BIOTECH MIDTERM

What is DNA

• DNA stands for deoxyribonucleic acid and is the molecule that stores the biological instructions for building and running a living organism

• It contains instructions for making proteins, which do lots of work in the cells

What are some of its main properties?

• DNA properties:

  • Stores genetic information

  • Can be copied

  • Can be passed from parent to offspring

  • Twisted ladder double helix structure

  • Uses 4 chemical bases to store information: A, T, C, and G

What are the 3 main components of a nucleotide and where in a nucleotide is the actual genetic "code"?

• Nucleotides are the building blocks of DNA and are made up 3 parts

  • Phosphate group

  • Deoxyribrose sugar

  • Nitrogenous base

    • A (Adenine)

    • T (Thymine)

    • C (Cytosine)

    • G (Guanine)

• The actual genetic code is in the order/sequence of the bases

  • A always pairs with T

  • C always pairs with G

What is the difference between DNA, chromosomes, genes, and traits?

• DNA is the molecule containing genetic information, 

• Chromosomes are a very long piece of DNA that has been tightly packaged with proteins

  • Humans have 46 chromosomes arranged into 23 pairs

• Genes are sections of DNA that contain instructions for making a product, usually a protein or functional RNA

  • Chromosomes contain many genes

• A trait is a characteristic of an organism such as:

  • Eye color

  • Blood type

    • Genes can influence traits by controlling which proteins cells make

    • Traits are also influenced by environment

What is RNA, and how is it different from DNA?

• RNA stands for ribonucleic acid and is another molecule that helps cells use genetic information

  • DNA stores instructions, RNA helps carry out/use the instructions

  • DNA is double stranded, RNA is single stranded

  • DNA uses A, T, C, G bases, RNA uses A, U, C, G bases

    • Thymine (T) is swapped for Uracil (U)

What are the different kinds of RNA?

• 3 main types of RNA:

  • mRNA: messenger RNA

    • Carries genetic instructions from DNA to the ribosome

  • tRNA: transfer RNA

    • Brings amino acids to the ribosome during protein production

  • rRNA: ribosomal RNA

    • Makes up structure of ribosomes, where proteins are assembled

How does protein synthesis work (hint: what happens during transcription and translation)?

• Step 1: Transcription   ~   DNA → mRNA

  • The cell needs to use the information stored in the DNA

  • The DNA stays inside the nucleus, so the cell makes an RNA copy of the gene

  • This copy is mRNA

  • This process is called transcription, so mRNA can leave the nucleus

• Step 2: Translation

  • The mRNA travels to a ribosome

  • The ribosome reads the mRNA sequence three bases at a time 

    • A group of three bases is called a codon

  • Each codon corresponds to a particular amino acid

    • Amino acids are the building blocks of proteins

  • The ribosome connects the amino acids together in the correct order, producing a protein

Why is protein synthesis so important for all living organisms

• DNA is the information storage system, while proteins are the molecules that perform our cellular functions

  • DNA = blueprint, RNA = copy of relevant instructions, Protein = the machine and product

Why do viruses enter and replicate in host cells (as opposed to doing this on their own)?

• Viruses are unusual because they aren’t complete living cells

• A virus consists of genetic material surrounded by a protective protein structure, and some viruses also have a lipid envelope

  • Viruses do not have the full machinery necessary to reproduce themselves

    • No complete ribosomes

    • No energy-producing systems

    • No cellular machinery for protein production

  • Therefore, they need a host cell to make copies of them

In general, how do viruses use host cell machinery to replicate?

• Virus enters cell → releases genetic material → uses host machinery → makes viral components → assembles new viruses → releases them

  • Different viruses do this differently because their genomes can be DNA or RNA

• Connection to central dogma: genetic information has to be used to make viral proteins

• Viruses hijack the host cell machinery

What are the key components of the SARS-CoV2 virus?

• SARS-CoV-2 is the virus that causes COVID-19

  • It is an RNA virus

• Main components:

  • RNA genome: this is the viruses genetic information

  • Spike protein: sticks out from the surface of the virus, helps the virus attach to and enter host cells. The immune system recognizes the spike protein as something foreign

  • Other proteins: helps it replicate RNA, process viral proteins, assemble new virus particles, interact with host cells

  • Lipid envelope: the fatty membrane surrounding the virus containing viral proteins including spike protei

How does the SARS-CoV-2 virus replicate in a host cell?

• SARS-CoV-2 replication process:

  • Attachment:

    • The spike protein attaches to a receptor on a host cell

  • Entry:

    • The virus enters the cell

  • Release of RNA:

    • The viral RNA becomes available inside the cell

  • Viral proteins produced:

    • Viral RNA provides instructions that allow host cell ribosomes to produce viral proteins

  • Viral RNA copied:

    • Viral machinery copies the viral RNA genome

  • Assembly:

    • New viral RNA and viral proteins are put together to form new virus particles

  • Release:

    • New virus particles leave the cell to infect other cells

What is the immune system?

• The immune system is our body’s defense system against things that cause harm, such as pathogens

  • Pathogens include:

    • Viruses

    • Bacteria

    • Fungi

    • Parasites

• The immune system has many different components:

  • White blood cells

  • Antibodies

  • Immune cells

  • Organs and tissues involved in immune defense

How does the immune system respond to a pathogen?

• How does it respond to a pathogen?

  • Detect

    • The immune system detects something foreign

  • Respond

    • Innate immune response is activated: immune cells become activated and attack the pathogen or infected cells

  • Make antibodies

    • Adaptive/acquired immunity response: B cells produce antibodies that specifically recognize parts of the pathogen, cytotoxic T cells kill virus-infected and damaged cells, helper T cells help cytotoxic T cells and B cells in their functions 

  • Develop memory

    • The immune system develops memory cells that will help it if it encounters the same pathogen again. 

How are vaccines designed to impact the immune system?

• Vaccines can cause the immune system to develop antibodies, memory B cells, or memory T cells

• Then if the pathogen is encountered later, the immune system can respond faster and more effectively

How did the world end up with multiple potential SARS-CoV2 vaccines in development within months of the publishing of the SARS-CoV2 genome?

• Scientists already knew a lot about coronaviruses from SARS and MERS, they weren’t starting from zero

• Scientists had spent years developing technologies such as:

  • mRNA vaccines

  • Viral-vector vaccines

  • protein-based vaccines

• The viral genome was published very quickly, thus scientists could identify important viral proteins and begin designing the vaccine

• The vaccine received mass amounts of funding and volunteers which helped research

What are the main types of vaccines (aka what they're made up of)?

• Live attenuated vaccines

  • Use a weakened version of the pathogen, the pathogen is alive but weakened so it doesn’t cause disease

• Inactivated vaccines

  • Use a pathogen that has been inactivated/killed so it cannot replicate but your immune system can still recognize it

• Protein/sub unit vaccines

  • Use only a specific protein or piece of the pathogen

    • For example using the spike protein in SARS CoV-2

• Viral vector vaccines

  • Use a virus as a delivery vehicle to carry genetic instructions for a pathogen protein

• mRNA vaccines

  • They give mRNA instructions for making the routine that the cells make for the immune system to recognize

What does 3’ and 5’ indicate?

• DNA is made up of Nucleotides, nucleotides have3 parts

  • Phosphate group

  • A 5 carbon sugar called Deoxyribrose

    • the 5 carbons are labelled 1’, 2’, 3’, 4’, 5’

  • Nitrogenous base

• The end of the strand where the 5’ carbon sugar is attached to the phosphate group is the 5’ end

• The opposite end of the strand where the 3’ carbon sugar is attached to a hydroxyl group

• A single strand of DNA always runs from 5’ to 3’

• in a double helix two strands that run side-by-side in opposite directions:

  • one runs 5' —> 3', and the partner runs 3' —> 5'

• Cellular machinery like DNA polymerase can only read and build DNA in the 5’ —> 3’ direction