Understanding DNA: Structure and Function

• DNA (deoxyribonucleic acid) is a double-stranded molecule storing genetic information
• The repeating units are called nucleotides (nucleic acid)
• Eukaryotes have DNA in the nucleus of all cells except Red Blood Cells (RBC)
• DNA in prokaryotes is found in the cytoplasm and is called circular DNA
• DNA directs the production of genes then proteins

Nucleotides

• Nucleic acid has 4 types (nitrogenous bases)
• Each nucleotide consists of a sugar (deoxyribose), a phosphate group, and a nitrogenous base (adenine [A], guanine [G], thymine [T], or cytosine [C])

Base Pairing

• DNA strands are held by hydrogen bonds between nitrogenous bases
• Adenine pairs with Thymine (A-T)
• Guanine pairs with Cytosine (G-C)
• Specific pairing allows accurate copying of genetic information during cell division
• The bond between nucleotides is called a sugar-phosphate bond (phosphodiester bond)
• Nucleic acids, such as DNA and RNA, are essential for life as they carry genetic instructions
• They are built from smaller subunits called nucleotides
• Nucleotides are the monomers or building blocks, forming long chains called polymers or nucleic acid

Monomer vs. Polymer

• Monomer (Nucleotide) is the single unit containing a sugar, phosphate group and a nitrogenous base
• Polymer (Nucleic Acid) is a long chain formed when many nucleotides are linked together, called a nucleic acid (DNA or RNA)
• Histones are proteins that tightly wrap DNA around them to prevent damage and conserve space

Differences between DNA and RNA

• DNA is double-stranded, forming a twisted ladder (helix)
• It has sugar-phosphate backbones on the outside and nitrogenous bases paired in the middle with A-T and C-G
• RNA is single-stranded, with a sugar-phosphate backbone and nitrogenous bases sticking out
• DNA contains deoxyribose, lacks a hydroxyl group, and is more stable
• RNA contains ribose, which has an extra hydroxyl group
• DNA contains adenine (A), guanine (G), thymine (T), and cytosine (C)
• RNA contains adenine (A), guanine (G), uracil (U) which replaces thymine (T), and cytosine (C)
• Uracil is simpler to make than Thymine
• DNA stores genetic information as a blueprint
• RNA acts as a messenger that carries instructions from DNA to make proteins

Types of RNA

• Messenger RNA (mRNA) carries genetic instructions copied from DNA to ribosomes, where proteins are built
• Ribosomal RNA (rRNA) forms the core of ribosomes, which translate the message from mRNA into proteins
• Transfer RNA (tRNA) acts like a "delivery truck" to bring the correct amino acids to the ribosome based on the instructions on the mRNA
• Each tRNA is specific to a single amino acid and has a "triplet code" that recognizes the matching code on the mRNA

Nitrogenous Bases

• There are 5 nitrogenous bases found in DNA and RNA (C,U,T,G,A)
• These are categorized into pyrimidines and purines, based on their size and structure
• Pyrimidines (smaller): Cytosine (C), Thymine (T) in DNA (replaced by Uracil (U) in RNA)
• They have a single ring structure made of carbon and nitrogen atoms
• Purines (larger): Adenine (A), Guanine (G)
• They have a double ring structure, one similar to a pyrimidine and the other a five-membered nitrogen ring
• Purines always pair with pyrimidines (A-T and C-G) to create stable rungs of the DNA ladder

Protein Synthesis

• There are two parts: transcription and translation
• Transcription: DNA -------> RNA and happens in the nucleus for eukaryotes
• Procedure
• DNA splits through breaking its hydrogen bonds
• mRNA is created using one of the strands from the DNA called the 'template strand'
• 'Junk' Information from the mRNA is taken out and additional molecules are added to the ends, so it can safely leave the nucleus

Translation

• Mature mRNA -------> Protein and happens in the cytoplasm, specifically in the ribosomes
• Procedure
• The mature mRNA travels out of the nucleus to the 2 subunits of the ribosomes, the protein-building factories in the cytoplasm
• The ribosome reads the code on the mature mRNA, one section of 3 at a time (codons). A,U,G are read first, they are the starting amino acids
• For each codon, a matching transfer RNA (tRNA) molecule delivers a specific building block (amino acid) and drops it off in the ribosome
• 3 nucleotides together code for 1 amino acid
• The ribosome links these amino acids together based on the instructions from the mature mRNA, ending the polypeptide chain if they are one of the 3 combinations (UAA, UAG, UGA) because our bodies do not have a matching amino acid for them
• The proteins are sent off to the Golgi Apparatus
• In transcription, DNA splits open by breaking hydrogen bonds
• An enzyme called RNA polymerase copies the instructions for making a protein from a gene in the cell's DNA into a molecule of messenger RNA (mRNA)
• mRNA is a single-stranded molecule that carries the genetic code from the DNA to the cytoplasm, where proteins are made
• In translation, ribosomes which are large protein-RNA complexes, read the instructions on the mRNA molecule
• They use these instructions to assemble amino acids into a protein
• Amino acids are the building blocks of proteins and there are 20 different kinds

The Immune System

• Pathogen: A biological agent that can cause disease whether microscopic or large
• Bacteria are single-celled organisms that can reproduce rapidly and can cause infections such as strep throat, food poisoning, and pneumonia
• Worms are multicellular parasitic organisms that live on or inside another organism
• Diseases include tapeworm infection, roundworm infection, and hookworm infection
• Parasites live on or inside another organism (the host) and benefit from the relationship, harming the host by causing infections
• Besides worms, they include mosquitoes that carry malaria
• Viruses are tiny particles that invade and hijack the cells of a host organism to reproduce
• The common cold, influenza, and HIV/AIDS are all caused by viruses
• Prion – Protein: A unique type of pathogen unlike bacteria or viruses
• It's a misfolded protein
• Proteins have a specific shape that allows them to function properly
• Bacteria reproduce asexually and spread through physical contact leading to food poisining and sore throats
• Worms replicate asexually and spread through poor hygiene leading to worms like tapeworm
• Parasites spread through being bit by a vector and cause Malaria and involve mosquitos
• Viruses are non-living, include Covid-19 and spread through droplets
• Fungi spreads through physical touch and involves tinea
• When the structure of a protein changes in an individual, that is the Prion and can cause mad cow disease or Kuru disease

First Line of Defence

• Defence is from innate (born with) and non-specific responses
• Responses do not act differently to a virus than a bacteria
• It is the same process for targeting pathogens and employs several strategies
• Physical barriers are the skin, the lining of our respitory etc, which prevent germs from entering the body
• Nose hairs blocks pathogens from entering the nose
• Cilia is basically hair in our windpipe, which allows coughs
• Mucus can come under both physical and chemical barriers because it traps phlegm which tracks the pathogens
• Ear wax is sticky and is healthy to some degree, acting to trap pathogens
• Chemical Barriers create a hostile environment with enzymes and acids to kill or inhibit pathogens
• Sweat has salt that contains sodium chloride, which can dehydrate bacteria
• Tears are an enzyme called lysozyme, that tears down certain bacteria (not to be confused with Lysosome)
• Stomach acid is Hydrochloric acid (HCL) helps kill many viruses or bacteria
• Saliva contains lysozyme
• Sebum is an oily secretion from the skin
• Friendy forces are the beneficial bacteria on our skin and in our gut
• Phagocyte Patrol is the specialized white blood cells, which can engulf

Plants

• Physical Barriers:
• Thorns
• Waxy cuticle
• Bark
• Sap
• Chemical Barriers
• Coffee

Second Line of Defence

• The innate immune system is with you from birth
• Reacts the same way to invaders, whether it's a bacteria, virus, or fungus
• Acts very quickly
• Key players are white blood cells (WBCs) called phagocytes that engulf intruders in a process called phagocytosis
• Phagocytes include macrophages, found in tissues, and neutrophils, which circulate in the bloodstream
• Steps for Phagocyte Engulfing Pathogens
• Phagocyte engulfs the pathogen by reaching its arms out (pseudopods)
• The pathogen fuses with the lysosome and breaks down the pathogen
• The phagocyte displays pieces of the pathogen (antigen) in its membranes
• The body sends other white blood cells to do surveillancs
• Inflammation is from damage tissue or invading leading to chemicals or histamine
• Vasodilation is these chemicals on blood vessels close, widening etc
• Cellular mobilisation is the blood flow of the WBC
• Migration helps with the squeezing of the vessels
• Red Alert!
• Inflammation involves vasodilation and increased permeability to prevent infections
• Phagocytes gobble up invaders
• It is important to try and maintain a minor fever for about 20 minutes
• Complementary Proteins don't directly put holes, but direct the protiens (opsonins)

Antibodies and Antibiotics

• Antibodies are specialized proteins made by your immune system in response to a specific infection
• Molecules with a unique shape that can fit perfectly onto a particular invader
• Antibiotics are medicines specifically designed to target and kill bacteria
• Are not made by your body
• Disrupt the bacteria's cell wall in order to interefe with reproducing
• Antibodies are immune sysytems, target specific invaders and attach for destruction
• Antibiotics come from scientists, target bacetria and kill it or stop thier ability to grow

T cells and B Cells

• T cells and B cells are both important types of white blood cells called lymphocytes
• The key players in the adaptive immune system, which recognize and fight specific pathogens disease causing germs and toxins
• B cells are responsible for producing antibodies, which are Y-shaped proteins that can bind to specific antigens foreign substances on pathogens
• T cells don't produce antibodies directly. Instead, they attack infected cells or cancer cells directly

Genes and Chromosomes

• Chromosomes are thread-like structures made of DNA and protein that carry genes
• A chromosome contains many genes, which are specific sequences of DNA
• Genes determine the inherited traits of an organism
• Alleles are different versions of genes that code for traits
• Haploid is cells with one set of chromosomes eg sperm
• Diploid is cells with two sets of chromosomes with two copies eg normal cells
• Mitosis allows for growth, repairment and reproduction

Phases of Mitosis

• Prophase: chromsomes
• Prometaphase: the nuclear envelopes disappear
• Metaphase when chromosomes line up
• Anaphase when copies seperate
• Telophase when a copy of the envelops reapear

Endocrine System

• Endocrine Glands release hormones directly into the bloodstream
• Includes the metabolism of the thyroid gland and regulation of glucagon

Homeostasis

• Refers to maintaining stable environment despite external changes
• Common mechanism of the equilibirum
• Blood regulation involves hormones that regualte high and low levels