LECTURE 5A and EXERCISE 4: Chemical Basis of Heredity

The last quarter of the lec 5 was moved to lec 6 handout so it doesn't conflict with the timeline of the teaching the central dogma

Chromatin

It is the extended form of the chromosome

Chromatin

It is part of the chromosome thats made of DNA and many proteins

DNA Packaging

It is the proper folding of long DNA molecules in an orderly manner to pack them inside the nucleus

Nucleosomes

basic repeating unit of chromatin

Nucleosomes

“beads on a string“

Nucleosomes

composed of (a) linker DNA and (b) nucleosome core

Linker DNA

DNA not wrapped around histones

nucleosome core

147 bp of DNA wrapped around a histone octamer

histone octamer = 2 copies each of H2A, H2B, H3, H4

histone octamer = _ copies each of ___, ___, ___, ___

Explain the structural detail of the chromosome from DNA to Chromosome

Nucleic acids

It is the storage of biological information; genetic material

many nucleotides

What does polynucleotides mean?

1.DNA

genetic material of all organisms and some viruses

2.RNA

genetic material of some viruses

nucleotides

Nucleic acids are a polymer of ________.

Nucleotides = phosphate group + pentose sugar + nitrogenous base

Nucleotides = _____________ + _____________ + _____________

phosphodiester bonds

Adjacent nucleotides are connected by _________________.

Phosphate Group

It is found along the DNA backbone and gives DNA its negative charge

DNA packaging

The negative charge from the Phosphate Group is important for proper ____________.

It is a monosaccharide sugar that is a key component of DNA.

A simple sugar and carbohydrate that is a main component of RNA.

Nitrogenous Base

carry the genetic sequence information

DNA: A, C, G, T

RNA: A, C, G, U

What are the Nitrogenous Base of DNA and RNA respectively?

Deoxyribonucleic Acid (DNA)

has a double-helix structure composed of a sugar-phosphate backbone on the outside and base pairs on the inside

• Double-stranded – two DNA strands are held together by hydrogen bonds

• Antiparallel – two DNA strands run in opposite orientations

• Complementary – the two DNA strands have complementary bases

What are the Universal Characteristics of DNA?

two DNA strands are held together by hydrogen bonds

Universal Characteristics of DNA:

Double-stranded

two DNA strands run in opposite orientations

Universal Characteristics of DNA:

Antiparallel

the two DNA strands have complementary bases

Universal Characteristics of DNA:

Complementary

For any DNA molecule, the number of purines is always equal to the number of pyrimidines.

1 purine: 1 pyrimidine

What is Chargaff’s Rules?

• Hydrogen bonds

• Base stacking – hydrophobic interactions build up among stacked bases
  

• Covalent bonds – β-N- glycosidic bonds, phosphoester bonds, phosphodiester bonds

What are the reasons for the High Stability of DNA?

hydrophobic interactions build up among stacked bases

High Stability of DNA:

Base stacking

Covalent bonds

High Stability of DNA:

β-N-glycosidic bonds, phosphoester bonds, phosphodiester bonds

• β-N-glycosidic bond – between β-D-2-deoxyribose and nitrogenous base

• phosphoester bond – between β-D-2-deoxyribose and phosphate group
  

• phosphodiester bond – between adjacent nucleotides

What are the Covalent Bonds in DNA?

Covalent Bonds in DNA:

between β-D-2-deoxyribose and nitrogenous base

Covalent Bonds in DNA:

between β-D-2-deoxyribose and phosphate group

Covalent Bonds in DNA:

between adjacent nucleotides

Dimensions of DNA

• Conformations: A-DNA, B-DNA, Z-DNA

  • Diameter = 2 nm or 20 Å

  • 1 turn = 3.4 nm or 34 Å

  • 1 turn = 10 base pairs

Dimensions of DNA

• Conformations: A-DNA, B-DNA, Z-DNA

  • Diameter = __ nm or __ Å

  • 1 turn = __ nm or __ Å

  • 1 turn = __ base pairs

sequence

DNA _________ determines genetic information.

DNA sequence is commonly described from __ to __.

What is the length (in μm) of a DNA molecule with 500 bp?

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HINT:

What is the DNA sequence in the 3’ to 5’ strand given the following sequence in the first strand?

Ribonucleic Acid (RNA)

genetic material of some viruses; gene products in cells

Ribonucleic Acid (RNA)

produced by transcription

Ribonucleic Acid (RNA)

usually single-stranded

Ribonucleic Acid (RNA)

made up of ribonucleotides

In 1930, R.A. Fisher, a quantitative geneticist, proposed two viewpoints the genes could be regarded from:

• As a hypothetical entity by which one could explain the results of breeding experiments; or

• As a chemical compound or molecule

In 1930, ___________ , a quantitative geneticist, proposed two viewpoints the genes could be regarded from:

• _________________________________

• _________________________________

Chemical composition of the Chromosome:

1. Lipids

2. Proteins

   • Histones or protamine (basic proteins)

   • Non histone chromosome proteins (acidic proteins)

3. Nucleic acids

   • DNA and RNA

Chemical composition of the Chromosome:

1. ______________

2. ______________

   • ________ or ________ (basic proteins)

   • ______________ (acidic proteins)

3. ______________

   • ______________

Characteristics of Genetic Material (H.J. Muller)

1. Can duplicate itself with extra fidelity. 

   • 1/1 M copies 

   • The reported error rate is one or less per one million copies.

2. Stable molecular structure 

   • very low frequency of mutation

3. Mutation is duplicated faithfully. 

   • inheritance of mutation 

   • genetic source of variation 

4. Can carry all necessary biological information.

5. Can transmit the information from generation to generation. 

6. Stored information must be decoded and translated into action.

Characteristics of Genetic Material (H.J. Muller)

1. Can _______ itself with extra _______. 

   • 1/1 M copies 

   • The reported error rate is _______ per _______ million copies.

2. Stable _______

   • very low frequency of _______

3. _______ is _______ faithfully. 

   • _______ of _______

   • genetic source of _______

4. Can carry all necessary _______.

5. Can transmit the _______ from _______ to _______. 

6. Stored _______ must be _______ and _______ into action.

proteins; proteios

Events leading to the discovery of DNA

In the 1830s, ________ were thought to be the most important molecules (________ (Greek) “of first importance”)

Friedrich Miescher

Events leading to the discovery of DNA

Late 1860 _____________

• While characterizing proteins from pus cells, a molecule different from protein was isolated from the nucleus and called it DNA.

• Ernst Haeckel

Events leading to the discovery of DNA

• 1866

  • ___________ discovered that the most obvious cellular component of a cell was the nucleus

Edmund Wilson

Events leading to the discovery of DNA

1866

• _____________, using a staining technique, he observed that the most important nuclear element handed from cell to cell was the DNA.

Frederick Griffith

Events leading to the discovery of DNA

1928

• _____________ (US Medical Officer) did a transformation experiment using Streptococcus pneumoniae and declared the presence of transforming principle. The avirulent (R) strain was transformed into virulent (S) type.

• There was a transforming factor, wherein the rough strain took something from the smooth strains, making it virulent.

• Small pieces of DNA or molecules were acquired by the rough strain, which made it deadly like the smooth strain, proving that the DNA called the biological information for virulence.

Events leading to the discovery of DNA

1928

• Frederick Griffith (US Medical Officer) did a transformation experiment using Streptococcus pneumoniae and declared the presence of transforming principle. The avirulent (R) strain was transformed into virulent (S) type.

Explain the experiment, the methodology and the interpretation.

• Oswald Avery, Colin Macleod, and Maclyn McCarty

Events leading to the discovery of DNA

1944

• ____________, ____________, and _____________ identified that the transforming principle (TP) was DNA. 

• When the DNA is treated with proteinases and RNases, its transforming ability is retained but when treated with DNases, transforming ability is lost. 

• When TP was treated to remove proteins and RNA, the composition of the substance left matched the composition of the DNA.

Events leading to the discovery of DNA

1944

• How did Oswald Avery, Colin Macleod, and Maclyn McCarty identify that the transforming principle (TP) was DNA?

Alfred Hershey and Martha Chase

Events leading to the discovery of DNA

1952

• _________ and __________, using the famous blender experiment, they proved that the DNA is the genetic material of bacterial viruses which is injected into the cell during infection. 

The DNA labeled with ³²P is injected into the cell while the labeled protein coat with ³⁵S remained outside.

Events leading to the discovery of DNA

1952

• Alfred Hershey and Martha Chase, using the famous blender experiment, they proved that the DNA is the genetic material of bacterial viruses which is injected into the cell during infection.
  

Explain the experiment, the methodology and the interpretation.

Norton Zinder, Joshua and Esther Lederberg

Events leading to the discovery of DNA

1952 

• ___________, and _________ and ___________, using a transduction experiment in Salmonella typhimurium, further proved that DNA is the genetic material.

Norton Zinder, Joshua and Esther Lederberg

Events leading to the discovery of DNA

The scientists, through their experiment, wherein:

When a bacteriophage infects a bacterial cell (cell A), a transducing phage picks a gene, infects and integrates the gene into a recipient (cell B) cell.

further proved that DNA is the genetic material.

Rosalind Franklin, Maurice Wilkins, James D. Watson, and Francis C. Crick

Events leading to the discovery of DNA

1953

• The structure of the DNA was discovered by ___________, _____________, ____________, ______________.

Events leading to the discovery of DNA

What were the results of Watson and Crick’s paper?

• Purine double ring, bigger

• Pyrimidines single ring, smaller

In terms of size differentiate the nitrogenous bases.

Features of DNA 

• It is composed of two polynucleotide strands. 

• The two strands are anti-parallel. 

• Specific pairing

  • A = T

  • C = G 

• It forms a helical coil. 

• Sugar is 2-deoxy-D-ribose.

Features of DNA 

• It is composed of ____ ____________ strands. 

• The ___ strands are __________. 

• Specific pairing of

  • _ = _

  • _ = _ 

• It forms a ______ coil. 

• Sugar is ____________.

• Its 2-deoxy because there's no oxygen at the second carbon if there was, then it would just be ribose

• Phosphodiester and Phosphoester bonds are the same but the former is called that because the phosphate group makes two ester bonds simultaneously

Why is it called 2-deoxyribose and phosphodiester?

• Why is it called 5’ and 3’ end? because it's connected to the 5th carbon

• The carbon starts to count at one beside the base

• Why is it called 5’ and 3’ end?
  

• Also, draw two pairs of nucleotides while labeling all the significant bonds. Use squares for the bases and circles for the phosphate group.

Evidences to show that DNA is the genetic material 

1. Relative constancy of DNA in all diploid tissues. 

   • in starvation, DNA is unchanged 

2. Haploid cell has half the amount of DNA in diploid cell. 

3. Doubling of DNA content at S phase.

Evidences to show that DNA is the genetic material 

1. Relative _________ of DNA in all _________ tissues. 

   • in starvation, DNA is unchanged 

2. _________ cell has half the amount of DNA in _________ cell. 

3. _________ of DNA content at S phase.
   

Evidences to show that DNA is the genetic material 

4. Cells with extra sets of chromosomes have a proportional increase in DNA content. 

   • polyploidy, polyteny 

5. Parallelism of UV absorption with mutation rates 

6. Transformation and transduction in bacteria

   
   

• Polyploidy or polyteny increases the number of chromosomes without division of the chromosome

• DNA is sensitive to UV, so the longer the exposure to UV, the higher the mutation rate, which explains the parallelism.

Evidences to show that DNA is the genetic material 

4. Cells with extra sets of _________ have a proportional increase in _________ content. 

   • polyploidy, polyteny 

5. Parallelism of _________ absorption with _________ rates 

6. Transformation and transduction in bacteria

Evidences to show that DNA is the genetic material 

7. Production of new viral particles in bacterial cells. 

8. RNA content of tobacco mosaic virus (TMV) caused infection and not the protein coat.

Note: Production of new viral particles is more on the nucleic acid, not the DNA specifically

Evidences to show that DNA is the genetic material 

7. Production of new _________ particles in bacterial cells. 

8. _________ content of tobacco mosaic virus (TMV) caused infection and not the _________.

They coated RNA A with the protein coat of virus B, wherein an infection led to type A progeny; this proves that the genetic material encodes for virus A, not virus B, so the RNA is the genetic material.

Evidences to show that DNA is the genetic material 

How was the RNA content of the tobacco mosaic virus (TMV) proven to be the cause of infection and not the protein coat?

RNA Structure is composed of the following:

1. one polynucleotide strand 

2. D-ribose as its sugar

3. no Thymine but instead Uracil; Adenine Cytosine Guanine

RNA Structure is composed of the following:

1. ___ ____________ strand 

2. _________ as its sugar

3. no ________ base but instead ________; with ________, ________, and ________ still the same
   

Difference between Ribose and Deoxyribose

• Ribose 

  • At carbon-2, a hydroxyl group is attached

  • Single-stranded

  • Same nucleotide bases but has uracil instead of thymine

• Deoxyribose

  • At carbon-2, only hydrogen

  • Double-stranded

  • Same nucleotide bases but has thymine instead of uracil.

Difference between Ribose and Deoxyribose

• Ribose 

  • ________________

  • ________________

  • ________________

• Deoxyribose

  • ________________

  • ________________

  • ________________

1. Before replication, the parent molecule has two complementary strands of DNA Each base is paired by hydrogen bonding with its specific partner, A with T and G with C. 

2. The first step in replication is separation of the two DNA strands. 

3. Each "old" strand now serves as a template that determines the order of nucleotides along "new" complementary strands. Nucleotides plug into specific sites along the template surface according to the base-pairing rules. 

4. The nucleotides are connected to form the sugar-phosphate backbones of the new strands. Each DNA molecule now consists of one "old" strand and one "new" strand. We have two DNA molecules identical to the one molecule with which we started.

1. Before replication, the parent molecule has two complementary strands of DNA Each base is paired by hydrogen bonding with its specific partner, A with T and G with C. 

2. The first step in replication is separation of the two DNA strands. 

3. Each "old" strand now serves as a template that determines the order of nucleotides along "new" complementary strands. Nucleotides plug into specific sites along the template surface according to the base-pairing rules. 

4. The nucleotides are connected to form the sugar-phosphate backbones of the new strands. Each DNA molecule now consists of one "old" strand and one "new" strand. We have two DNA molecules identical to the one molecule with which we started.

Three models of DNA replication

1. Conservative model: The parental double helix remains intact, and a second, all-new copy is made. 

2. Semiconservative model: The two strands of the parental molecule separate, and each functions as a template for the synthesis of a new complementary strand. 

3. Dispersive model: Each strand of both daughter molecules contains a mixture of old and newly synthesized parts/segments.

What are the models of DNA replication? Explain each one.

Matthew Meselson and Franklin Stahl

1958

• By growing E. coli in ¹⁵N and ¹⁴N, isolating the DNA, and centrifugation in cesium chloride, they determined which mode of replication the cells followed, which they found to be the semi-conservative mode. 

Initially, the DNA from bacterial cells contained heavy nitrogen (15N), represented by red strands. After centrifugation, the dense DNA appeared at the lower end of the tube indicating that it was dense.

After one round of replication, the red 15N strand was complemented with a blue 14N strand, creating a hybrid that was lighter than the red DNA. 

After two rounds of replication, both strands were separated, with each red and blue strand complemented by a newly synthesized blue strand. Centrifugation revealed two bands: one lighter consisting of 14N and a hybrid band of both 15N and 14N.

Explain the experiment done by Matthew Meselson and Franklin Stahl (1958).

• Histone octamer (emphasized)

• Histones are positively charged while the DNA due to the phosphate groups are negative this is how its able to super coil.

How is DNA able to super coil in terms of charge?

• Base stacking

  • Hydrophobic because the phosphate group is outside or hides the inner bases, preventing degradation and interaction with water.

Why do DNA molecules have to be hydrophobic? How?