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3/19/2020

Virus Biology

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What is a virus?



A virus reproduces inside the cells of living hosts, a host cell is forced to produce thousands of identical copies of the original virus.
​


Viruses
 consist of nucleic acid and a protein coat.

Usually the nucleic acid is RNA; sometimes it is DNA. ... 

Viruses are much smaller than bacteria.
​

​They lack the means for self-reproduction outside a host cell and are therefore generally not considered to be true living organisms.


Virus Anatomy


Influenza
Picture

​https://micro.magnet.fsu.edu/cells/viruses/influenzavirus.html


Coronavirus


Picture

​https://asm.org/Articles/2020/January/2019-Novel-Coronavirus-2019-nCoV-Update-Uncoating
​

HIV Virus


Picture

​https://micro.magnet.fsu.edu/cells/viruses/hivvirus.html


EBola VIrus


Picture

​https://pdb101.rcsb.org/motm/178

Picture

​https://microbiologyinfo.com/structure-of-ebola-virus/
​

Bacteriophage



​Without a host cell, viruses cannot carry out their life-sustaining functions or reproduce.

They cannot synthesize proteins, because they lack ribosomes and must use the ribosomes of their host cells to translate viral messenger RNA into viral proteins.

​Viruses cannot generate or store energy in the form of adenosine triphosphate (ATP), but have to derive their energy, and all other metabolic functions, from the host cell. They also parasitize the cell for basic building materials, such as amino acids, nucleotides, and lipids (fats). 

All viruses contain nucleic acid, either DNA or RNA (but not both), and a protein coat, which encases the nucleic acid. Some viruses are also enclosed by an envelope of fat and protein molecules.

​
Picture

https://micro.magnet.fsu.edu/cells/virus.html
​

Immune Response



Vaccines



Pandemic Spread


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3/13/2020

coronavirus break

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3/11/2020

Synapse

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The Place where nerve communication Ends and begins 


Synapse: 

A junction between two nerve cells, a gap across which impulses pass by diffusion of a neurotransmitter.
​
Picture

​https://socratic.org/questions/how-do-impulses-travel-across-a-synapse
​
Picture
https://www.neuroscientificallychallenged.com/glossary/synaptic-cleft
​


Acetylcholine


Acetylcholine:

An organic chemical that functions in the brain and body of many types of animals as a neurotransmitter—a chemical message released by nerve cells to send signals to other cells, such as neurons, muscle cells and gland cells.

​-Wikipedia


Picture

https://www.getbodysmart.com/nervous-system/neurotransmitter-release


Endocannabinoid System


Picture

​https://www.researchgate.net/figure/The-human-endocannabinoid-system_fig1_316545895


Endocannabinoid-enhancing foods
​
  • Hemp seeds and hemp oil.
  • Flax seeds (grind at home in a coffee grinder) and flax oil.
  • Chia seeds.
  • Walnuts.
  • Sardines and anchovies.
  • Eggs (pasture-fed or omega-3 enriched only)
​
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3997295/

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3/9/2020

Types of Proteins

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What do ribosomes make?


Picture
http://nnhsbiology.pbworks.com/w/page/26126310/Transcription%20%20Translation


​Guiding Questions

1.  What is transcription?

2. Where does it take place?

3. What is translation?

4. Where does it take place?

5. What is a codon? Where is it?

6. How does DNA three letter code get converted into an amino acid? ​
​

Types of Proteins


Hemoglobin: 

a red protein responsible for transporting oxygen in the blood of vertebrates. It contains an iron atom bound to a heme group.

​
Picture

​http://www.chemistry.wustl.edu/~edudev/LabTutorials/CourseTutorials/Tutorials/Hemoglobin/Hemoglobin.htm

Picture
https://courses.lumenlearning.com/suny-ap2/chapter/erythrocytes/

Picture

​https://www.pinnaclehealth.org/wellness-library/blog-and-healthwise/wellness-collection/article/en-us/tp10337/
​

Skin


Keratin:

Insoluble, usually high-sulfur content and filament-forming proteins.

The bulk of epidermal appendages such as:

hair, nails, claws, turtle scutes, horns, whale baleen, beaks, and feathers.

These keratinous materials are formed by cells filled with keratin and are considered ‘dead tissues’.

​Keratin structures are among the toughest biological materials, serving as a wide variety of interesting functions, e.g. scales to armor body, horns to combat aggressors, hagfish slime as defense against predators, nails and claws to increase prehension, hair and fur to protect against the environment

​Keratin is in skin.


Picture

https://www.newworldencyclopedia.org/entry/Keratin
​

Picture
https://www.sciencedirect.com/science/article/abs/pii/S0079642515000596

Picture
https://www.researchgate.net/figure/Molecular-structure-of-keratin_fig1_334421596

https://www.newworldencyclopedia.org/entry/Keratin

Skin Anatomy


Picture

Keratin production related illness



Harlequin ichthyosis:

Mutations in the ABCA12 gene cause harlequin ichthyosis.

The ABCA12 gene provides instructions for making a protein that is essential for the normal development of skin cells.

​This protein plays a major role in the transport of fats (lipids) in the outermost layer of skin (the epidermis).
​
This condition is inherited in an autosomal recessive pattern, which means both copies of the gene in each cell have mutations.

The parents of an individual with an autosomal recessive condition each carry one copy of the mutated gene, but they typically do not show signs and symptoms of the condition.
​

Picture
https://ghr.nlm.nih.gov/condition/harlequin-ichthyosis
​

https://dermnetnz.org/topics/harlequin-ichthyosis/
​


Nerve Cell


Picture

​https://en.wikipedia.org/wiki/Axon
​

​
​Myelin:


A mixture of proteins and phospholipids forming a whitish insulating sheath around many nerve fibers, increasing the speed at which impulses are conducted.
​
Picture

https://www.researchgate.net/figure/The-structure-of-the-myelin-sheath-The-myelinated-axon-A-myelin-sheath-B-bilayer_fig1_24011701

Picture

​https://www.adooq.com/myelin-basic-protein-87-99.html
​

Picture

http://highered.mheducation.com/sites/dl/free/0071402357/156721/figure345_2.html
​

Picture
http://www.people.vcu.edu/~kentbh/Sato-Bigbee-2008/support1.html
​


Nerve Cells COnnect to Muscles


Picture

​http://humanbiologylab.pbworks.com/w/page/69996625/Muscle%20Contraction%C2%A0by%20Talia%20Castano
​

Picture
https://www.dentistrytoday.com/news/industrynews/item/3178-grant-to-explore-schwann-cells-role-in-oral-cancer-pain
​

Schwann cell:

Also called neurilemma cell, any of the cells in the peripheral nervous system that produce the myelin sheath around neuronal axons. Schwann cells are named after German physiologist Theodor Schwann, who discovered them in the 19th century.

https://www.britannica.com/science/Schwann-cell


Worksheets


Picture
Picture

We are made of many elements


Picture

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3/8/2020

Protein Structure and FUnction

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Protein Folding 



Protein Structure as a result of Folding



DNA Nucleotide Bonding


Picture
https://www.quora.com/How-many-hydrogen-bonds-form-between-guanine-and-cytosine

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3/4/2020

Biochemistry: A closer look at DNA

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What is DNA?


So far we have said that DNA:

is a double helix

Has a sugar phosphate backbone

contains instructions to make proteins

coils into a chromosome

is in the nucleus of a cell

has nucleotides

​has nucleotide pairs
​


We will now learn more about what this means



The following are some of the components, they will help us learn prefixes, how to dissect words:

Pentose monosaccharide: 
a pentose is a monosaccharide (simple sugar) with five carbon atoms.

pent-five

mono- one

​saccharide- sugar​

Picture
https://isabellaacostabioportfolio.weebly.com/26-structure-of-the-dna-and-rna.html

Deoxyribose: 

a sugar derived from ribose by replacing a hydroxyl group with hydrogen.

etymology:
de- (expressing reduction) + oxy-2 + ribose.
​
Picture
https://www.sciencedirect.com/topics/nursing-and-health-professions/2-deoxyribose
​


RNA has ribose, 
DNA has deoxyribose

Picture
DNA RNA comparison

Picture
http://www.phschool.com/science/biology_place/biocoach/bioprop/ribose.html

Triphosphate, diphosphate, monophosphate:

Mono- one
Di- two
Tri- three
​
phosphate- phosphorous groups
​

Picture
https://www.sciencedirect.com/topics/medicine-and-dentistry/adenosine-triphosphate

​Nitrogenous base: a nitrogen-containing molecule that has the same chemical properties as a base.

They are particularly important since they make up the building blocks of DNA and RNA: adenine, guanine, cytosine, thymine and uracil.


Picture
https://ib.bioninja.com.au/standard-level/topic-2-molecular-biology/26-structure-of-dna-and-rna/nitrogenous-bases.html
​


​Purines and Pyrimidines


Picture
https://www.diffen.com/difference/Purines_vs_Pyrimidines

​Bonding:
​

Picture
https://socratic.org/questions/why-do-purines-pair-with-pyrimidines
​


​Bases found in DNA are ATCG

Bases found in RNA are AUCG
​

RNA is usually single stranded, 
​
DNA is usually double stranded

mRNA is a small "photocopy" of genetic information

DNA is the cell's archive for genetic information passed down from one generation to the next generation 

A gene is a part or segment of DNA
​


Organic Compounds


Alkane:

any of the series of saturated hydrocarbons including methane, ethane, propane, and higher members.

Nomenclature of alkanes


Picture
https://www.quora.com/How-can-I-compare-the-boiling-point-of-alkanes
​

Phosphate: 

In chemistry, a phosphate is an anion, salt, functional group or ester derived from a phosphoric acid.
​
Picture
http://www.chem.ucla.edu/~harding/IGOC/P/phosphate_group.html
​


Carbonyl Group (aldehyde and ketones): 

a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O
​
Picture
http://www.chem.ucla.edu/~harding/IGOC/P/phosphate_group.html
​

Picture
http://biology.reachingfordreams.com/chemistry-cheat-sheet/organic-chemistry/32-aldehydes-and-ketones
​

R group:

An abbreviation for any group in which a carbon or hydrogen atom is attached to the rest of the molecule.
​

https://www.youtube.com/watch?v=pyRmpNIKfeA
​

Carboxylic Acid Group: 

an organic compound that contains a carboxyl group (C(=O)OH).[1] The general formula of a carboxylic acid is R–COOH, with R referring to the alkyl group.

Carboxylic acids occur widely. Important examples include the amino acids and acetic acid.
​

https://en.wikipedia.org/wiki/Carboxylic_acid
​

Picture

​https://www.sciencedirect.com/topics/neuroscience/carboxylic-acids
​
Hydroxyl:

Have O-H

Groups are polar, and the oxygen side is always negative, while the hydrogen side is always positive.
​
Picture

​https://www.youtube.com/watch?v=pyRmpNIKfeA

Picture
https://slideplayer.com/slide/733051/
​

Amines:


Picture
https://socratic.org/questions/what-are-the-reactions-for-amines-and-amides
​

Picture

​https://revise.im/chemistry/rpa/amines-amino
​

​Amide:


An amide is a functional group containing a carbonyl group linked to a nitrogen atom or any compound containing the amide
 functional group.
​
Picture

​http://www.chem.ucla.edu/~harding/IGOC/A/amide.html

Picture
https://www.masterorganicchemistry.com/2019/10/07/amide-hydrolysis/

Picture

​https://www.askdifference.com/amide-vs-amine/



Amino Acid Structures


Picture

https://www.quora.com/Does-every-amino-acid-contain-nitrogen
​

Picture

​https://www.quora.com/What-is-the-difference-between-amide-and-amino-acid-regarding-N2

Picture

https://openi.nlm.nih.gov/detailedresult?img=PMC4282886_pathogens-03-00791-g001&req=4
​


Polarity


Picture

The water molecule is made up of oxygen and hydrogen, with respective electronegativities of 3.44 and 2.20.

The electronegativity difference polarizes each H–O bond, shifting its electrons towards the oxygen (illustrated by red arrows).

These effects add as vectors to make the overall molecule polar.
​

https://en.wikipedia.org/wiki/Chemical_polarity
​

Picture

​https://www.quora.com/How-do-I-know-if-an-amino-acid-is-polar-or-nonpolar


FUnctional Groups


Picture

https://www.vanderbilt.edu/vicb/discovery_archives/discovery_new_functional_group.html

Picture

https://wou.edu/chemistry/courses/online-chemistry-textbooks/ch105-consumer-chemistry/ch105-chapter-9-organic-compounds-oxygen/


Picture

​https://chem.libretexts.org/Courses/Purdue/Purdue%3A_Chem_26505%3A_Organic_Chemistry_I_(Lipton)/Chapter_2._Functional_Groups_and_Nomenclature/2.050_Functional_Groups
​

Peptide bond


Picture

​https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/a/introduction-to-proteins-and-amino-acids
​
Sulfhydryl group (thiol)
​

Picture
https://commons.wikimedia.org/wiki/File:Thiol-group.svg

Esther and Ether


Picture

https://byjus.com/chemistry/difference-between-ester-and-ether/

Picture

​
http://www.ilpi.com/msds/ref/ether.html


Picture

https://glossary.periodni.com/glossary.php?en=ester

Picture
https://socratic.org/questions/what-is-ester-linkage-in-lipids
​

Picture

https://courses.lumenlearning.com/wm-biology2/chapter/archaea-vs-bacteria/

https://course-notes.org/flashcards/campbell_biology_ninth_edition_chapter_5_the_structure_and_function_of_large_biological_molecules_flashcards

Bonds in DNA
​

Picture
https://ppt-online.org/279894
​


Acids and Bases


Picture

​https://opentextbc.ca/chemistry/chapter/14-3-relative-strengths-of-acids-and-bases/

Acids donate H ions, bases take them

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3/1/2020

Gene COde

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Connect Genetics to Protein Synthesis



WHat is a gene?



DNA Transcription and Translation



​RNA is synthesized from DNA by an enzyme known as RNA polymerase during a process called transcription.

The new 
RNA sequences are complementary to their DNA template, rather than being identical copies of the template. 

RNA is then translated into proteins by structures called ribosomes.
​

Messenger RNA (mRNA) carries the instructions to make a particular protein of the DNA from the nucleous to the ribosomes. 

The process of producing mRNA from instructions in the DNA is called transcription. 

During transcription, the DNA molecule unwinds and separates exposing the nitrogenous bases. 

Free RNA nucleotides pair with the exposed bases. 

No thymine (T) is in RNA.  Uracil (U) pairs with adenine (A) instead. 

RNA contains the sugar ribase instead of deoxyribose. 

The mRNA molecule is completed by the formation of bonds between the RNA nucleotides, and it then separates them from the DNA. 

The mRNA molecule is a single strand, unlike DNA.
​

Picture

https://socratic.org/questions/how-would-you-describe-the-steps-in-protein-synthesis
​

Picture
https://kids.britannica.com/students/assembly/view/53364
​


Protein FOlding


Picture
https://www.nature.com/articles/d41586-019-01357-6
​

https://www.sciencedaily.com/releases/2014/01/140113154211.htm
​

https://news.uchicago.edu/story/discovery-new-fossils-reveals-key-link-evolution-hind-limbs
​


Chitin is a protein in mushrooms, also sea sponges, crustaceans, and insects



The theory of fish:

​https://www.fishkeepingworld.com/evolution-of-fish/


Agnathan
​

Picture
https://www.britannica.com/animal/sea-lamprey
​

https://www.pnas.org/content/101/36/13273

They have chitinous teeth:

https://books.google.com/books?id=bvAqAAAAYAAJ&pg=PA288&lpg=PA288&dq=agnathan+chitin&source=bl&ots=oKX_Dmfsa1&sig=ACfU3U27yAJg3uH8zRExhYjBPxjDQN8bxw&hl=en&sa=X&ved=2ahUKEwit7-uQs_vnAhUB2qwKHcg8Cts4ChDoATADegQIChAB#v=onepage&q=agnathan%20chitin&f=false

https://books.google.com/books?id=t4jjBwAAQBAJ&pg=PA881&lpg=PA881&dq=agnathan+teeth+are+made+of+chitin&source=bl&ots=QVyP0p5TWf&sig=ACfU3U04pCpZXzJNvBioh-gVzhHMyD8fLg&hl=en&sa=X&ved=2ahUKEwiSnOXCs_vnAhUJ26wKHYnxAvIQ6AEwFXoECA0QAQ#v=onepage&q=agnathan%20teeth%20are%20made%20of%20chitin&f=false


Chondrichthyes



Fish with cartilage skeletons
​

There is a chitin/fish connection here:

https://www.scirp.org/journal/PaperInformation.aspx?paperID=82188
​


​Chitin based barrier in some fish:
Picture
https://www.researchgate.net/figure/A-chitin-based-barrier-immunity-model-a-A-model-The-intestinal-mucosal-surface-of-the_fig2_327210331
​


Chitin Molecular Structure


Picture

​https://www.degruyter.com/view/j/psr.2016.1.issue-9/psr-2016-0048/psr-2016-0048.xml
​

Structure and FUnction



​Pg 331
​


Fossil Record



Geological Timescale


Picture
http://prehlife.weebly.com/paleozoic.html

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