Posted in P2 SBI4U Biology

SBI4U Image of Your Protein

I was asked by a student for a good source for an image of their protein. The most authoritative source for an image is the RCSB Protein Data Bank. As an example I input HLA-DQB1 and selected the first link for Homo sapiens. This data bank will have the images for proteins from any species that have had research done on their version of the protein. Here are some screenshots:

This is the default view they give you, but if you mouse over the image, you can twirl it around to see it from other views as shown below:

This is another image found by a simple Google search from this site: https://www.researchgate.net/figure/Figure-3-Identical-by-state-SNPs-affecting-HLA-DQB1-binding-groove-The-three_fig1_301588887. As you can see this is from a primary research paper and in this image HLA-DQB1 is being affected by SNPs (single nucleotide polymorphisms).

Any one, or all of these images could be submitted. The point to this question in your task is so you get a sense of what your gene product (protein) actually looks like. You can see mine is made of mostly beta sheets with a couple alpha helices. You only have to submit one, but a few from different angles would be good if possible.

Posted in P2 SBI4U Biology

SBI4U Exam Review Topics

  • atomic Lewis structures of carbon, nitrogen, oxygen and hydrogen atoms
  • Electronegativity and bonding – ionic, polar covalent and non-polar covalent
  • Functional Groups
  • VSEPR Theory
  • Molecular Polarity
  • Intermolecular Forces
  • anabolic & catabolic reactions
  • carbohydrates
  • lipids
  • proteins
  • nucleic acids
  • cellular transport: diffusion, facilitated diffusion, osmosis (tonics), active transport
  • homeostasis – components and positive and negative feedback loops
  • thermoregulation
  • kidney structure and function
  • the brain – structures and their functions
  • the nervous system – CNS vs PNS
  • action potential
  • chemical synapse
  • how specific drugs work in our brain (know the ones from Mouse Party, other than marijuana)
  • DNA replication
  • gel electrophoresis
  • central dogma in general
  • mutations – harmful, maybe harmful, harmless?
  • PCR
  • gel electrophoresis
  • plasmids and their components
  • restriction endonucleases
  • how to make a recombinant plasmid
  • transcription
  • mRNA processing
  • splicing
  • translation
  • Sanger sequencing
  • cycle sequencing
  • mitochondrial structure
  • cellular respiration – overall chemical reaction
  • glycolysis
  • pyruvate oxidation
  • Krebs cycle
  • electron transport chain in the mitochondrion
  • substrate level phosphorylation vs oxidative phosphorylation
  • photosynthesis general reaction
  • chloroplast structure
  • light reactions – electron transport chain in the chloroplast
  • Calvin cycle (aka dark reactions)

Format:  multiple choice, diagrams, problem-solving/analysis, explanations

Posted in P2 SBI4U Biology

SBI4U Molecular Genetics Unit Test Wednesday June 12

This test will be made of multiple choice, a diagram section, and problem-solving/analysis questions but not a long answer section.

  • replication – p. 222 in your textbook as well as the notes we took
  • PCR – purpose, ingredients, how it works (go through three cycles)
  • central dogma in general – DNA to RNA to Protein
  • mutations – types and how to analyze if they are harmful, definitely harmful, or maybe harmful
  • gel electrophoresis – how this works in general and how to analyze a gel
  • recombinant DNA techniques – plasmids (what are the necessary components), genes of interest, restriction endonucleases; basically, what are the ingredients and steps required to make a recombinant plasmid
  • transcription in detail
  • mRNA processing – in detail – 5’methyl-G capping and 3′ Poly A tailing processes
  • splicing – removal of introns and the pasting of exons
  • translation – from mRNA to proteins in detail
  • Sanger vs cycle sequencing – what are the ingredients, how do these techniques work, how to read the data they output

Posted in P2 SBI4U Biology

SBI4U DNA Sequencing Techniques

Go here. Click on “Techniques”, then “Sorting & Sequencing”.

Click on “Early DNA Sequencing” and watch this animation.

Click on “Cycle Sequencing” and watch this animation.

Tomorrow we will be doing a hands-on activity that models Cycle Sequencing.

On Wednesday we will be doing an in-class multiple choice/true-false/fill in the blanks activity that counts to your Application category of learning based on these animations.