DNA structure: answers to questions What is wrong with this diagram?

Transcription

1 answers to questions What is wrong with this diagram? Lecture 2: 1 Answer questions based on the figure. 1.Write down the sequence of the double-stranded DNA using common abbreviations for four nucleotides, G, A, T, and. 2. Assuming that the double-stranded DNA is separated into two single strands by heat denaturation, can you determine whether the two single strands have the same mass or not? Why? 3. ow many picograms does one such molecule weigh? Answer to question 1: 5 -AGA-3 3 -TTGG-5

2 answers to questions Lecture 2: 2 Answer questions based on the figure. 1.Write down the sequence of the double-stranded DNA using common abbreviations for four nucleotides, G, A, T, and. 2. Assuming that the double-stranded DNA is separated into two single strands by heat denaturation, can you determine whether the two single strands have the same mass or not? Why? 3. ow many picograms does one such molecule weigh? Answer to question 2: Yes or no. It depends on the sequence composition of a particular DNA. The most simplest example for yes is a sequence similar to this: 5 -GAT-3 3 -TAG-5 The simplest example for NO is a sequence of 5 -GA-3 3 -T-5 The key point is that the two strands of a DNA molecule are complementary but not identical.

3 answers to questions Answer questions based on the figure. 1.Write down the sequence of the double-stranded DNA using common abbreviations for four nucleotides, G, A, T, and. 2. Assuming that the double-stranded DNA is separated into two single strands by heat denaturation, can you determine whether the two single strands have the same mass or not? Why? 3. ow many picograms does one such molecule weigh? The wt of 10 nucleotides =(10 X 330) X (1.66X X ) =3.3 X10 3 X1.66 X =3.3 X1.66 X 10-9 =5.478 x 10-9 picogram 1. lkb of double-stranded DNA (sodium salt) = 6.6 x 105 Daltons. 2. lkb of single-stranded DNA (sodium salt) = 3.3 x 105 Daltons. 3. lkb of single-stranded RNA (sodium salt) = 3.4 x 105 Daltons. 4. The average MW of a nucleotide = 330 Daltons. The unified atomic mass unit (u), or dalton (Da), is a small unit of mass used to express atomic and molecular masses. It is defined to be 1 12 of the mass of one atom of carbon-12. Lecture 2: 3 One atomic mass unit (1 u) is defined as onetwelfth the mass of an atom of carbon-12. Since the experimentally measured mass of an atom of carbon-12 is x g, 1 u = X g. Answer to question 1: 5 -AGA-3 3 -TTGG-5 1 base pairs = x 10-9 /5 =1.1 x 10-9 picogram 1 picogram = 1/(1.1 X10-9 ) =0.909 X 10 9 base pairs =909 x 10 6 base pairs = 909 Mega base pairs (Mb) 1 ton=1000 g 1 kg =1000 g 1 g = 1000 mg 1 mg =1000 µg 1 µg = 1000 ng 1 ng =1000 pg 1 pg = 1000 fg 1 kg = 2.20 lb

4 topics Lecture 2: 4 Topic 1: Structure of the Atom Topic 2: hemical Bonds Topic 3: Primary Structure of DNA

5 Structure of the Atom/subatomic particles Lecture 2: 5 What is atom? An atom is the smallest unit of matter, which retains the chemical properties of that element. It consisting of a dense, central, positively charged nucleus surrounded by a system of negatively electrons. What is an element? What is an element? An element is a substance that is made entirely from one type of atom. Electrons Nucleus What is the atomic nucleus made of? The nucleus of atoms is made of protons and neutrons except that of hydrogen atoms, whose nucleus has one proton and no neutron. Protons are positively charged while neutrons has no charge. A neutron has no electrical charge. It can decay into a proton plus an electron. The number of protons in the atom is called atomic number.

6 Structure of the Atom/subatomic particles Lecture 2: 6 What are isotopes? Isotopes are atoms with the same number of neutrons, but different numbers of neutrons, thus different masses. For example, the hydrogen element has three isotopes: Protium 1 1 : one proton, no neutron, and a mass of 1 Da; Deuterium 2 1 : one proton, one neutron and a mass of 2 Da); and Tritium 3 1 : one proton, two neutrons and a mass of 3 Da Electrons Nucleus What are radioisotopes? Since excessive neutrons in tritium makes the atoms unstable, thus cause emission of radiation (beta rays), tritium is referred to as RADIOATIVE ISOTOPE. The radiation can damage cells. Tritium has a half-life of years What is atomic weight? It is equal to the total mass of all subatomic particles including protons, neutrons and electrons. A single proton weighs X gram. A neutron with a weight of X gram is slightly more massive than a proton. The mass of an electron is grams. The atomic weight is usually expressed in Daltons (Da). One Da has the equivalent mass of one proton. A teaspoonful of tightly packed neutrons would weigh millions of tons at the earth's surface.

7 Structure of the Atom/subatomic particles Lecture 2: 7 What are the sizes of atoms? N O 1.2 Ǻ 2.0 Ǻ 1.5Ǻ 1.4 Ǻ Electrons, what you are? Electrons Nucleus A electron carries a negative charge of 1.60 X oulomb. Electrons can be free or orbit around the nucleus of an atom. An electron is lighter than a proton by 1,836 times. Electrons in atoms exist in spherical shells of various radii, representing energy levels. The larger the spherical shell, the higher the energy contained in the electron.

8 hemical Bonds/orbitals Lecture 2: 8 Shell Orbital Number of electrons ENERGY LEVEL K 1s 2 L 2s 2 2p 6 M 3s, 3p, 3d 18 N 4s, 4p, 4d, 4f 32 Y Y Y Y X X X X Z 1S Z P X Z P Y Z P Z

9 hemical Bonds/orbitals Lecture 2: 9 1S 2S 2P x 2P y 2P z 3S 1 1S N 7 1S 2 2S 2 2P 3 O 8 1S 2 2S 2 2P 4 6 1S 2 2S3P 3 P 15 1S 2 2S 2 2P 6 3S 2 3P 3 Na 11 1S 2 2S 2 2P 6 3S hemical bonds is driven by atoms propensity for minimizing the unpaired electron.

10 hemical Bonds/ionic and covalent bonds Lecture 2: 10 Ionic Bonds: Electrostatic attractions between two opposite charge ions such as Na + and - in NaL (table salt). In this interaction, sodium atom loses its electron in the outmost shell to the chloride atom, becoming positively charged, while chloride atom receives an electron from the sodium atom and turns into a negatively charged ion. ovalent bonds: Atoms form a stable linkage by sharing electrons. ydrogen gas (2): : arbon dioxide (o2): O::O = 2 0 o

11 hemical Bonds/ydrogen bonds Lecture 2: 11 ydrogen bonds: A hydrogen is shared by two electroneative atoms (e.g. N and O) to give a hydrogen bond. 1 Ǻ long 1 Ǻ long

12 hemical bonds/weak interactions Lecture 2: 12 Van der Waals forces: Electronstatic attractions or repulsions between two atoms due to fluctuating electrical charges. ydrophobic interaction forces: Atoms can be forced to clump together when non-polar molecules are mixed with water, which is strongly polar.

13 hemical Bonds/their energy levels Lecture 2: 13 haracteristics of covalent and noncovalent chemical bonds One calorie: The quantity of energy need to raise the temperature of 1 gram of water by 1 o under one atmosphere pressure calories are one kilocalories (kcal), which is equal to 4.17 kilojoules (kj).

14 hemical Bonds/molecules Lecture 2: 14 A molecule is: the most basic unit of a substance, consisting two or atoms of one or types, bound to each other by chemical forces. It retains the chemical and physical properties of that substance. DNA is a molecule: made up of hydrogen, carbon, nitrogen, oxygen, phosphor and metal atoms. What is a mole of substance? A mole of substance is the amount of molecules is also called Avogadro's number, named after Amedeo Avogadro. The value of one mole is equal to the mass in grams given by the formula weight (FW) or relative molecular weight (Mr). For example, the formula weight of NaL is So, a mole of sodium chloride weighs grams on earth. arbon has a Mr of 12. That means 12 grams of carbon contain a mole of carbon. The concept of mole has been applied to define other particles such as atoms. one mole of water is equivalent to about 18 grams of water and contains one mole of 2O molecules, but three moles of atoms (two moles and one mole O).

15 hemical Bonds/molecule weight&mass Lecture 2: 15 Two ways to quantify the amount of a molecule: molecular weight and molecular mass Molecular weight (FW, Mr): the relative ratio of the amount of a mass of a molecule of that substance to one-twelfth the mass of carbon isotope 12. The value of molecular weight is the same as those of the formula weight (FW) or the relative molecular weight (Mr). Molecular mass (m): the total mass of the atoms in a molecule. So, its unit is dalton. One dalton is equivalent to one-twelfth the mass of carbon-12; a kilodalton (kda) is 1,000 daltons; a megadalton (MDa) is 1 million daltons. What is the difference between molecular weight and molecular mass? The former varies with the amount of gravity but the latter does not. Generally, the two numbers are the same, since substances we deal with are on Earth. Molar concentration: One molar denotes one mole (in grams) of a substance (solute) per one liter of a solvent, expressed in [mole/l). Milimolar: mm; micromolar: µm.

16 Primary Structure of DNA/building blocks (,, O) Lecture 2: 16 ß-D-2-deoxyribose (sugar) (,, O, N) 5 4 O O 3 2 O (P, O,?) Phosphate 1 O 8 N 7 9 N Adenine (a base) N N N O - - O P O - O

17 Primary Structure of DNA/nucleosides ß-D-2-deoxyribose (sugar) 5 4 O 3 O O Adenine (base) N 7 9 N O 5 4 N2 6 3 N 1 N O Sugar + Base = Nucleotide O 2 8 deoxyadenosine (deoxynucleoside) N 7 9 N Lecture 2: 17 N2 6 3 N 1 N 2 N-glycosidic bond O

18 Primary Structure of DNA/two configurations of adenosine Lecture 2: 18

19 Primary Structure of DNA/nucleotides Lecture 2: 19 Phosphate - O O - P O O O O + O 2 8 N 7 9 N N2 6 3 N 1 N 2 N-glycosidic bond Adenosine (nucleoside) Phosphoester - 2 O phosphoester bond bond Deoxyadenosine 5 -monophosphate (damp) Adenine deoxynucleotide

20 Primary Structure of DNA/nucleotides Lecture 2: 20 As in damp As in damp As in dadp As in datp

21 Primary Structure of DNA/nucleotides Lecture 2: 21 ytosine deoxynucleotide

22 Primary Structure of DNA/nucleotides Lecture 2: 22 BASE DEOXYNULEOSIDE (Base + deoxyribose) DEPXYNULEOTIDE 5 -MONOPOSPATE (Nucleotide)(Base + deoxyribose + phosphate) Adenine Guanine ytosine Thymine deoxyadenosine deoxyguanosine deoxycytidine deoxythymidine deoxyadenosine 5 -monophosphate (damp) or adenine nucleotide; A deoxyguanosine 5 -monophosphate (dgmp) or guanine nucleotide; G deoxycytidine 5 -monophosphate (dmp) or cytosine nucleotide; deoxythymidine 5 -monophosphate (dtmp) or thymine nucleotide; T

23 Primary Structure of DNA/dinucleotides Lecture 2: 23 DNA is polar Phosphodiester linkage

24 Primary Structure of DNA/polynucleotide Lecture 2: 24 DNA is a polar, linear polymer made up of four types of deoxyribose nucleotide connected by phosphodiester linkage.

25 Primary Structure of DNA/chemical properties of bases Lecture 2: 25 Bases can be present in two tautomeric forms: a keto or its enol form. Two forms differ in the arrangement of single and double bonds in the rings of purines and pyrimidines. Ke Ke Tautomerization affects the formation of hydrogen bonds (base-pairing)

26 Primary Structure of DNA/alternative base pairing and modified bases Lecture 2: 26

27 Primary Structure of DNA/base pairing Lecture 2: 26

28 Secondary Structure of DNA Lecture 2: 26

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30 Primary Structure of DNA/base pairing Lecture 2: 26