July 12, 2013

[BIOCHEMISTRY: NUCLEIC ACIDS AND THE CENTRAL DOGMA PART 1]

Other scientists did not believe the conclusion due to contamination issues. Thomas Hunt Morgan published the mechanism of Mendelian Heredity wherein it showed that the genes were lined up along the chromosomes 1950.

LECTURER: Mr. Noel S. Quiming HISTORY Walter Sutton proved that chromosomes the cells units of inheritance and that it follows the Mendellian Law in 1902. Chromosomes highly folded, long strand of DNA molecules associated with proteins. *different organisms can be differentiated by their number of chromosomal pairs. e.g Humans 23 pairs Dogs 39 pairs Tomato - 12 pairs *1 fragment of a chromosome represents a gene, and a gene corresponds to particular protein/s. Prokaryotes - 1 gene = several proteins Eukaryotes 1 gene = 1 protein Frederick Griffith demonstrated the transforming factors of bacterial cells in 1928. Griffith Experiment concludes that heatkilled S-strain can transform the R-strain.

Genes fragments of DNA molecules that are found in the chromosomes.

Martha Chase and Alfred Hershey proved that the DNA is the substance that transmits genetic information in 1952.

Note: Proteins undergo denaturation. AveryMacLeodMcCarty Experiment (1944) Proved that DNA is the substance that causes bacterial transformation and that it carries the hereditary traits.

*bacteriophages- virus that is parasitic (reproduces itself) in bacteria. Conclusion: Bacteriophages infect using their DNA and not with their proteins, hence, DNA are the genetic materials. UPCD 2017 |Amiel Apostol, Rogielyn Bandoja 1

July 12, 2013

[BIOCHEMISTRY: NUCLEIC ACIDS AND THE CENTRAL DOGMA PART 1]

2. Phosphate Group 3. Nitrogenous Base 2 TYPES OF NUCLEIC ACIDS BASED ON SUGAR COMPONENT 1. DNA (found in nucleus, mitochondria) 2. RNA (found in nucleus, cytoplasm)

Erwin Chargaff - Discovered the key facts needed to determine the structure of DNA by measuring the 4 nitrogenous bases in DNA molecules of different species.

Franklin and Wilkins - their detailed measurements using x-ray gave the key to Watson and Crick to determine that the shape of the DNA molecule was a double helix in 1952. * Both sugars are pentoses NUCLEIC ACIDS Polymers of nucleotides (building blocks) 1'C Nitrogenous bases is attached 3'C free hydroxyl group (OH) 5'C connects to phosphate group

Determination of the Structure of Nucleotides 1. Use detergent to separate protein from nucleic acid components from nucleoproteins. 2. Nucleic acid was subjected to nuclease (enzyme that hydrolyzes nucleic acids). *Nucleic acids degraded into nucleotides. 3. Using Phosphatase or Nucleotidase, nucleotides are separated into phosphate group and nucleoside. 4. Nucleosides upon the action of nucelosidase are degrade into sugar component and nitrogenous bases. As a result we should know that nucleotides are compose of: 1. Sugar Component (Ribose or Deoxyribose)

NUCLEOSIDE VS NUCLEOTIDE Nucleoside- no phosphate group at 1C Nucleotide- with phosphate group at 1C

UPCD 2017 |Amiel Apostol, Rogielyn Bandoja

July 12, 2013

[BIOCHEMISTRY: NUCLEIC ACIDS AND THE CENTRAL DOGMA PART 1]

* DNA is double stranded, therefore Strand A would run from 5 to 3 direction while Strand B would run from 3 to 5 direction. * The two strands are connected through the pairing of the nitrogenous bases through hydrogen bonds. A-T Low melting point (region if rich in A-T) 2 hydrogen bonds C-G Stronger bond 3 hydrogen bonds

CONFORMATION 1) Syn- ring of nitrogenous base and ring of sugar are in the same plane 2) Anti- ring of nitrogenous base and ring of sugar are in opposite planes -nucleosides and nucleotides are usually found in this conformation 2 TYPES OF NUCLEIC ACIDS BASED ON NITROGENOUS BASES 1. Purines (A, G) 2. Pyrimidines (C, T, U)

Structures of Ribonucleotides (Sugar: Ribose) - building blocks of RNA Molecules 1. 2. 3. 4. Adenosine Guanosine Uridine Cytidine

Forms of DNA

Structures of Deoxyribonucleotides (Sugar: Deoxyribose) - building blocks of DNA Molecules 1. 2. 3. 4. Deoxyadenosine (adenine) Deoxyguanosine (guanine) Deoxythymidine (thymine) Deoxycytidine (cytosine)

* Phosphodiester Bond binds the structure of DNA; sugar-phosphate backbone; formed through the reaction of 3C OH of one nucleotide to 5C PO43- of another nucleotide

1. aDNA 2. zDNA 3. bDNA (most common form of DNA) *aDNA can be obtained from bDNA through dehydration

UPCD 2017 |Amiel Apostol, Rogielyn Bandoja

July 12, 2013

[BIOCHEMISTRY: NUCLEIC ACIDS AND THE CENTRAL DOGMA PART 1]

Loop or Hairpin, Cruciform Structure may form due to intrastrand pairing (pairing occurs within a single strand)

*zDNA is irregular and seem to zigzag because the purine bases are in the syn conformation while the pyrimidine bases are in the anti conformation Form Helical twist Base pairs per turn Occurrence A Right 11 RNA, DNA B Right 10 DNA Z Left 12 DNA

Remember: 1. Prokaryotes - Double stranded Circular DNA 2. One Single unit = Plasmid = Encode Several Proteins 3. Eukaryotes = Double Stranded Linear DNA 4. Chromatin = DNA Molecules associated with proteins and RNA.

OTHER FORMS OF DNA

Notes: 1. Chromatin - DNA Molecules associated with proteins and RNA. 2. Several Nucleosomes joined together by linker DNA strand into a solenoid and folded into nuclear scaffold folded into chromosome. 3. Chromosome = Histone Octamer Proteins + Nucleosome + Double Stranded DNA Histone Octamer - Compose of 8 Proteins; Cylindrical Part where the DNA is coiled Total of 8 Proteins UPCD 2017 |Amiel Apostol, Rogielyn Bandoja 4

July 12, 2013 1. H2A (2) 2. H2B (2) 3. H3 (2) 4. H4 (2)

[BIOCHEMISTRY: NUCLEIC ACIDS AND THE CENTRAL DOGMA PART 1]

Components of Replication Apparatus 1) dnaA- binds to origin DNA sequence 2) Primasome- composed of: a) dnaB- helicase *function of helicase- unwind DNA duplex (double stranded DNA) ahead of DNA polymerase creating a single stranded DNA that can be used as template - unwind DNA at origin b) dnaC- binds dnaB c) dnaG- primase (synthesizes RNA primer to initiate DNA synthesis) 3) DNA gyrase (Topoisomerase II) -enzymes that relieve supercoiling of double stranded DNA -DNA usually supercoils, BUT in needs to be relieved to prevent instability - bacteria replication is also inhibited through this (ex. Ciprofloxacin, ofloxacin) 4) Single Stranded Binding Protein (SSB) -prevent intrastrand pairing *looped conformation is not wanted since ideally, we want all Nitrogenous bases to be exposed; this is where SSB protein comes in to prevent intrastrand pairing 5) DNA polymerase Bacterial cells: (3 types of DNA polymerase) I II III 1) 5->3 / / / polymerase activity 2) 3->5 / / / exonuclease activity 3) 5->3 / x x exonuclease activity UPCD 2017 |Amiel Apostol, Rogielyn Bandoja 5

*Histone Octamer is basic therefore positively charged in order for the negatively charged DNA molecule to coil around it. CENTRAL DOGMA OF GENETICS 3 processes: 1) Replication- DNA produce DNA 2) Transcription- DNA template produce RNA *reverse transcription- RNA template produce DNA 3) Translation- RNA produce protein Characteristics of DNA Replication 1) DNA replication is semiconservative -one strand is used as template; complementary strand as newly synthesized template -newly synthesized strand has lighter isotope of nitrogen * conservative- product of 1st generation double sided DNA with 2 newly synthesized strands with a parent strand -DNA strands with heavy nitrogen isotope 2) DNA replication begins at an origin 3) DNA replication is bidirectional -two replication forks are made which move in opposite directions Ex. Formation of Okazaki fragments *replication bubble 4) DNA replication proceeds in a 5 -> 3 direction and is semidiscontinuous

July 12, 2013

[BIOCHEMISTRY: NUCLEIC ACIDS AND THE CENTRAL DOGMA PART 1]

1) 5->3 polymerase activity- can synthesized from 5 to 3 direction; meaning it starts at 3 end -both strands used as template *perfect template is strand running from 3 to 5 2) 3->5 exonuclease activity - they can remove nucleotide from 3 to 5 direction -proofreading ability= removal of mismatched pair 3) 5->3 exonuclease activitynucleotide from 5 to 3 direction removal of

- remove RNA primer and replace it by newly synthesized DNA fragment Replication of E. Coli 1) Initiation 2) Elongation 3) Termination- once replication bubble is formed, at some point, both ends will meet (when entire bacterial gene has been replicated) causing termination

UPCD 2017 |Amiel Apostol, Rogielyn Bandoja