General Biology 2 Midterms Reviewer PDF

GENERAL BIOLOGY 2 | MIDTERMS REVIEWER GB2 1ST SEMESTER | 2024-2025 | PROF. JULIE ANNE QUINONES ○ Antiparallel strands running in CENTRAL DOGMA OF MOLECULAR BIOLOGY...

GENERAL BIOLOGY 2 | MIDTERMS REVIEWER GB2 1ST SEMESTER | 2024-2025 | PROF. JULIE ANNE QUINONES ○ Antiparallel strands running in CENTRAL DOGMA OF MOLECULAR BIOLOGY opposite directions (5’ to 3’ and 3’ to 5’) ○ Nucleotides THE DNA Sugar (deoxyribose - deoxy “no oxygen” attached in 2’ WHAT IS DNA? carbon atom) Phosphate group DNA or Deoxyribonucleic Acid is: Nitrogenous bases ○ Complex molecule that contains ○ Nitrogenous bases - building genetic instructions for blocks of DNA & RNA; carry genetic development, functioning, growth information and reproduction of all living Purines – larger molecules organisms. with double ring structure ○ Genetic material passed on from Adenine (A) and parents to offspring Guanine (G) ○ “Blueprint of life” Pyrimidines - smaller ○ Discovered in 1953 by James molecules with Watson & Francis Crick 6-membered ring structure Cytosine (C ) and FUNCTION OF DNA Thymine (T) Base pairing: A - T, C - G The functions of the DNA are: ○ Responsible for carrying all hereditary information ○ Capable of replication which is essential for passing traits ○ Crossing over which produces recombination ○ Changes in sequence and number of nucleotides cause mutation ○ Controls all metabolic reactions of cells through RNAs and synthesis of proteins Chargaff’s Rule - DNA from any cycles of all STRUCTURE OF DNA organisms should have a 1:1 ratio (base pair rule) of purine & pyrimidine bases The structure of the DNA can be characterized by the following: LOCATION OF DNA ○ Double-helix structure (twisted ladder) The DNA can be found in the: ○ Nucleus (Eukaryotes) ○ Cytoplasm (Prokaryotes) GB 2 GENERAL BIOLOGY 2 1  GENERAL BIOLOGY 2 | MIDTERMS REVIEWER GB2 1ST SEMESTER | 2024-2025 | PROF. JULIE ANNE QUINONES THE RNA STRUCTURE OF RNA WHAT IS RNA? The structure of the DNA can be characterized by the following: RNA or Ribonucleic Acid is: ○ Single-stranded helix structure ○ A nucleic acid present in all living ○ Nucleotides cells. Sugar (ribose) ○ “Working copy” Phosphate group ○ Acts as a messenger carrying Nitrogenous bases instructions from DNA for ○ Nitrogenous bases controlling the synthesis of Adenine (A) proteins. Uracil (U) (replaces thymine ○ In viruses, it carries the genetic in DNA) information. Cytosine (C ) Guanine (G) TYPES & FUNCTIONS OF RNA The types of RNA and their functions are: ○ Messenger RNA (mRNA) Carries genetic information from DNA to the ribosome, where proteins are synthesized. Transcribed from DNA and serves as a template for translation. ○ Transfer RNA (tRNA): LOCATION OF RNA Brings amino acids to the ribosome during protein The RNA can be found in the: synthesis. ○ Cytoplasm (mRNA and tRNA) Each tRNA molecule has an ○ Nucleus (rRNA) anticodon that pairs with a specific mRNA codon, ensuring the correct amino acid sequence. ○ Ribosomal RNA (rRNA): Structural and functional component of ribosomes Helps catalyze the formation of peptide bonds between amino acids. GB 2 GENERAL BIOLOGY 2 2  GENERAL BIOLOGY 2 | MIDTERMS REVIEWER GB2 1ST SEMESTER | 2024-2025 | PROF. JULIE ANNE QUINONES 3 CORE PRINCIPLES OF THE CENTRAL DOGMA ○ Helicase - binds to the DNA at the origin of replication and unwinds the double helix, separating the WHAT IS DNA REPLICATION? two strands into single strands. This creates a Y-shaped DNA replication: structure known as the replication fork. ○ Copies DNA molecule to create an ○ Replication fork - where the DNA identical copy strands are separated and where ○ Essential for cell division as each the actual synthesis of new DNA daughter cell receives a complete occurs. set of genetic instructions ○ RNA primase - synthesizes short ○ Semiconservative mechanism as RNA primers complementary to the DNA template. each new DNA molecule consists of one original strand and one newly synthesized strand. RNA Primers - RNA primers are essential ○ Composed of enzymes and because DNA polymerases cannot initiate the synthesis of new DNA strands; they can only proteins: add nucleotides to an existing strand. Primase - synthesizes a short RNA primer (starting Elongation point for DNA synthesis) ○ DNA Polymerase III - binds to the Ligase - joins together primer and begins adding DNA fragments of DNA nucleotides to the 3’ end of the Helicase - unwinds and newly synthesized strand (5’ to 3’ separates the DNA direction) Polymerase - synthesizes Adds nucleotides that are complementary to the new DNA strands by adding template strand complementary nucleotides ○ Continuous vs. Discontinuous ○ Ensures that genetic information Synthesis: is accurately passed on during cell Leading Strand - division, allowing for growth and synthesized continuously repair. toward the replication fork. Lagging Strand - synthesized discontinuously, forming short segments called Okazaki fragments away from the replication fork. Okazaki fragments Japanese molecular biologist Reiji Okazaki and Tsuneko Okazaki (1960s). Formed because DNA is synthesized discontinuously away from the replication fork, resulting in these PROCESS OF DNA REPLICATION fragments that are later joined together by DNA ligase. Initiation GB 2 GENERAL BIOLOGY 2 3  GENERAL BIOLOGY 2 | MIDTERMS REVIEWER GB2 1ST SEMESTER | 2024-2025 | PROF. JULIE ANNE QUINONES Termination ○ Converting genetic information ○ DNA polymerase III - continues to encoded in DNA to mRNA add nucleotides until it reaches a molecule section of DNA that has already ○ Carried out by RNA polymerase been replicated or a termination (reads DNA and builds signal. complementary RNA strand) ○ RNA primers are removed by DNA ○ mRNA carries the information to polymerase I, which clears the RNA the ribosomes for protein nucleotides from the newly synthesis synthesized strand. ○ DNA ligase then seals the gaps between Okazaki fragments on the lagging strand, forming a continuous double-stranded DNA molecule. PROCESS OF DNA TRANSCRIPTION Initiation: Why Semi-Conservative? ○ RNA polymerase - attaches to the It refers to the way in which DNA DNA at a region called the replication occurs promoter. ○ After replication, each new DNA ○ It unwinds the DNA strands, molecule consists of one original exposing the template strand for (parental) strand and one newly synthesized strand transcription. One of the strands is conserved (the original strand) while the other is new. Genetic information is accurately preserved and passed on during cell division. Elongation: Accurate replication with high fidelity, ○ RNA polymerase - moves along minimizing errors and mutations. the DNA, synthesizing a single strand of mRNA by adding complementary ribonucleotides in DNA TRANSCRIPTION the 5’ to 3’ direction. DNA transcription: ○ Process of synthesizing RNA from a DNA template GB 2 GENERAL BIOLOGY 2 4  GENERAL BIOLOGY 2 | MIDTERMS REVIEWER GB2 1ST SEMESTER | 2024-2025 | PROF. JULIE ANNE QUINONES Termination: the growing polypeptide chain, ○ RNA polymerase - continues until forming a functional protein it reaches a specific sequence Final products of central known as the terminator, which dogma (collagen, enzymes, signals the end of transcription. hemoglobin, e.g.) The newly synthesized mRNA is released. mRNA Modifications PROCESS OF DNA TRANSLATION RNA Splicing ○ The initial mRNA (pre-mRNA) has introns (non-coding parts) Initiation and exons (coding parts). Introns ○ Ribosomal subunits - attach to the are removed, and exons are 5' end of the mRNA and scan joined together to make mature along the strand until they find the mRNA. start codon, AUG. 5' End Capping ○ A special cap is added to the 5' ○ tRNA - brings the first amino acid end of the mRNA. This cap to the ribosome protects the mRNA and helps it Each tRNA has an leave the nucleus and be used anticodon, which is a set of by ribosomes for translation. three bases that matches Poly-A Tail the corresponding codon ○ A string of adenine nucleotides on the mRNA. is added to the 3' end. This tail protects the mRNA from Elongation degradation and helps with ○ Ribosome - moves along the translation efficiency. mRNA, and new tRNA molecules bring the appropriate amino acids based on the mRNA codons. DNA TRANSLATION These amino acids are linked together to form a growing polypeptide chain. DNA translation: Termination ○ Converting mRNA sequence into a ○ When the ribosome reaches a stop protein codon (UAA, UAG, or UGA), ○ Ribosomes are complex molecular translation ends. machines that read mRNA codons The completed protein is and recruit tRNA molecules released, and the ribosome ○ Each tRNA molecule carries a disassembles. specific amino acid that binds to GB 2 GENERAL BIOLOGY 2 5  GENERAL BIOLOGY 2 | MIDTERMS REVIEWER GB2 1ST SEMESTER | 2024-2025 | PROF. JULIE ANNE QUINONES CODONS GENETIC ENGINEERING & RECOMBINANT DNA WHAT ARE CODONS? GENETIC ENGINEERING Codons - sequences of three nucleotides WHAT IS GENETIC ENGINEERING? in mRNA that correspond to specific amino acids or stop signals during Genetic engineering - process of altering protein synthesis genes found in all living organisms ○ Each codon is part of the genetic ○ Transfer of genes or parts of DNA code that dictates how proteins are from one organism to another made. ○ Transgenic organisms - organisms whose genes are altered or CODON CHART modified for specific purposes HOW IS DNA USED IN GENETIC ENGINEERING? Genetic engineering - achieved through manipulation of DNA ○ Made possible because DNA is present in all living organisms Genes from one organism can be read by another Since DNA contains genes in building certain proteins by changing its sequence, engineers are able to provide a new gene or cell for an organism to create a different protein ○ New instruction may supplement old instruction (extra trait is exhibited) or completely replace it (trait is changed) GENETIC ENGINEERING TECHNIQUES Identification of the organism that contains a desirable gene To read a codon chart, find the first base in the Extraction of the entire DNA from the row, the second base in the column, and the organism third base on the side to identify the corresponding amino acid. For example, AUG Isolation of the gene by removing it from codes for Methionine. the rest of the DNA GB 2 GENERAL BIOLOGY 2 6  GENERAL BIOLOGY 2 | MIDTERMS REVIEWER GB2 1ST SEMESTER | 2024-2025 | PROF. JULIE ANNE QUINONES ○ Restriction enzyme - searches GENETICALLY MODIFIED ORGANISMS (GMOs) specific nucleotide sequences where they will cut the DNA Genetically modified organisms (GMOs) - Preparing the target DNA organisms whose genetic material has ○ Plasmid - circular piece of DNA is been synthetically manipulated in a removed from bacterial cell laboratory through genetic engineering ○ Special proteins also used to cut ○ Produced when selected plasmid ring individual genes are transferred Insertion of DNA into plasmid from a given donor organism into ○ Host DNA that produces wanted a target organism protein is inserted into the opened ○ Conferring desired properties to plasmid ring new organism ○ Special cells close the ring ○ Include plants, animals, and Insertion of plasmid back to cell enzymes ○ Circular plasmid DNA with host gene inserted back into bacterial GMOs are typically approved by agencies cell for commercial production and Recombinant DNA - consumption bacteria cell with a gene ○ Others undergoing evaluation from different organism ○ USDA (2012) Plasmid multiplication 93% soybeans, 94% cotton, ○ Plasmid multiplies to make 88% corn several copies of the wanted gene to make proteins HISTORY OF GMOs Target cells reproduction ○ When the bacterial cells reproduce by dividing, inserted gene is reproduced in newly created cells Cells produce proteins ○ Can be purified and used for medicine, agriculture, industrial, etc. GB 2 GENERAL BIOLOGY 2 7  GENERAL BIOLOGY 2 | MIDTERMS REVIEWER GB2 1ST SEMESTER | 2024-2025 | PROF. JULIE ANNE QUINONES CLASSICAL BREEDING VS GENE ENGINEERING Recombinant plasmids added to cells ○ Some bacteria will take in plasmid from a solution during the process Classical Breeding Genetic Engineering called “transformation” As cells reproduce (mitosis), recombinant Focuses on Done through mating with insertion of plasmid is copied organisms genetic Introduced gene can produce protein via with desirable material transcription and translation characteristics Does not occur Develop new in nature RECOMBINANT DNA TECHNOLOGY plant varieties (gene in selection gun/bacterial process truck inserts WHAT IS RECOMBINANT DNA? Expression of GM to host genetic plant cells, material within promoter gene Recombinant DNA (rDNA) technology - species to let inserted changes phenotype of an organism Nature-based gene express (host) when a genetically altered vector processes itself) is introduced and integrated into the (sexual and Profoundly genome of an organism asexual different from ○ Scientific method that allows reproduction) conventional researchers to combine DNA from Emphasizes breeding certain different organisms to create new characteristics genetic combinations. and not new ○ Introduction of new traits or for species characteristics into living organisms. Inserting desired gene into the genome GENE CLONING of a host involves: ○ Selection of desired gene for Gene cloning is a process where: administration into the host ○ Large quantities of a specific, ○ Selection of perfect vector with desired gene or section of DNA which the gene has to be may be cloned or copied once integrated desired DNA has been isolated ○ Recombinant DNA formed need to be introduced to the host PROCESS OF GENE CLONING ○ Maintained in host and carried forward to offspring Desired DNA/gene is isolated using restriction enzymes PRIMARY TOOLS IN RECOMBINANT DNA Desired gene and plasmid with same restriction enzymes to produce identical Restriction enzymes - Special proteins sticky ends that cut DNA at specific sequence DNAs mixed and treated with DNA ligase Sticky ends - bond with complementary to splice together DNA sequences, join DNA pieces during rDNA has been formed recombination GB 2 GENERAL BIOLOGY 2 8  GENERAL BIOLOGY 2 | MIDTERMS REVIEWER GB2 1ST SEMESTER | 2024-2025 | PROF. JULIE ANNE QUINONES PROCESS OF RECOMBINANT DNA Production of Transgenic Plants: DNA extraction, where DNA is isolated ○ Plants engineered to express from the source organism desired traits Next, restriction enzymes are used to cut Production of Transgenic Animals: the DNA at specific locations. ○ Animals modified to produce A desired DNA fragment is then inserted beneficial traits, such as increased into a plasmid, which is a small circular growth rate or disease resistance. DNA molecule, creating recombinant Production of Hormones: DNA. This recombinant plasmid is ○ Hormones like insulin produced by introduced into host cells, such as inserting human genes into bacteria, through a process called bacteria or yeast. transformation. Production of Vaccines: As the host cells multiply, they replicate ○ Vaccines created using the recombinant DNA along with their recombinant DNA to generate own DNA. immune responses (e.g., hepatitis B Scientists then identify and select the vaccine). cells that contain the recombinant DNA. Biosynthesis of Interferon: Finally, these host cells express the ○ Production of interferon, a protein desired proteins or traits encoded by the that helps fight viral infections, inserted DNA. using recombinant methods. Production of Antibiotics: ○ Developing new antibiotics by modifying bacterial genes to enhance their efficacy. Production of Commercially Important Chemicals: ○ Creating biofuels, biodegradable plastics, and other valuable chemicals through engineered organisms. Application in Enzyme Engineering: ○ Designing enzymes with specific To be useful, recombinant DNA needs to functions for use in industry (e.g., replicate and work inside a cell. One way to do detergents, food processing). this is by using plasmid DNA from bacteria. Scientists can insert small DNA fragments into Prevention and Diagnosis of Diseases: these plasmids and then introduce them into ○ Using recombinant DNA to develop bacterial cells. As the bacteria multiply, they diagnostic tests and preventive also copy the recombinant plasmids. This measures for various diseases. process creates a colony of bacteria where the Gene Therapy: foreign gene has been successfully cloned. ○ Correcting genetic disorders by delivering functional genes into a APPLICATIONS OF RECOMBINANT DNA patient's cells. GB 2 GENERAL BIOLOGY 2 9