Nucleic Acids CHEM 43 Biochemistry I PDF

Nucleic Acids  CHEM 43: Biochemistry I NUCLEIC ACIDS I. Structure of Nucleotides Genetics inherited phenotypes, focused on genes a...

Nucleic Acids  CHEM 43: Biochemistry I NUCLEIC ACIDS I. Structure of Nucleotides Genetics inherited phenotypes, focused on genes and functions. Nucleotide: basic unit of NA’s, arranged in two Biochem chemistry of living organisms long strands (spiraled, double helix). Consists of 3 covalently-linked units: Molec. Bio molecular basis of bio. activity Genomics study of genomes Nitrogenous Purine: A, G Bases Pyrimidine: C, T, U A genome is an organism’s complete set of genetic information (blueprint!). Pentose Ribose: has OH at at C2 Sugar This includes all hereditary instructions Deoxyribose: no O at C2 for creating (reproduction) and maintaining life. Phosphate Monophosphate ○ 23 pairs (22 autosome, 1 sex chromosome) Diphosphate Triphosphate Chromosome: long strand of DNA, packed together with proteins and other molecules. DNA: long polymers of nucleotides. Purine two hydrogen-carbon rings pyrimidine ring fused with imidazole ring. and four nitrogen atoms. DNA info. is encoded in four chemical bases: adenine (A), guanine (G), cytosine (C), and Pyrimidine one hydrogen-carbon ring thymine (T). and two nitrogen atoms. pair up as A+T and C+G to form base pairs. each base connects to a sugar & phosphate molecule, forming the DNA backbone. Base + Sugar + Phosphate = Nucleotide ★ Nucleoside = Nitrogenous base + Sugar ★ Nucleotide = Nucleoside + Phosphate Prepared by: Dhenz  CHEM 43: Biochemistry I NUCLEIC ACIDS Researchers Year Process Findings Signif. Oswald Avery, 1944 Mixed heat-killed S strain with live R Only when Established Colin Macleod, strain; destroyed components with DNA was DNA as the Maclyn McCarty enzymes. destroyed did genetic transformatio material 1. S strain (virulent) was heat-killed, n stop. making it non-virulent. 2. The heat-killed S strain was mixed DNA is the with live R strain (non-virulent). transforming 3. Transformation occurred, creating substance live S strain. 4. Extracted and purified the transforming factor (DNA). 5. Used enzymes to destroy proteins, RNA, and DNA separately. Martha Chase & 1952 Used labeled bacteriophages to infect Only the DNA, not Alfred Hershey bacteria; separated components. phosphorus- the protein, labeled DNA, is the 1. Labeled phages were allowed to not protein genetic infect E. coli. (sulfur), material 2. Phages were separated from the entered the responsible bacteria. bacteria for heredity. 3. Measurements were taken to see during which component entered bacteria. infection. James Watson & 1953 Built models using X-ray diffraction Proposed the Discover Francis Crick data (images from Rosalind Franklin double helix DNA and Maurice Wilkins). structure with structure base pairing Erwin Chargaff 1950s Analyzed DNA from various organisms: Discovered Provided key base pairing evidence for [A] = [T] and [C] ≡ [G] rules in all DNA organisms structure. Prepared by: Dhenz  CHEM 43: Biochemistry I NUCLEIC ACIDS 1. B DNA (right-handed double helix) most common Anti-parallel BP’s are parallel to the axis of the helix Axis passes through the center of BP’s 2. A DNA (right-handed) ○ found in solutions with higher salt DNA Forms concentration or with alcohol added 3. Z DNA (left-handed) ○ its bases seems to zigzag (hence, Z!) ○ found in DNA molecules w/ alternating G-C sequences in alcohol or high salt solution. Glycosidic Pentose Nitrogenous Bonds Sugar Bases Purine (A) C1 N9 distance between base pairs: 0.34 nm Pyrimidine (B) C1 N1 distance covered by one full 3.4 nm helical turn (pitch): (34 A) base pairs per turn of helix 10.4 bp’s base pair rotation relative to 35.4* the adjacent base pair (360/10.4) length of genome 3 x 10^9 bp’s Prepared by: Dhenz  CHEM 43: Biochemistry I NUCLEIC ACIDS Naming Nucleotides Hydrogen Bonds For DNA (deoxy if deoxyribose) A forms 2 hydrogen bonds with T G forms 3 hydrogen bonds with C Deoxyadenosine monophosphate (dAMP) Practice Problem: One strand found in Base Adenine Phosphate 1 the coding sequence of DNA fragment isolated from E. coli reads 5’-GTAGCCTA-3’. Sugar Deoxyribose (basis if DNA or RNA) How many H bonds are present between this strand and its complementary strands? For RNA (no prefix for ribose) Complementary sequence: 3’-CATCGGAT-5’ Uridine triphosphate (UTP) Count the H-bonds: 20 hydrogen bonds! Base Uracil Phosphate 3 4 pairs of G ≡ C: 12 H bonds 4 pairs of A = T: 8 H bonds Sugar Ribose (basis if DNA or RNA) DNA PACKAGING Nucleosome – DNA wrapped around histone proteins. Histones – Proteins that help package DNA (H2A, H2B, H3, H4, and H1). Chromatin – DNA-protein complex; euchromatin (loose, active) & heterochromatin (tight, inactive). Linker DNA – DNA between nucleosomes, bound by histone H1. Chromosome – The most condensed form of DNA during cell division. Topoisomerase – Enzyme that prevents DNA tangling. Condensins – Proteins that compact chromosomes during mitosis. Scaffold proteins – Structural proteins supporting chromatin loops. Prepared by: Dhenz  CHEM 43: Biochemistry I NUCLEIC ACIDS III. Central Dogma of Molecular Biology The central dogma of molecular biology outlines the flow of genetic information within a biological system. 1. DNA: Stores genetic instructions. ‘ 2. RNA: Acts as the messenger, carrying instructions from DNA. 3. Protein: The functional molecule responsible for most of the cellular structure and processes DNA → RNA → Protein The Steps in the Central Dogma: (1) Transcription DNA → Nucleus (in RNA eukaryotes) During transcription, a specific segment of DNA is copied into messenger RNA (mRNA) by the enzyme RNA polymerase. (2) Translation RNA → Ribosome (in Codons and the Genetic Code Protein cytoplasm) Codons: Sequences of three nucleotides In translation, the mRNA is used as a template on mRNA that correspond to specific to synthesize proteins. Transfer RNA (tRNA) amino acids. matches amino acids to the corresponding codons on the mRNA. Type Start Stop Sequence AUG UAA, UAG, UGA (3) Post- Protein Cytoplasm or Translation folding organelles Function Initiates Terminates protein translation After synthesis, proteins fold into specific shapes synthesis and may undergo modifications (e.g., glycosylation) to become fully functional. Amino Acid Methionine None (stop signal) Prepared by: Dhenz  CHEM 43: Biochemistry I NUCLEIC ACIDS In prokaryotes, transcription and translation happen quickly. In DNA, need to process transcription dahil sa labas ng nucleus ang translation. In eukaryotes, may introns and exons (in prokaryotes, exons only). REMAINING NOTES FROM FIRST MEETING Length of genome = 3 x 10^9 base pairs (3 x 10^9 bp) * 0.34 nm = 1 m length of DNA na pinagsisiksikan in a 1 mm cell, particularly sa nucleus Nucleotides can only target the portion of DNA na may histone linker, not yung naka-wrap sa histone. Genes in a genome do not have any effect on cellular function until they are expressed. 20k protein-coding genes. Gene: Has a transcriptional and regulatory region. Transcriptional region: Part of DNA that will be transcribed to mRNA. Promoter (3’ to 5’) transcription start site → mRNA enzymes that help the promoter Prepared by: Dhenz  DNA Replication  CHEM 43: Biochemistry I DNA REPLICATION I. The Basic Idea DNA replication occurs during cell division, producing daughter cells with identical DNA sequences as the parent. This happens through semi-conservative replication. Types of Replication Model Template New Strand Semi Each original One original conservative strand as a + one new template strand per helix Conservative Original DNA One fully old, stays intact one fully new helix Dispersive DNA Both strands fragmented, have mixed both strands old and new as template DNA Characteristics of DNA Replication: Semi-Conservative: Each new DNA molecule has one original and one new strand. Specific Start Point: Replication begins at designated origins in the chromosome. Enzyme Requirement: Strand separation is facilitated by specific enzymes. Meselsohn-Stahl Experiment (1958) Bidirectional Fork: Replication occurs Meselson and Stahl grew E. coli in heavy nitrogen (¹⁵N) in two directions from the origin, forming to make their DNA denser. After switching to normal a replication fork. nitrogen (¹⁴N), they observed that, after one replication, Catalyzed by DNA Polymerases: DNA the DNA had an intermediate density—one strand from synthesis is driven by DNA polymerase the ¹⁵N and one from the ¹⁴N. This hybrid DNA enzymes. provided strong evidence for the semi-conservative model, where each new DNA helix consists of one RNA Primer: An RNA primer is required original and one newly synthesized strand. to initiate DNA synthesis. Prepared by: Dhenz and Mai