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Origami membrane protein

All cell membranes have proteins embedded in them. Each protein has its own job.

Students often draw the proteins in the cell membrane them like this:

With more detail we can see that proteins are three-dimensional machines, with movable parts.

Creative Biomart Lipidsome-Based-Membrane-Protein-Production

Adding more detail, we can now see molecules going in and out of a cell. The membrane proteins open or close as needed to let certain molecules in, and other ones out.

Cell membrane lipid bilayer animation

Here, a student in our class build a three dimensional model of a membrane protein. He made one monomer; and then attached several of them to make a polymer.

Monomer Polymer Lego analogy

Instead of attaching eight monomers in a straight line, he’ll form them into a circle:

This becomes a model of a protein that floats in a cell’s membrane,

It can have two shapes, closed or opened, depending on how it’s folded.

It allows certain molecules in or out of a cell, as needed.

protein folding 1

protein folding 2

protein folding 3

protein folding 4

protein folding 5

protein folding 6

protein folding 7

For instructions we may refer to a video from AskABiologist:

Proteins are made of building blocks called amino acids, and have their own special shape. Not only do they look different, but they have different jobs to do inside the cell. Some proteins help move things around in the body, others act like support structures or glue to hold parts of the cell together, and some can help reactions in the cell go faster. The protein we’re making is a channel that sits in the outer cell surface, or membrane, and works like a door that lets certain molecules pass through. Some channels are open all the time while others can be closed depending on signals from the cell or the environment.

Narration by Rebecca Elaine Ryan
Original origami design by Florence Temko

Step-by-step directions

Here’s the video from AskABiologist

Proteins fold into biological machines

Here is a great app that teaches us about protein folding – Protein folding

Individual amino acids have side chains with varying properties of electrical charge. When suspended in water, chains of amino acids can move, bend, and interact with one another along the chain and with the surrounding environment. Forces of electrical attraction and repulsion cause the chain to eventually settle into a conformation that maximizes the molecule’s stability.

Explore the folding of proteins using the free educational simulations and activities below. These scientifically accurate models are great for the classroom, homework assignments, or independent learning. Use them to explore some of the forces involved in the creation of three-dimensional structures in proteins:  1. Where do proteins come from. 2. A closer look at amino acids. 3. The impact of electrical charge. 4. The impact of the surrounding medium.

Protein folding: The Concord Consortium

Learning Standards

Massachusetts Curriculum Frameworks: Biology

8.MS-PS1-1. Develop a model to describe that (a) atoms combine in a multitude of ways to produce pure substances which make up all of the living and nonliving things that we encounter, (b) atoms form molecules and compounds that range in size from two to thousands of atoms, and (c) mixtures are composed of different proportions of pure substances.

HS-LS1-6. Construct an explanation based on evidence that organic molecules are primarily composed of six elements, where carbon, hydrogen, and oxygen atoms may combine with nitrogen, sulfur, and phosphorus to form monomers that can further combine to form large carbon-based macromolecules.

Disciplinary Core Idea Progression Matrix: PS1.A Structure of matter: That matter is composed of atoms and molecules can be used to explain the properties of substances, diversity of materials, how mixtures will interact, states of matter, phase changes, and conservation of matter.

Teaching about evolution

So, we’re supposed to teach our students about evolution – but where to start? What topics to cover? And in what order should we cover them? And for each topic, what are the relevant learning standards? This sequence works for me:

Chicken or the egg

Abiogenesis & spontaneous generation

Abiogenesis – modern discoveries

Charles Darwin’s Voyage of Discovery and Darwin’s notebook

Darwin’s finches

Fossils: Evidence of evolution over time and Dating of fossils

Convergent evolution and Homologous and analogous structures

Natural selection

Artificial selection

clades & phylogenies

clades rotate = equivalent phylogenies

Gradualism vs. Punctuated Equilibrium

Examples of evolution

Evolution of our kidneys

Evolution of humans

Evolution of whales

Where did the idea of evolution develop? How has the idea of evolution changed over time?

Advanced topics

Evolution of the first animals

Ontogeny and Phylogeny: Addressing misconceptions

Did nerves evolve twice?

Horizontal Gene Transfer and Kleptoplasty

Evolution and the 2nd law of thermodynamics

Scars of evolution

Teaching about cells

So, we’re supposed to teach our students biology – but where to start? What topics to cover? And in what order should we cover them? And for each topic, what are the relevant learning standards? This sequence works for me:

Characteristics of Life
Organelles, an introduction
Organelles: In more depth

What is the role of enzymes in cells?

Diffusion

Osmosis

Endocytosis and exocytosis

Then we move on to types of cells

Bacteria

Archaea

Now the nitty-gritty: Cell reproduction

Mitosis

Asexual reproduction

Meiosis

For those teaching Honors Biology

Active transport across cell membranes

Ion channels and carrier proteins

Endosymbiosis: origin of eukaryotic cells from prokaryotes

Psychiatry

Psychiatry is a medical  field devoted to the diagnosis, study, and treatment of mental disorders.

The following intro has been adapted from Wikipedia:

ai-brain

Psychiatric assessment of a person typically begins with a case history and mental status examination.

Physical examinations and psychological tests may be conducted.

On occasion, neuroimaging or other neurophysiological techniques are used.

Mental disorders are often diagnosed in accordance with criteria listed in diagnostic manuals. Examples include:

Diagnostic and Statistical Manual of Mental Disorders (DSM),
by the American Psychiatric Association (APA),

and the International Classification of Diseases (ICD),
by the World Health Organization (WHO).

Psychopharmacology became important starting with Otto Loewi‘s discovery of the neuromodulatory properties of acetylcholine. This is the first-known neurotransmitter.

Neuroimaging was first utilized as a tool for psychiatry in the 1980s.

subpage_people_brain_scans_03

The discovery of chlorpromazine‘s effectiveness in treating schizophrenia in 1952 revolutionized treatment of the disorder.

Another major discovery (1948) was the chemical lithium carbonate. This molecule can stabilize mood highs and lows in bipolar disorder.

Biopsychiatric research – This has shown us how biology is related to psychiatry.

We have discovered that there are relationships between certain mental illnesses, and certain abnormalities of brain structure. This includes schizophrenia.

We have also discovered that some genetic mutations are related to psychiatric disorders. This includes schizophrenia, bipolar disorder, and autism.

In general, though, science has not progressed to the stage that we can identify clear biomarkers of these disorders.

In other words, we don’t have specific biochemical tests for mental disorders.

Mental disorders don’t exist on their own

From The hidden links between mental disorders

Psychiatrists have a dizzying array of diagnoses and not enough treatments.
Hunting for the hidden biology underlying mental disorders could help.
Michael Marshall, Nature 581, 19-21 (2020). doi: 10.1038/d41586-020-00922-8

In 2018, psychiatrist Oleguer Plana-Ripoll was wrestling with a puzzling fact about mental disorders. He knew that many individuals have multiple conditions — anxiety and depression, say, or schizophrenia and bipolar disorder. He wanted to know how common it was to have more than one diagnosis, so he got his hands on a database containing the medical details of around 5.9 million Danish citizens.

He was taken aback by what he found. Every single mental disorder predisposed the patient to every other mental disorder — no matter how distinct the symptoms. “We knew that comorbidity was important, but we didn’t expect to find associations for all pairs,” says Plana-Ripoll, who is based at Aarhus University in Denmark.

The study tackles a fundamental question that has bothered researchers for more than a century. What are the roots of mental illness? In the hope of finding an answer, scientists have piled up an enormous amount of data over the past decade, through studies of genes, brain activity and neuroanatomy. They have found evidence that many of the same genes underlie seemingly distinct disorders, such as schizophrenia and autism, and that changes in the brain’s decision-making systems could be involved in many conditions.

They have a few theories. Perhaps there are several dimensions of mental illness — so, depending on how a person scores on each dimension, they might be more prone to some disorders than to others. An alternative, more radical idea is that there is a single factor that makes people prone to mental illness in general: which disorder they develop is then determined by other factors. Both ideas are being taken seriously, although the concept of multiple dimensions is more widely accepted by researchers.

The details are still fuzzy, but most psychiatrists agree that one thing is clear: the old system of categorizing mental disorders into neat boxes does not work. They are also hopeful that, in the long run, replacing this framework with one that is grounded in biology will lead to new drugs and treatments. Researchers aim to reveal, for instance, the key genes, brain regions and neurological processes involved in psychopathology, and target them with therapies. Although it might take a while to get there, says Steven Hyman of the Broad Institute of MIT and Harvard in Cambridge, Massachusetts, “I am long-term optimistic if the field really does its work.”

 

Related articles

Neuroscientist argues that addiction is not a disease

Is a ‘Spectrum’ the Best Way to Talk About Autism?

Learning styles and multiple intelligences

Psychopathy

Psychopaths Don’t Care If They Hurt You. This Is Why. New research shows why the psychopathic are so likely to harm others.

Detecting genetic disorders with 3d face scans

Link between marijuana and pyschosis, and depression, hyperactivity, and inattention in children.

Mysterious link between immune system and mental illness – He Got Schizophrenia. He Got Cancer. And Then He Got Cured.

 

Article on mental health disorders

NIMH Disruptive Mood Dysregulation Disorder

 

Learning Standards

Massachusetts Comprehensive Health Curriculum Framework

PreK–12 STANDARD 5: Mental Health. Students will acquire knowledge about emotions and physical health, the management of emotions, personality and character development, and social awareness; and will learn skills to promote self-acceptance, make decisions, and cope with stress, including suicide prevention.

Benchmarks: American Association for the Advancement of Science

Stresses are especially difficult for children to deal with and may have long-lasting effects. 6F/H1
Biological abnormalities, such as brain injuries or chemical imbalances, can cause or increase susceptability to psychological disturbances. 6F/H2
Reactions of other people to an individual’s emotional disturbance may increase its effects. 6F/H3
Human beings differ greatly in how they cope with emotions and may therefore puzzle one another. 6F/H4
Ideas about what constitutes good mental health and proper treatment for abnormal mental states vary from one culture to another and from one time period to another. 6F/H5
Psychological distress may also affect an individual’s vulnerability to biological disease. 6F/H6** (SFAA)
According to some theories of mental disturbance, anger, fear, or depression may result from exceptionally upsetting thoughts or memories that are blocked from becoming conscious. 6F/H7** (SFAA)

Organelles in depth

Cell membrane

Made of 2 layers of lipids (fats); aka lipid bilayer.

We sometimes see simplified 2D drawings of this.

This drawing shows a small section of the lipid bilayer: 2 layers of lipids and some proteins floating in these lipids.

A more accurate visualization would be to show this in three dimensions:

We sometimes see simplified 2D drawings of this. This drawing shows a small section of the lipid bilayer: 2 layers of lipids and some proteins floating in these lipids.

Cytoplasm

A thick viscous liquid filling the cell.

All the organelles float in it.

Filled with millions of enzymes, dissolved salt ions, and other chemicals.

Dancing Queen molecules in cytoplasm

Here is a (false color) visualization of proteins floating in a cell’s cytoplasm. Densely packed!

Densely packed proteins in cytoplasm

Nucleus

The command-and-control center of the cell.

Chromosomes (made of DNA) are stored in here. In this animation we see DNA in the nucleus, and a copy of it (RNA) leaving the nucleus and going out into the rest of the cell.

Nucleus DNA RNA mRNA ribosome transcription translation.gif

Here we see a more realistic image of the nucleus (lower left); we see mRNA copies of DNA coming out of the nucleus through nuclear pores.

Nucleus to ribosomes to ER GIF Protein synthesis NPR

Nucleus to ribosomes to ER GIF from NPR: Protein synthesis

Chromosomes

If we magnify a cell we see chunks floating in the nucleus called chromosomes. They are made of a chemical called DNA.

organism cell chromosome DNA 2

Here we see a cell nucleus being lysed (broken open) and all the chromosomes are spilling out on the right.

The color was added by hand to make it easier to tell them apart. We cut-and-paste each of the chromosomes, number them, and line them up (lower left.)

In humans we find 23 pairs of chromosomes in every cell.

These X shaped chromosomes are not solid; they are like objects made of wound-up yarn.

A chromosome could be unwound into a long, thing string.

This string is made of DNA molecules.

chromosomes 1

Each section of the chromosome has difference sequences of DNA.

A complete sequence of DNA is called a gene; it is an instruction on how to build a protein.

Mitochondrion

Plural is mitochondria.

Converts energy from food molecules into a form usable by the cell.

and

 

Ribosomes

Little organic machines that take in amino acids (from our food) and turn them into proteins.

They are very tiny compared to the size of a cell – often seen as mere dots. 

plant and animal cell ribosomes

Here we see the ribosomes picking up RNA, and using that instruction to build a protein.

Nucleus to ribosomes to ER GIF Protein synthesis NPR

Nucleus to ribosomes to ER GIF from NPR: Protein synthesis

Ribosomes struck on an organelle

On the right we can just barely see the ribosomes as small dots stuck to the ER (endoplasmic reticulum.)

On the left we see the ER magnified.

The ribosomes are a bit clearer here (although we still don’t see their details.)

When the ER is covered with ribosomes we call it the “rough ER.”

Darryl Leja, NHGRI Rough endoplasmic reticulum and ribosomes

Darryl Leja, NHGRI Rough endoplasmic reticulum and ribosomes

Other ribosomes float freely in the cytoplasm.

Here we see mRNA copies of DNA coming out of a cell nucleus, and moving to a ribosome floating nearby.

Here’s how we remember this:

Beyonce look like the rough ER

ER (endoplasmic reticulum)

This manufactures lipids and proteins.

Like an assembly line which makes our products.

Rough ER GIF

Next, molecules from the ER are packaged into vesicles, and transported to the Golgi apparatus.

Vesicles transport from ER to Golgi-min

Golgi body

This organelle packages proteins into vesicles, tags them with an “address” and send them to their destination.

Golgi GIF

another image will be here:

Details of Golgi bodies function and organization

ER Golgi stack Cis Medial Trans vesicle

From The Cell: A Molecular Approach, 5th ed. Cooper & Hausman. 2009

The Endomembrane system

Here we see the while system, from products leaving the nucleus, going to the ER, then to the Golgi, and then secreted as a vesicle.

In this case the products are going out to the cell membrane (“plasma membrane.)

endomembrane ER Golgi Exocytosis

From Biotech Review YouTube channel.

More details: The endomembrane system is composed of the different membranes that are suspended in the cytoplasm within a eukaryotic cell.

Endomembrane system by Mariana Ruiz Villarreal LadyofHats

Endomembrane system by Mariana Ruiz Villarreal, LadyofHats

 

Cytoskeleton

These thin protein tubes give the cell its shape and mechanical resistance to deformation.

With the right stains, one can take a beautiful photo of the cytoskeleton.

Lysosome

Contain enzymes that can break down virtually all kinds of biomolecules. Garbage disposal.

Lysosome GIF

Vacuoles

A lipid bag that can store organic molecules.

Vacuole GIF

Chloroplasts

In this movie of plant cells, we some small, green discs moving around: these are chloroplasts.

Chloroplasts in plant cell 6 smaller

They contain a light-absorbing pigment (colored molecule), chlorophyll.

This molecules captures the energy from some wavelengths of light.

The plant cell stores this energy in chemical bonds. The plant builds ATP and sugar molecules which store this energy.

In this image we see some chloroplasts floating within a plant cell.

Here we see a single chloroplast, vastly magnified with a TEM (transmission electron microscope.)

We see that there is quite a bit of detail within them.

Chloroplast structure Thylakoid Granum

Cell wall

Note that animal cells don’t have this organelle. Only plants and bacteria have it.

Made of cellulose – a special sugar used to provide structure, and not used for energy.

If the cell membrane is like a balloon, then the cell wall is like a cardboard box around the balloon, protecting it.

Gives strength and support. Allows plants like bamboo and trees to grow tall.

Animal cell versus plant cell

Here we see a typical boxy shaped plant cell, clearly showing the cell wall (green) and the lipid bilayer (yellow, aka plasma membrane.)

Plant cell has a wall adapaproject

Plant cell has a wall adapaproject

Large central vacuole

A membrane that stores watery bags of food or waste molecules.

How do we know what these organelles really look like?

Visualizing cells and organelles in 3D

Sample questions

Feb 2016 MCAS: Which of the following types of organisms have cell walls composed of cellulose?

A. amoebas     B. birds    C. grasses        D. worms

==========

Feb 2016 MCAS.  Antibiotics are medicines used to treat bacterial infections in humans. Some antibiotics work by interfering with the bacteria’s ribosomes. Other antibiotics work by interfering with the bacteria’s plasma membrane.

a. Describe the function of the ribosomes and explain why interfering with the ribosomes would kill the bacteria.

b. Describe the function of the plasma membrane and explain why interfering with the plasma membrane [lipid bilayer] would kill the bacteria.

Medicines called antifungals are used to treat infections caused by fungi. One way antifungals work is by targeting cell parts that are present in fungal cells but not in human cells.

c. Identify one cell part other than a ribosome or a plasma membrane that human cells and fungal cells have in common.

d. Describe what would happen to a human cell if the cell part you identified in part (c) were affected by an antifungal. Explain your answer based on the function of the cell part.

==========

External resources

http://www.amoebasisters.com/gifs.html

Biology MCAS exams

Previous MCAS exams from the Massachusetts Department of Elementary and Secondary Education

Feb 2017 Biology MCAS

Feb 2016 Biology MCAS

Feb 2015 Biology MCAS

Feb 2014 Biology MCAS

Feb 2013 Biology MCAS

Below you will find each released short-response question, open-response question, and writing prompt that was included on High School Biology MCAS tests; the scoring guide for each question; and a sample of student work at each score point for that question. Taken together, these provide a picture of the expectations for student performance on the MCAS tests.

 

Special Education accommodations

February 2018 MCAS Biology Test Administration Resources

MCAS Accessibility and Accommodations

SAMPLE MCAS High School Biology Reference Sheet For Students with Accommodation 20

]MCAS Access & Accommodations Manual Spring 2018

MCAS TEST ACCOMMODATIONS FOR STUDENTS WITH DISABILITIES (PDF document)

 

MCAS Standard Accommodations

Frequent Breaks: The test is administered in short periods with frequent breaks

Time of Day: The test is administered at a time of day that takes into account the student’s medical or learning needs (IEP or 504 plan must specify time of day)

Small Group: The test is administered in a small group setting (no more than 10 students)

Separate Setting: The test is administered in a room other than the one used by the rest of the class

Individual: The test is administered to the student individually

Specified Area: The test is administered with the student seated at the front or other specified area of the room, in a study carrel, or in another enclosed area (IEP or 504 plan must specify where)

Familiar Test Administrator: The test is administered by a test administrator familiar to the student

Noise Buffers: The student wears noise buffers, after test administration instructions have been read (headphones with music playing are not allowed)

Magnification or Overlays: The student uses magnifying equipment, enlargement devices, colored visual overlays, or specially tinted lenses (IEP or 504 plan must specify which)

Test Directions: The test administrator clarifies general administration instructions No portion of the test items themselves (eg, the introduction to a reading selection) may be read or signed

Large-Print: The student uses a large-print version of the test

Braille: The student uses a Braille version of the test

Place Marker: The student uses a place marker

Track Test Items: The test administrator assists the student in tracking test items (eg, moving from one test question to the next) or by redirecting the student’s attention to the test

Amplification: The student uses sound amplification equipment

Test Administrator Reads Test Aloud (except ELA Reading Comprehension test): Test Administrator reads entire test session word-for-word exactly as written

Test Administrator Reads Test Aloud (except ELA Reading Comprehension test): Test administrator reads selected words, phrases, and/or sentences as directed by the student. The student points to the word, phrase, or sentence that he or she needs read aloud.

Test Administrator Signs Test (except ELA Reading Comprehension test): The test administrator signs the ELA Composition writing prompt or the Mathematics, Science and Technology/Engineering, and/or History and Social Science passages and test items to a student who is deaf or hard of hearing

Electronic Text Reader (except ELA Reading Comprehension test): The student uses an electronic text reader for the ELA Composition writing prompt or the Mathematics and Science and Technology/Engineering tests

Scribe Test (except ELA Composition): For open-response test items (and multiple-choice items if needed), the student dictates responses to a scribe or uses a speech-to-text conversion device to record responses

Organizer, Checklist, Reference Sheet, or Abacus: The student uses a graphic organizer, checklist, individualized mathematics reference sheet, or abacus

Student Signs or Reads Test Aloud: The student reads the test aloud to himself or herself, or student reads the test and records answers on audiotape, then writes responses to test items while playing back the tape; a student who is deaf or hard of hearing signs test items/responses onto video, then writes answers while playing back the tape

Monitor Placement of Responses: The test administrator monitors placement of student responses in the student’s answer booklet

Word Processor: The student uses a word processor, Alpha-Smart, or similar electronic keyboard to type the ELA Composition and/or answers to open-response questions

Answers Recorded in Test Booklet: The student records answers directly in the test booklet

Other Standard Accommodation: Other standard accommodation that is identified by the IEP Team or team, documented in the student’s IEP, and not on this list

Alternate Assessment (Portfolio)

MCAS Nonstandard 

Test Administrator Reads Aloud ELA Reading Comprehension Test: The test administrator reads the ELA Reading Comprehension test to a student

Test Administrator Signs ELA Reading Comprehension Test for a Student Who Is Deaf or Hard of Hearing

Electronic Text Reader for the ELA Reading Comprehension Test: The student uses an electronic text reader for the ELA Reading Comprehension test

Scribe ELA Composition: The student dictates the ELA Composition to a scribe or uses a speech-to-text conversion device to record the ELA Composition

Calculation Devices: The student uses a calculator, arithmetic table (including multiplication and division charts), or manipulatives on all sections of the Mathematics or Science and Technology/Engineering test

Spell- or Grammar-Checking Function on Word Processor, Spell-Checking Device, or Word Prediction Software for the ELA Composition: The student uses a spell- or grammar-checking function, spelling device (including hand-held electronic spellers), or word prediction software (IEP must specify which device) for the ELA Composition

Other Nonstandard Accommodation: Other nonstandard accommodation that is identified by the IEP Team or team, documented on the student’s IEP, and not on this list

 

 

.

 

Organelles

A car is a working machine – made from smaller systems working together.

A cell is an organic, living machine – made from organelles working together.

No part of a car, by itself, is functioning.

No part of a cell, by itself, is alive.

What we a “functioning car” is the way that parts work together.

What we call “life” is the way that organelles work together.

Let’s compare the parts of a car with the parts of a cell

 

 

Consider: The transmission, the axles and the engine.

Yet disconnect just one of these systems, and we effectively no longer have a car.

We’d just have an inert 2000 pound block of metal and plastic.

A car is not a car unless the parts are connected and working together.

The same is true for cells.

drive-train-transmission xpertechautorepair

Inside the engine, what would happen if we removed or froze the pistons?

We’d effectively no longer have an engine.

The same is true for organelles inside cells.

four-stroke-engine-gif

Similarly, consider the ways that organelles and organic molecules are interacting within our cells.

This is mitochondrial ATP synthase. See how it is just like a machine? This is a machine with organic parts.

GIF mitochondrial ATP synthase

All parts of the body, when examined in detail, turn out to work in the same way: Like a simple machine, with parts that move against other parts, and objects that move from one place to another.

Nucleus to ribosomes to ER GIF Protein synthesis NPR

Nucleus to ribosomes to ER GIF from NPR: Protein synthesis

What would happen if we removed some of these parts?

We’d effectively no longer have a living cell.

You’ve seen parts inside cars. Now let’s look at the organelles (parts inside cells)

First, a note of caution about artwork: Many books simplify what a cell looks like, with a 2D black & white drawing, like this. This picture is “true” – but simplified.

In reality cells are 3D.

Organelles are suspended in cytoplasm throughout the cell.

c6026-animal252bcell252blabeled252bblue252blavendar

 

Now let’s learn the job of each organelle using analogies:

CPO Life science organelle analogy

 Organelle

 Function

 Analogy

 lipid bilayer

 Controls which molecules go in/out of the cell

 Walls and doors

 cytoplasm

 Suspends and holds all the organelles

 the factory floor, where all the work is done.

 nucleus

 Chromosome (DNA) storage

 Control center

 chromosomes

(made of DNA)

 Instructions for building and running the cell

 blueprints and instructions

 mitochondrion

 Converts energy from food molecules into a form usable by the cell

 Powerhouse

 ribosomes

 biological protein synthesis (translation)

 Workers on the assembly line, building our product.

 cytoskeleton

 gives the cell its shape and mechanical resistance to deformation

 Walls & studs, support and structure

golgi body

 Packages proteins into vesicles inside the cell, and send them to their destination.

 Receives product from ER. Like UPS, its packages and distributes the products.

endoplasmic reticulum

(ER)

 Manufactures lipids and proteins

 Assembly line which makes our products

 lysosome

 Contain enzymes that can break down virtually all kinds of biomolecules.

 garbage disposal

 vacuoles

 Multiple uses, often related to storing molecules.

 Storage

 

Organelles unique to plants

Plant organelles chloroplast vacuole

Click here to read about the organelles in more depth.

 

Endomembrane system

More details here: The endomembrane system

Endomembrane system by Mariana Ruiz Villarreal LadyofHats

Endomembrane system by Mariana Ruiz Villarreal, LadyofHats

Learning Standards

2016 Massachusetts Science and Technology/Engineering Curriculum Framework

6.MS-LS1-2. Develop and use a model to describe how parts of cells contribute to the cellular functions of obtaining food, water, and other nutrients from its environment,
disposing of wastes, and providing energy for cellular processes.

2006 Massachusetts Science and Technology/Engineering Curriculum Framework

Biology High School Standards: Cells have specific structures and functions that make them distinctive. Processes in a cell can be classified broadly as growth, maintenance, and reproduction.

2.1 Relate cell parts/organelles (plasma membrane, nuclear envelope, nucleus, nucleolus, cytoplasm, mitochondrion, endoplasmic reticulum, Golgi apparatus, lysosome, ribosome, vacuole, cell wall, chloroplast, cytoskeleton, centriole, cilium, flagellum, pseudopod) to their functions. Explain the role of cell membranes as a highly selective barrier (diffusion, osmosis, facilitated diffusion, active transport).

Benchmarks for Science Literacy, AAAS

By the end of the 12th grade, students should know that

  • Every cell is covered by a membrane that controls what can enter and leave the cell. 5C/H1a
  • In all but quite primitive cells, a complex network of proteins provides organization and shape and, for animal cells, movement. 5C/H1b
  • Within the cells are specialized parts for the transport of materials, energy capture and release, protein building, waste disposal, passing information, and even movement. 5C/H2a

SAT Biology Subject Area Test

Cellular and molecular biology: Cell structure and organization, mitosis, photosynthesis, cellular respiration, enzymes, biosynthesis, biological chemistry

External links

Wayback archive of RegentsPrep.Org on Cells

Amoeba Sisters.com gifs

Khanacademy Eukaryotic-cells

tablesgenerator.com

Evolution of the first animals

Animals probably evolved from marine protists, although no group of protists has been identified from an at-best sketchy fossil record for early animals.

Cells in primitive animals (sponges in particular) show similarities to collared choanoflagellates as well as pseudopod-producing amoeboid cells.

Multicellular animal fossils and burrows (presumably made by multicellular animals) first appear nearly 700 million years ago, during the late precambrian time….

All known Vendian animal fossils had soft body parts: no shells or hard (and hence preservable as fossils) parts.

Animals in numerous phyla appear at (or in many cases before) the beginning of the Cambrian Period ( 540 million years ago)

from http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookDiversity_7.html

Nicole King explains “All animals, from sponges to jellyfish to vertebrates [animals with a backbone], can be traced to a common ancestor. So far, molecular and fossil evidence indicate that animals evolved at least 600 million years ago. The fossil record does not reveal what the first animals looked like or how they lived. Therefore, my lab and other research groups around the world are investigating the nature of the first animals by studying diverse living organisms….. Choanoflagellates are a window on early animal evolution. Both cell biological and molecular evidence indicate that choanoflagellates are the closest living relatives of multicellular animals.

http://www.actionbioscience.org/evolution/king.html

————————————–

http://www.wired.com/2014/08/where-animals-come-from/

Between 620 and 550 million years ago (during the Vendian Period) relatively large, complex, soft-bodied multicellular animals appear in the fossil record for the first time. While found in several localities around the world, this particular group of animals is generally known as the Ediacaran fauna, after the site in Australia where they were first discovered.

The Ediacaran animals are puzzling in that there is little or no evidence of any skeletal hard parts i.e. they were soft-bodied organisms, and while some of them may have belonged to groups that survive today others don’t seem to bear any relationship to animals we know. Although many of the Ediacaran organisms have been compared to modern-day jellyfish or worms, they have also been described as resembling a mattress, with tough outer walls around fluid-filled internal cavities – rather like a sponge.

http://sci.waikato.ac.nz/evolution/AnimalEvolution.shtml

A new study mapping the evolutionary history of animals indicates that Earth’s first animal–a mysterious creature whose characteristics can only be inferred from fossils and studies of living animals–was probably significantly more complex than previously believed… the comb jelly split off from other animals and diverged onto its own evolutionary path before the sponge. This finding challenges the traditional view of the base of the tree of life, which honored the lowly sponge as the earliest diverging animal. “This was a complete shocker,” says Dunn. “So shocking that we initially thought something had gone very wrong.”

But even after Dunn’s team checked and rechecked their results and added more data to their study, their results still suggested that the comb jelly, which has tissues and a nervous system, split off from other animals before the tissue-less, nerve-less sponge.

The presence of the relatively complex comb jelly at the base of the tree of life suggests that the first animal was probably more complex than previously believed, says Dunn.

http://www.astrobio.net/topic/origins/origin-and-evolution-of-life/earths-first-animal/

http://news.nationalgeographic.com/news/2014/05/140521-comb-jelly-ctenophores-oldest-animal-family-tree-science/

Is this possible? for this to be true, it would seem that complex structures – neurons – have evolved twice! Independently? See here for more amazing details:

Did neurons evolve twice? The curious case of comb jellies

What kinds of radiation cause cancer

For most people the biggest cancer risk from radiation hovers in the sky above us giving us all warmth and light. There is no cancer risk from Wi-Fi or microwaves.

Wear sunscreen, but use WiFi without fear. (Image: Spazturtle/SMS (CC))

What is radiation, and where does it come from? nuclear chemistry

What is cancer? How is caused?  Cancer

Microwaves, Radio Waves, and Other Types of Radiofrequency Radiation: American Cancer Society

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Organic food and farming

Organic food

“People got in their head, well, if it’s man-made somehow it’s potentially dangerous, but if it’s natural, it isn’t. That doesn’t really fit with anything we know about toxicology. When we understand how animals are resistant to chemicals, the mechanisms are all independent of whether it’s natural or synthetic. And in fact, when you look at natural chemicals, half of those tested came out positive [for toxicity in humans].” –Bruce Ames

Organic food is food produced by organic farming, a set of techniques that mixes scientific knowledge of soil depletion and enrichment with anti-scientific beliefs and myths about nature and the natural.

A key belief of groups like the International Federation of Organic Agriculture Movements (IFOAM) and the Soil Association, which oppose conventional farming in favor of organic farming, is that pesticides and fertilizers are so harmful that they should be avoided unless they are “natural.”

This belief is contradicted by the vast majority of scientific studies that have been done on these subjects (Morris and Bate 1999Taverne 2006NCPA study). The United States Department of Agriculture (USDA) has put in place a set of national standards that food labeled “organic” must meet, whether it is grown in the United States or imported from other countries.

“USDA makes no claims that organically produced food is safer or more nutritious than conventionally produced food. Organic food differs from conventionally produced food in the way it is grown, handled, and processed.”*

Harm from bacterial contamination is a much greater possibility from natural fertilizers (Stossel 2005: 194). (For those of you who hate John Stossel, read the newspaper. The most dangerous bacteria in America’s food supply is E. coli, which is found in abundance in cattle manure, a favorite “natural” fertilizer of organic farming.)

The residues from pesticides on food, natural or synthetic, are not likely to cause harm to consumers because they occur in minute quantities.* (This fact does not make either kind of pesticide safe for those who work with them and are exposed to large quantities on a regular basis. I refer to residues on foods you and I are likely to find on fruits and vegetable we buy at the store or market.)

Using natural biological controls rather than synthetic pesticides is more dangerous to the environment (Morris and Bate 1999). The amounts of pesticide residue produced by plants themselves or introduced by organic farmers are significantly greater than the amounts of synthetic pesticide residues.

Almost all of the pesticides we ingest in food are naturally produced by plants to defend themselves against insects, fungi, and animal predators (Ames and Gold 1997). The bottom line is that fresh fruits and vegetables are good for you and it doesn’t matter whether they’re organic.

Over 30 separate investigations of about 500,000 people have shown that farmers, millers, pesticide-users, and foresters, occupationally exposed to much higher levels of pesticide than the general public, have much lower rates of cancer overall (Taverne 2006: 73.)

Groups like IFOAM refer to synthetic pesticides as “toxic,” even though the amount of pesticides people are likely to ingest through food are always in non-toxic amounts.

Many toxic substances occur naturally in foods, e.g.,arsenic in meat, poultry, dairy products, cereals, fish, and shellfish, but usually in doses so small as not to be worthy of concern. On the IFOAM website you will find the following message:

Although IFOAM has no official position on the quality of organic food, it’s easy to conclude that the overall nutritional and health-promoting value of food is compromised by farming methods that utilize synthetic fertilizers and toxic pesticides.

It’s easy to conclude—as long as you ignore the bulk of the scientific evidence that is available.

the myth of organic superiority

The evidence for the superiority of organic food is mostly anecdotal and based more on irrational assumptions and wishful thinking than on hard scientific evidence. There is no significant difference between a natural molecule and one created in the laboratory. Being natural or organic does not make a substance safe* nor does being synthetic make a substance unsafe. 

Organic food does not offer special protection against cancer or any other disease. Organic food is not “healthier” than food produced by conventional farming, using synthetic pesticides and herbicides. Organic farming is not necessarily better for the environment than conventional farming. There is scant scientific evidence that most people can tell the difference in taste between organic and conventional foods. The bottom line is: fresher is better. Organic produce that travels thousands of miles to market is generally inferior to the same produce from local farmers, organic or not.

Is there any difference between organic and conventional fruits and vegetables? According to one scientific paper, there are several differences:

Based on the results of our literature review and experiment we conclude that there are substantial differences between organic and conventional fruits and vegetables. They differ with respect to production method, labeling, marketing, price and potentially other parameters.

You don’t need to do a scientific study to know that organic foods are produced differently from conventionally farmed foods. Anyone who has been to the market knows that you will pay substantially more for food labeled “organic.”

The aforementioned scientific study did find that the literature provides evidence for one nutritional difference between organic and conventional foods: vitamin C was found to be higher for organic food.

coddling by the media

The way the media treat “green” issues accounts for one reason that the organic-is-better myth is pervasive. Here’s an example from BBC News:

Growing apples organically is not only better for the environment than other methods but makes them taste better than normal apples, US scientists say.

The study is among the first to give scientific credence to the claim that organic farming really is the better option.

The researchers found organic cultivation was more sustainable than either conventional or integrated farming, which cuts the use of chemicals.

The scientists, from Washington State University in Pullman, found the organic apples were rated highest for sweetness by amateur tasting panels.

They reported: “Escalating production costs, heavy reliance on non-renewable resources, reduced biodiversity, water contamination, chemical residues in food, soil degradation and health risks to farm workers handling pesticides all bring into question the sustainability of conventional farming systems.”

The headline for the story reads: Organic apples tickle tastebuds.

Most people might stop reading the story after five paragraphs of nothing but positive statements about organic farming and the mention of a number of problems ahead for conventional farming. For those who persevere, however, the following bits of information are also provided:

…organic farming systems were “less efficient, pose greater health risks and produce half the yields of conventional farming”.

…the tests “found no differences among organic, conventional and integrated apples in texture or overall acceptance”.

…Growers of more sustainable systems may be unable to maintain profitable enterprises without economic incentives, such as price premiums or subsidies for organic and integrated products.

Apparently, the measure used to determine that organic farming was “better for the environment” was based on physical, chemical, and biological soil properties. The scientists created their own index and found that organic was better mainly because of the addition of compost and mulch.

Certainly, there are going to be some organic farms that use methods of composting and mulching that improve growing conditions. But there are also methods conventional farmers can use to accomplish the same thing.

Finally, there are some organic farmers who used methods of composting and mulching that don’t improve anything except the chances of bacterial infection. Only a “green” journalist or scientist could turn being less efficient, posing greater health risks, no different in texture or appearance, and producing half the yields of conventional farming into “better than conventional farming.”

I’ll provide just one more example of how the media and scientists with agendas distort the results of scientific studies that compare organic with conventional agricultural practices. In 2003, Alyson Mitchell, Ph.D., a food scientist at the University of California, Davis, co-authored a paper with the formidable title of “Comparison of the Total Phenolic and Ascorbic Acid Content of Freeze-Dried and Air-Dried Marionberry, Strawberry, and Corn Grown Using Conventional, Organic, and Sustainable Agricultural Practices.”

The article was published in the Journal of Agricultural and Food Chemistry, a peer-reviewed journal of the American Chemical Society. The article got some good press from “green” journalists, who proclaimed that the study showed that organic foods have significantly higher levels of antioxidants than conventional foods. 

(Examples of glowing press reports can be found here and here.) There is a strong belief among promoters of organic foods that there is good scientific support for the claim that diets rich in antioxidants contribute to significantly lower cancer rates. 

The data, however, do not support this belief. “Study after study has shown no benefit of antioxidants for heart disease, cancer, Parkinson’s disease, Alzheimer’s disease, or longevity” (Hall 2011).

The study compared total phenolic metabolites and ascorbic acid in only two crops, marionberries and corn. Both crops were grown organically and conventionally on different farms. The organic berries were grown on land that had been used for growing berries for four years; the conventional berries were grown on land that had been used to grow conventional berries for 21-22 years.

The crops were grown on different soil types: the organic soil was “sandy, clay, loam”; the conventional was “sandy, Ritzville loam.” The soil for the conventional corn had been used before for wheat; the soil for the organic corn had been used for green beans. The conventional farm used well water; the organic farm used a combination of well and creek water. (I don’t mention the strawberry listed in the title of the article because no organic strawberries were tested.)

As you can tell from the title of the article, the metabolites measured were not taken from fresh berries or corn but from samples that had been freeze-dried and air-dried. Though not mentioned in the title, the scientists also compared samples that were simply frozen.

The data provided by the authors in their published study shows clearly that there was not enough measurable ascorbic acid (AA) in either of the marionberry samples to compare the organic to the conventional. As already noted, no organic strawberries were studied. There was not enough measurable AA for the freeze-dried or air-dried corn to be compared.

So, the only data on AA is for the frozen corn: organic had a value of 3.2 and conventional had a value of 2.1. You can read the study yourself to find out what these numbers represent, but whatever they represent they do not merit the conclusion drawn by the authors of the study: “Levels of AA in organically grown … samples were consistently higher than the levels for the conventionally grown crops.”

The study also compared what it calls “sustainable agricultural practices” to organic and conventional practices. Sustainable practices in this study included the use of synthetic fertilizers.

“Our results indicate,” the authors write, “that TPs [total phenolics] were highest in the crops grown by sustainable agricultural methods as compared to organic methods.” Dr. Mitchell is quoted in the press as saying that their study “helps explain why the level of antioxidants is so much higher in organically grown food.” Yet, her study clearly states that the evidence for this claim is anecdotal. In fact, the authors write of the comparative studies that have been done:

These data demonstrate inconsistent differences in the nutritional quality of conventionally and organically produced vegetables with the exception of nitrate and ascorbic acid (AA) in vegetables.

distortion of evidence by scientists

One thing these “green” advocates are good at is distorting data to make lead appear to be gold. Another study led by Mitchell claims that organic tomatoes have “statistically higher levels (P < 0.05) of quercetin and kaempferol aglycones” than conventional tomatoes. The increase of these flavonoids corresponds “with reduced manure application rates once soils in the organic systems had reached equilibrium levels of organic matter.”

In fact, the study suggests that it is the nitrogen “in the organic and conventional systems that most strongly influence these differences.” The authors suggest that “overfertilization (conventional or organic) might reduce health benefits from tomatoes.” The argument is that the flavonoids are a protective response by the plants and one of the things they respond to is the amount of nitrogen in the soil.

In any case, the thrust of these and similar studies is that both organic and conventional crops can be manipulated to yield higher levels of antioxidants. At least one study has found “organic food products have a higher total antioxidant activity and bioactivity than the conventional foods.”* That study, however, involved only ten Italian men, aged 30-65 years.

I have to say that I am underwhelmed by the studies I have reviewed that claim to have found organic foods are more nourishing or healthy than conventional fruits and vegetables. At present, there is no strong body of scientific evidence that supports the contention that organic fruits and vegetables are superior to conventional produce.

A best case scenario for the organic folks would be that to achieve the recommended nutrients from five helpings a day of fruits or vegetables you might have to eat four or five more conventionally grown strawberries or two or three more baby carrots to get the same amount of vitamins, minerals, or antioxidants as provided by organic fruits and vegetables. But I’m not sure the evidence supports even that weak position.

History of the term “organic”

The term ‘organic’ as a descriptor for certain sustainable agriculture systems appears to have been used first by Lord Northbourn in his book Look to the Land (1940).

“Northbourn used the term to describe farming systems that focused on the farm as a dynamic, living, balanced, organic whole, or an organism.”* T

he term ‘organic’ was first widely used in the U.S. by J. I. Rodale, founder of Rodale Press, in the 1950s. “Rodale failed to convince scientists of the validity of his approach because of his reliance on what were perceived to be outrageous unscientific claims of organic farming’s benefits.”*

The USDA standards for organic food state:

Organic food is produced without using most conventional pesticides; fertilizers made with synthetic ingredients or sewage sludge; bioengineering; or ionizing radiation.

These standards capture the essence of the organic mythology:

  1. Conventional pesticides should be avoided.

  2. Synthetic fertilizers should be avoided.

  3. Food should not be genetically altered.

  4. Food should not be subjected to ionizing radiation.

The bit about sewage sludge is there because some organic farmers follow the “law of return” as proposed by Sir Albert Howard (1873-1947), a founder and pioneer of the organic movement. He advocated recycling  all organic waste materials, including sewage sludge, in farmland compost. The practice of adding human and animal feces to the soil is an ancient practice found in many cultures even today.

The fact that these cultures developed their practices without benefit of modern knowledge of such things as bacteria or heavy metals is trumped by the romantic notion that farm life was idyllic in those times and places when life expectancy was half that of today.

Rudolf Steiner, the founder of a set of superstitious agricultural practices known as biodynamics, also advocated using manure as fertilizer but it had to be prepared according to a magical formula based on his belief that cosmic forces entered animals through their horns. Steiner also romanticized farming. Commenting on some peasants stirring up manure, he said:

“I have always had the opinion … that [the peasants’] alleged stupidity or foolishness is wisdom before God [sic], that is to say, before the Spirit. I have always considered what the peasants and farmers thought about their things far wiser than what the scientists were thinking.”* 

Steiner gave lectures on farming, but did no scientific research to test his ideas.

A central concept of these lectures was to “individualize” the farm by bringing no or few outside materials onto the farm, but producing all needed materials such as manure and animal feed from within what he called the “farm organism.”

Other aspects of biodynamic farming inspired by Steiner’s lectures include timing activities such as planting in relation to the movement patterns of the moon and planets and applying “preparations,” which consist of natural materials which have been processed in specific ways, to soil, compost piles, and plants with the intention of engaging non-physical beings and elemental forces. Steiner, in his lectures, encouraged his listeners to verify his suggestions scientifically, as he had not yet done.*

Steiner opposed the use of synthetic fertilizers and pesticides, not on scientific grounds but on spiritual grounds. He claimed there were “spiritual shortcomings in the whole chemical approach to farming.”* He had a mystical idea of the farm as an organism, “a closed self-nourishing system.”*

This article has been excerpted from The Skeptic’s Dictionary,  http://skepdic.com/organic.html