclease activity 3) Rates of polymerization 4) Processivity
DNA replication is bi-directional. Use the diagram below to explain bi-directional DNA replication from a single origin of replication (represented by the dots in the middle of the single
stranded region). Use squiggled lines to represent RNA primers and straight lines for DNA. Use arrow heads pointing from 5’ to 3’ to denote the direction of polynucleotide
synthesis.
