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10/30/2020

Ancient Life Forms and Evidence of Adaptation

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Taxonomy



​The science of naming, describing and classifying organisms and includes all plants, animals and microorganisms of the world.

Every species is organized by Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.


Picture
https://www.biologyjunction.com/classification-of-living-things


Phylogenetic Tree

Picture

https://www.thoughtco.com/three-domain-system-373413

The three Domains are Bacteria, Eukaryota, and Archaea

Bacteria are prokaryotes, they do not have a nucleus

Eukaryotes have a nucleus, this group includes plants, animals, fungi, and many single celled eukaryotes

Archaea are very ancient, some live in environments that few living beings can thrive in



Stromatolites



Are about 3.5 billion years old, calcareous mound built up of layers of lime-secreting cyanobacteria and trapped sediment, found in Precambrian rocks as the earliest known fossils, and still being formed in lagoons in Australasia.

Cyanobacteria are very ancient life forms, perhaps only Archaea are older.

Picture

​https://sciencestruck.com/what-are-stromatolites-how-do-they-form
​


FOssil Dating


Radiometric Dating 

The use of radioactive isotopes as a measure for determining the age of a rock or fossil
​
Radioactive isotope

An unstable form of an element that decays into another element by radiation, that is, by emitting energetic particles

Half-Life

The amount of time it takes for one half of a substance to decay

Uranium-238

Has a half life of 4.5 billion years

Potassium-40

Has a half life of 1.3 billion years


Types of life



​Prokaryotes

Found to have existed 3.5 billion years ago, a microscopic single-celled organism that has neither a distinct nucleus with a membrane nor other specialized organelles.


Prokaryotes include the bacteria and cyanobacteria.
  • Unicellular organism who lacks membrane bound organelles
  • DNA not in a nucleus, it just floats around in cytoplasm
  • much smaller than eukaryotic cells
  • a prokaryote is about the size of a mitochondria in a eukaryote 
  • single DNA loops

Bacteria and Archaea are prokaryotes
​
Picture

https://www.khanacademy.org/science/high-school-biology/hs-cells/hs-prokaryotes-and-eukaryotes/a/prokaryotic-cells
​

Bateria may have:


Flagella


whip-like appendages used to move around, like arms


Pili

short, hair-like appendages extending from the surface, used to stick to surfaces


Capsule

​
sticky coating, used to stick to surfaces
​


Types of bacteria



​Cyanobacteria 

are a phylum of bacteria that obtain their energy through photosynthesis and are the only photosynthetic prokaryotes able to produce oxygen.


Round bacteria 

are referred to as cocci (singular: coccus),

an example is Streptococcus 
​
​C
ylindrical, capsule-shaped bacteria 

are named bacilli (singular: bacillus), 
bacteria that make yogurt: Lactobacillus bulgaricus ​

​Spiral bacteria 

are called spirilla (singular: spirillum) 
​Lyme disease and syphillis are caused by this type of bacteria
​
Picture

https://microbenotes.com/classification-of-bacteria/


Binary Fission



​Cell division in prokaryotes is called binary fission, asexual reproduction by a separation of the body into two new bodies, cells transfer genetic information by making contact. 

​Both Archaea and Bacteria can reproduce through binary fission. 


Picture

​https://simple.wikipedia.org/wiki/Binary_fission
​


are all bacteria bad?



​
​Some but not all bacteria are pathogens: a disease causing agent

Some bacteria are purely beneficial and help with symbiosis: the relationship in which two different organisms live together, often interdependently. 

Nitrogen Fixation:


Converting atmospheric nitrogen into a form that plants can use to grow
  • ​Two types of bacteria do this job: non-symbiotic bacteria in the soil and symbiotic bacteria that live in the roots of plants.
  • Bacteria in the genera Clostridium and Azotobacter are non-symbiotic nitrogen-fixing bacteria.
  • The genus Rhizobium are symbiotic bacteria.
​
Picture

https://en.wikipedia.org/wiki/Nitrogen_fixation


Archaea



The other domain of prokaryotic life, tend to live in extreme environments

Grouped according to where they live (pg 371):
​
  • Halophiles: live in very salty places
  • Hyperthermophile: extremely high temperatures (80 to 100 Celcius), (176 to 212 Fahrenheit) ​
​

Some Archaea live in hydrothermal vents



In deep sea vents, heated fluids rise to the surface through openings in the seafloor. Hydrothermal fluid temperatures can reach 400°C (750°F) or more, but the archaea do not boil under the extreme pressure of the deep ocean.

As they pour out of a vent, the fluids encounter cold, oxygenated seawater, causing another, more rapid series of chemical reactions to occur. Sulfur and other materials precipitate, or come out of solution, to form metal-rich towers and deposits of minerals on the seafloor. 

​The sea floor is an anaerobic environment, no oxygen

  • Serpentinization: H2, hydrogen is formed when mantle rock is exposed to seawater, the rock columns that are formed as gases emerge from the earth's crust in hydrothermal chimneys
​
  • Methanogens: archaea that produce methane as a by-product of converting energy from carbon dioxde, using hydrogen H2 as an energy source
  
  • Anaerobic Archaea: eat methane
​

Who lives there



It is theorized that this is where life on Earth originated



Deep sea mining might be connected to cobalt mining



Cobalt is used for phones and computer batteries, some companies are interested in mining it from the deep sea. 

​Alternatives to cobalt are needed so companies don't consider deep sea mining a viable option.



Most Cobalt currently comes from Democratic Republic of Congo


DR Congo produces 60% of the world's supply of cobalt. The mineral is used to produce lithium-ion batteries used to power electric cars, laptops and smartphones. However, the extraction process has been beset with concerns of illegal mining, human rights abuses and corruption.

https://www.bbc.com/news/world-africa-50812616#:~:text=DR%20Congo%20produces%2060%25%20of,human%20rights%20abuses%20and%20corruption.


What are alternatives to cobalt?



A good battery is able to store current and transfer it, conduct heat, and cool quickly.


Other possibilities



​Manganese:


https://www.azomining.com/Article.aspx?ArticleID=1438
​

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10/25/2020

Technologies in Biology

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Some of the methods that are used to develop Bio tech


Selective breeding

The ancestral form of trait selection, when people intentionally breed plants and animals to have certain characteristics.  When wild plants were bred into food crops.
​
Picture
https://www.businessinsider.com/brassica-oleracea-broccoli-kale-brussels-sprouts-2017-5


​Corn


Picture
https://en.wikipedia.org/wiki/Selective_breeding
​


Genetic Modification in a Lab



Genetic Engineering 



Genetic Engineering with Agrobaterium tumefaciens

Picture

https://sphweb.bumc.bu.edu/otlt/MPH-Modules/PH/GMOs/GMOs3.html



DNA samples are studied through PCR Electrophoresis to see if the target DNA is in the sample.


Picture
Picture

https://www.addgene.org/protocols/gel-electrophoresis/


https://www.addgene.org/protocols/gel-electrophoresis/


Results to read


Picture
https://openoregon.pressbooks.pub/mhccmajorsbio/chapter/dna-isolation-gel-electrophoresis-and-pcr/
​


Genetic Engineering of Mosquitoes



PCR in Crime Scene Investigation



But it is not perfect



What are some possible issues with this biotech?



That applies to plants, what if we GM people?



Emmanuelle Charpentier and Jennifer Doudna have been awarded the 2020 Nobel Prize in Chemistry for their development of CRISPR/Cas9 genetic editing, this video is from 2015.


there are many ethical issues to consider



Stem Cell Organs



Biomedical Engineering includes mechanical, Biological, chemical ENGINEERING and computer software



Upcoming issues to resolve



Antibiotic Resistance


Really, it's a very big deal



It is better to wash your hands than use hand sanitizer, otherwise, the bacteria that survive are the ones that get to pass on their genes

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10/17/2020

The Study of genetics, human and animal genetics

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Genetics Continued



​Chapters 11 and 12
​

​Gregory Mendel’s research on genetics.

What is a Punnett Square and how do we use it?

Natural 
selection and adaptation: insects and plants adapting to chemicals, how organisms find ways to survive.

Mutation

A change in the nucleotide sequence of DNA

Allele

Genetic trait

Recessive Allele

​An allele that is visible in the organism only if to copies of the allele are present

Dominant Allele

an allele that can mask the presence of a recessive allele

Heterozygous


Having two different alleles

Homozygous

Having two identical alleles

Phenotype

The visible or measureable features of an individual.

Genotype

The particular genetic makeup of an individual

Gametes

Specialized reproductive cells that carry one copy of each chromosome (they are haploid)

Haploid

Half the genetic information compared to most cells, one copy of every chromosome

Diploid

Having two copies of every chromosome

Homologous chromosomes

The two copies of each chromosome in a diploid cell.  

Meiosis

A specialized type of cell division that generated genetically unique haploid gametes

Recombination

An early stage of development in which maternal and paternal chromosomes pair and physically exchange DNA segments
​
Picture

​Independent Assortment


The principle that alleles of different genes are distributed independently of one another during meiosis

Picture

Stem Cell Technology to help Same Sex couples reproduce: In vitro Gametogenesis 




Zygote

A cell that is capable of developing into an adult organism.

Embryo

An early stage of development reached when a zygote undergoes cell division to form a multicellular structure.



Cystic Fibrosis


Carrier

An individual who is heterozygous for a particular gene of interest, and can pass the recessive allele to offspring.
​

Picture

Punnett Square

A diagram used to determine the probabilities of offspring having particular genotypes b looking at the genotypes of the parents

Picture

https://www.sciencedirect.com/science/article/pii/S1569199317309700



CRISPR  (/ˈkrɪspər/) (clustered regularly interspaced short palindromic repeats) 

​Gene editing technology.

The 2020 Nobel Prize in Chemistry has gone to Emmanuelle Charpentier and Jennifer A. Doudna “for the development of a method for genome editing.” That method, formally known as CRISPR-Cas9 gene editing but often called simply CRISPR, allows scientists to precisely cut any strand of DNA they wish.
 
https://cen.acs.org/biological-chemistry/gene-editing/CRISPR-genome-editing-2020-Nobel/98/i39#:~:text=The%202020%20Nobel%20Prize%20in,strand%20of%20DNA%20they%20wish.
​


CF is Recessive, Huntington's Disease is Dominant


Picture
https://en.wikipedia.org/wiki/Dominance_(genetics)
​


​With an autosomal dominant trait, if one parent has it, the children have a 50% chance of inheriting that gene, if they have that gene, they have the trait.


Picture
https://vanhornhuntingtonsdisease.weebly.com/


https://www.bbc.com/news/world-latin-america-10952800#:~:text=The%20village%20of%20Barranquitas%20in,work%20to%20find%20a%20cure.


​https://www.mayoclinic.org/diseases-conditions/huntingtons-disease/symptoms-causes/syc-20356117



Pedigree Chart


Picture

https://www.britannica.com/science/pedigree-genetics

Hemophilia is an inherited bleeding disorder in which the blood does not clot properly

Hemophilia is a sex-linked trait and recessive.

The recessive gene for hemophilia is carried on the X chromosome.

Males inherit one affected X chromosome from the mother and, less commonly, females inherit an affected X chromosome from both mother and father experience the disease.

Females who inherit an affected X chromosome from either mother or father are carriers for the disease. 



More genetic complexities



Autosomes

Paired chromosomes present in both males and females; all chromosomes except the X and Y chromosomes

X Linked trait

a phenotype determined by an allele on an X chromosome

Incomplete Dominance

Heterozygotes have a phenotype that is intermediate between the dominant and the recessive genes.

Wavy hair is an example

Codominance

Both alleles contribute equally to the phenotype

An example is Blood Type

The three blood types are A, B, and O

The possible combinations that we inherit from parent are:

OO, AO, BO, AB, AA, and BB


Both parental alleles contribute equally to the phenotype 

O is recessive

So if you are blood type A, you may be AA homozygous or AO heterozygous

Different blood types have different surface markers, not every blood type is compatible:


Picture

Genes move with individuals



​Genetic drift


a change in the frequency of an allele within a population over time

Picture

https://www.khanacademy.org/science/biology/her/heredity-and-genetics/a/genetic-drift-founder-bottleneck
​

As individuals move around we can observe genetic drift



​Bottleneck Effect


Something happens leaving only a few individuals to reproduce​
Picture
​https://www.nps.gov/articles/bison-bellows-12-3-15.htm
​

Picture

​https://www.mun.ca/biology/scarr/NS_02-03.html
​

​
​Founder Effect

The new population might not fully represent the ancestral population


Picture

https://socratic.org/questions/what-are-the-two-forms-of-genetic-drift-and-examples
​


Tasmanian devils and population bottleneck


Picture

http://tasmaniandevil.psu.edu/background.html


Natural Selection


Picture

https://microbenotes.com/natural-vs-artificial-selection/microbenotes.com/natural-vs-artificial-selection/

Picture
https://www.nationalgeographic.com/news/2018/02/animals-climate-change-winter-evolution/

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10/11/2020

Genetics intro

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GENETIC SEQUENCES IN CHROMOSOMES ARE CALLED GENES


Picture

https://www.sciencelearn.org.nz/resources/1328-mistakes-in-dna


Gene

plural noun: genes


A unit of heredity which is transferred from a parent to offspring and determines some characteristic of the offspring.

"proteins are coded directly by genes"


A distinct sequence of nucleotides forming part of a chromosome, the order of which determines the order of monomers in a polypeptide or nucleic acid molecule which a cell (or virus) may synthesize.
​
Allele

Variation of a genetic trait


Dominant allele
​

An allele that produces the same phenotype whether its paired allele is identical or different

​Recessive allele

An allele that produces its characteristic phenotype only when its paired allele is identical​


Coding DNA

Sequence of a gene's DNA that transcribes into protein structures

Phenotype

Physical genetic expression

Genotype

Internal genetic expression


Gene expression

Conversion of the information encoded in a gene first into messenger RNA and then to a protein
​

​https://www.lexico.com/en/definition/gene
​

Picture

https://www.pinterest.com/pin/560064903641420013/



CHROMOSOMES GO THROUGH CHANGES TO CREATE A VARIETY OF GAMETES



Gamete:

a Sex cell

​​
Crossing over
 

​occurs between prophase I and metaphase I 
of meiosis, some genes are swapped to create unique gametes.


Picture

https://www.quora.com/Does-crossing-over-occur-between-all-the-23-pairs-of-chromosomes


​Gamete production is meiosis. 

A gamete is a mature haploid male or female germ cell which is able to unite with another of the opposite sex in sexual reproduction to form a zygote.

​

Gregor Mendel


Picture

https://www.britannica.com/biography/Gregor-Mendel

Austrian Monk and botanist, he observed peas to see the traits that were inherited by their offspring.

Picture

​https://study.com/academy/lesson/gregor-mendel-genetics-experiments-laws-discovery.html



Punnett Square



​The 
Punnett square is a square diagram that is used to predict the genotypes of a particular cross or breeding experiment.

It is named after Reginald C. 
Punnett.

The diagram is used by biologists to determine the probability of an offspring having a particular genotype.
​
Picture
https://en.wikipedia.org/wiki/Punnett_square#/media/File:Punnett_Square.svg
​


Guinea Pig Fur Color

Picture

​​https://www.quora.com/How-can-a-Punnett-square


Cystic Fibrosis

Picture
https://twowomensci.wordpress.com/2019/04/21/cystic-fibrosis-the-disease-that-changed-our-family-forever/


Cystic Fibrosis


Picture
https://arkansascf.com/handout-cf-carrier
​


More COmplex Genetic COmbination



M
onohybrid cross
 

a breeding experiment between P generation (parental generation) organisms that differ in a single given trait. The P generation organisms are homozygous for the given trait.



​​Dihybrid cross 

A cross between two different lines/genes that differ in two observed traits. According to Mendel's statement, between the alleles of both these loci there is a relationship of completely dominant - recessive traits.


Picture

https://www.mun.ca/biology/scarr/Dihybrid_Cross.html

Picture

https://www.quora.com/How-did-you-get-a-genotype-ratio-in-mendel-dihybrid-cross
​

Codominance


Picture
https://www.genome.gov/genetics-glossary/Codominance
​

Picture
https://ibiologia.com/codominance/


X-Linked Traits


Picture
https://petcentral.chewy.com/behavior-pet-facts-are-all-orange-cats-male-all-calico-cats-female/
​

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10/2/2020

Genes, cell types, and Stem Cells

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let's learn more about Types of cells


Stem Cells

Adult Stem Cells/ Somatic Stem cells:  Not specialized yet

Pluripotent Stem Cells

H
ave the capacity to self-renew by dividing and to develop into the three primary germ cell layers of the early embryo during gastrulation and therefore into all cells of the adult body, but not extra-embryonic tissues such as the placenta.

Multipotent Stem Cells


A cell with the ability to differentiate into a limited number of cell types in the body.

Embryonic Stem Cells

Cells from embryonic blastocyst, a few day old fetus, they get these from "leftover" IVF clinic embryos.

Totipotent Stem Cells

Can form all the cell types in a body, plus the extraembryonic, or placental, cells. These are embryonic cells within the first couple of cell divisions after fertilization.

​

Picture

​https://www.businessinsider.com/how-old-are-cells-cellular-lifespan-2016-8
​

Types of cells



  • Bone Cells 
  • Blood Cells
  • Muscle Cells
  • Fat Cells
  • Skin Cells
  • Nerve Cells
  • Endothelial Cells
​

Bone Cells


Picture
Picture

https://www.sciencephoto.com/media/873252/view/osteocyte-bone-cells-sem

Picture

​https://cellapplications.com/bone


Picture

​https://boneresearchsociety.org/resources/gallery/7/


Blood Cells


Picture
Picture

​https://www.bbc.co.uk/bitesize/guides/z3pjsrd/revision/7


https://www.reddit.com/r/Damnthatsinteresting/comments/8f8z2s/scanning_electron_microscop
​

​Red blood cell and white blood cell


Picture

https://www.quora.com/What-does-an-animal-cell-look-like-under-an-electron-microscope

Picture
https://microbiologyinfo.com/blood-cells-types-functions/


Muscle Cells


Picture

​https://www.gettyimages.com/photos/skeletal-muscle

Picture

https://www.dkfindout.com/us/gallery/human-body/types-muscle-cells/

Picture
Picture

https://sciencing.com/structure-function-muscle-cells-6615020.html


https://www.dkfindout.com/us/gallery/human-body/types-muscle-cells/

​
Picture

https://biologydictionary.net/muscle-cell/

Picture

https://www.pinterest.com/pin/516577019754328886/


Fat Cells


Picture

https://www.livescience.com/62218-whats-in-a-fat-cell.html

Picture

https://www.nfpt.com/blog/uncovering-the-biology-behind-fat-cells


Skin Cells


Picture

https://www.quora.com/Why-are-skin-cells-more-likely-to-turn-into-cancer-than-a-muscle-cell

Picture

​https://wtamu.edu/~cbaird/sq/2015/11/23/how-does-the-outer-layer-of-skin-cells-



Stem cell technology for skin recovery


Nerve Cells


Picture

http://people.eku.edu/ritchisong/301notes2.htm



Stem Cell treatment for vision


epithelial cells



​Epithelial cells line the stomach the intestines, our whole digestive tract, they have structures that help them absorb nutrients
​
Picture

https://www.dreamstime.com/illustration/epithelial-cell.html


Cell Membranes



What all of these cells have in common is the cell membrane, membranes are made of a phospholipid bilayer an have channels that allow certain things in and out of the cell.


Picture

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

Picture

https://open.oregonstate.education/aandp/chapter/3-1-the-cell-membrane/


Extracellular: Outside of the cell

Intracellular: Inside the cell


​

Cell Membrane Review



Cholesterol in cell membranes

Around 25-30% of a cell membrane has cholesterol. Cholesterol can fit into spaces between phospholipids and prevent water-soluble molecules from diffusing across the membrane. Cholesterol helps cells keep their shape and stay flexible.


Picture
https://biology4ibdp.weebly.com/13-membrane-structure.html

Membrane proteins

Membrane
 proteins do a series of jobs for the cell, receptor proteins relay signals between the cell's internal and external environments. Transport proteins move molecules and ions across the membrane.
​
Picture
https://www.ck12.org/book/ck-12-biology-advanced-concepts/section/3.12/


​Transport Proteins


Are channels in the cell membrane, the fluid mosaic model, that allow things in and out of the cell.


Picture
https://stke.sciencemag.org/content/6/271/tr3
​



Aquaporins are water channels for the cell

​
Picture
https://www.water-channeling-life.com/en/themes/01.html

Receptor Proteins

Are like antennae, they signal other cells and communicate with the outside of the cell, they may receive hormones or other messages

Picture

​https://www.quora.com/What-are-receptor-proteins

Marker proteins

Extend across the cell membrane and serve to identify the cell. The immune system uses these proteins to tell friendly cells from foreign invaders. They are as unique as fingerprints.


Picture

https://quizlet.com/433904608/biology-unit-3-flash-cards/

These proteins and elements are all part of the

Fluid-mosaic model

A mosaic of components —including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character.

Picture
https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/5%3A_Structure_and_Function_of_Plasma_Membranes/5.1%3A_Components_and_Structure/5.1B%3A_Fluid_Mosaic_Model


Cell Transport Types


Osmosis 

the spontaneous, no energy needed, movement of solvent molecules through a selectively permeable membrane.  From higher concentration to lower concentration to equalize the solution on both sides.

Picture

http://biology4alevel.blogspot.com/2014/09/25-passive-and-active-transport-across.html



​Simple Diffusion

Moves with the flow, from high concentration to low concentration

Facilitated Diffusion

Movement with the flow/ with the concentration gradient, from high concentration to low, with the help of a transport protein.


Passive Transport

A movement of ions and other atomic or molecular substances across cell membranes without need of energy input, so no ATP needed, using a specialized channel protein in the cell membrane.



​Active Transport

Movement against the regular gradient flow, from low concentration to high concentration.

Movement of ions or molecules through a cell membrane using specialized proteins with enzymes, using ATP.

Endocytosis

Bringing things in, like large molecules, the cell will form a vesicle to bring something into the cell.

Receptor Mediated Endocytosis

The molecules that will enter the cell need to have a special signal so the cell can identify them

Pinocytosis

Taking in fluids, cell drinking

Exocytosis

Forming a vesicle to transport a molecule



Picture

https://quizlet.com/250540983/biology-cell-transport-diagram/


​Sodium Potassium Pump

A form of active transport, transports sodium ions out of the cell and potassium ions into the cell

Very important in the function of neurons so action potentials can be fired 




​Types of cell transport:

https://www.ck12.org/book/ck-12-biology/section/3.3/


Different Solutions



​Tonicity


​measure of the osmotic pressure gradient

Hypertonic

Lower concentration of water, more solute molecules, makes cells shrink like pickles

Hypotonic

Less concentrated solution, more solute inside the cell, water will enter the cell and the cell might burst

Isotonic

concentration (of let's say salt) inside and outside the cell are equal



We can see osmosis with an eggsperiment


View this post on Instagram

Egg soaked in vinegar, egg shell dissolves

A post shared by Jazmin Biology (@myinfinitespiral) on Oct 12, 2020 at 4:32pm PDT

View this post on Instagram

The egg weighs 2.7oz

A post shared by Jazmin Biology (@myinfinitespiral) on Oct 12, 2020 at 4:35pm PDT

View this post on Instagram

Let's put the egg in corn syrup, there is more solute outside of the egg than inside the egg, what do you think water will do to balance out the water content of the solution?

A post shared by Jazmin Biology (@myinfinitespiral) on Oct 12, 2020 at 4:39pm PDT

View this post on Instagram

Now it looks very different and weighs 1.6oz

A post shared by Jazmin Biology (@myinfinitespiral) on Oct 13, 2020 at 8:55am PDT


The ten major systems of the body



Parts of the brain
​

How the heart works
​

The respiratory system


Cell Specialization in Plants and anmals


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    Author: Jazmin Gannon

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