Topic 1. Cell Biology

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1.1 Introduction to cells

Lesson one: Cell theory

Essential questions: What is the basic unit of life?

Objectives: Understand what is meant by cell theory. Know exceptions to cell theory.

Keywords:

  • Cell theory: the theory that the cell is the basic unit of life for all living things
  • micrometre: one thousandth of a milimetre
  • nanometre: one thousandth of a micrometre 
  • Tissue: a group of highly similar cells with the same function
  • Protista: a kingdom of ‘amoeba-like’ single celled organisms eg. paramecium or Scenedesmus

Cell theory states that living organisms are made from cells. This establishes cells as the building blocks of living organisms. The most simple organisms are only made from one cell, such as Protists (in the kingdom Protoctista).

All cells have:

  • a cell membrane,
  • contain genetic material which stores all of the information needed for the cell’s activities,
  • have enzymes to catalyse their metabolic reactions,
  • and generate their own energy.

Life is an emergent property (it emerges from the interactions of their cellular components, as something extra to them).

Can you think of other examples of emergent properties?

The implicit assumption of cell theory is that nothing smaller than a cell can survive eg. a cell membrane cannot live on it’s own.

Single-celled organisms carry out all the functions of life:

  • Movement
  • Reproduction
  • Sensitivity
  • Growth
  • Respiration
  • Excretion
  • Nutrition

Task: Investigating two single celled organisms, Paramecium and Scenedesmus.

image credit: bioninja

image credit: bioninja

Exceptions to cell theory:

Some organisms cannot be neatly divided into cells. They are exceptions to cell theory

  1. Giant algae (A). Several species of Giant algae exist eg. Caleurpa.  which seem to have only one nucleus, and so seem to be made of one giant cell. They can be as long as 100mm.
  2. Striated muscle. Striated muscle is a type of muscle tissue found in skeletal muscle in mammals. It is not divided into cells, but compartments called sarcomeres instead. (B)
  3. Aspetate fungi. Some fungi are made out of thread like structures called hypha. Usually these are divided into cell like components by divisions called ‘septa’. Sometimes they aren’t, and the hypha appears to be multinucleate (many nuclei), without divisions into cells.(C)

A

giant algae

B

striated-muscle

C)

34d85e31_13a0db21dec__8000_00000003

Understanding relative sizes: Follow this link to compare the relative sizes of cells / organelles in the general framework of things.
http://learn.genetics.utah.edu/content/cells/scale/

Lab Microscopy (see lab handout):

You must know how to prepare a wet slide of plant and animal tissue, focus on the relevant cells, estimate cell size and make a clearly labelled tissue drawing ( a tissue drawing is where no individual cells are drawn). Please see the lab skills webpage of MrHorrocks.com for more details.

Examples of specimens prepared by IB Junior students

cheek cellIMG_8789

1.2 Ultrastructure of cells

Lesson one: Prokaryotic cells

Objectives: understand what is meant by a prokaryotic cell. Know some key differences between prokaryotic and eukaryotic cells. Know the structure of a prokaryotic cell.

Keywords:

  • Prokaryote: one of the three domains of life, along with eukaryote and archaea (each of the three domains covers multiple kingdoms including eubacteria, or ‘true bacteria’ ) Prokaryotic cells have certain characteristics, such as the lack of a true nucleus.
  • Flagella: a tail like structure that allows prokaryotes to move
  • Mesosome: an infolding of the cell membrane that has metabolic functions eg.respiration
  • Nucleoid: a region of the prokaryotic cell where naked DNA can be found (not with archaea, their DNA is found with histone proteins)
  • Peptidoglycan: a compound composed of protein and carbohydrate like elements, that forms the cell wall of a prokaryotic cell (not in archaea bacteria, their cell wall is made from carbohydrates)
  • Organelle: part of a cell with a recognised function
  • Ribosome: a non-membrane bound organelle, which occurs differently in all three domains (in eukaryotes they are larger 80S size, in prokaryotes they are smaller 70S size, in archaea they are smaller 70S size and a different shape)

The content of a Prokaryotic cell is quite different from that of a eukaryotic cell. Having seen your own cells (from the lab on cell theory), you can remember that ‘you’ have eukaryotic cells.

Task: make a high quality drawing of a prokaryotic cell on paper. Annotate the labels to add functions to the organelles, based on the last slide.

Q) Mesosome is missing, what is the function?

 

imagecredit:bioninja.au.net

imagecredit:bioninja.au.net

Lesson two: Why don’t we have giant cells?

Objective: understand that cell size is limited by decreasing surface area to volume ration

Keywords:

  • Surface area :volume ratio – a mathematical expression derived by dividing the surface area by the volume
  • Diffusion distance: the distance a molecule travels by diffusion eg. from the cell membrane to the nucleus.

 

image credit (US National department of wildlife and fisheries)

The jewel of the desert (giant bacteria) T Namibiensis
giant bacteria

Image credit: the alien project

This is unusual, why aren’t there giant man -eating cells running around?

Cells are limited by their surface area to volume ratio. As a cell get’s bigger, it’s surface area to volume ratio get’s smaller until they can no longer absorb the things they require by simple diffusion

Activity: Work out the surface area to volume ratio for a hypothetical Streptococcus bacteria of differing sizes.

View this excellent slideshow on cells, including surface area the aspect of surface area – to – volume ratio

[slideshare id=52022804&doc=c-150824214449-lva1-app6891]

this lesson uses slides 41-51.

Key points:

  • Larger cells have difficulty obtaining sufficient nutrients, as their surface volume ratio : volume ratio is too low.
  • Larger cells also suffer from greater diffusion distances, from the cell membrane to the centre.
  • Overall the effect is to limit cell size to 1-10 micrometres in Prokaryotic cells, and 10-100 micrometres in Eukaryotic cells.

 

Lesson three: Plant and Animal cells 

Objectives: Understand the differences between plant and animal cells.

Keywords:

  • Organelle: Part of a cell with a specialised function. This improves the efficiency of a cell as multiple processes happen simultaneously in different parts of the cell, in specially adapted areas eg. mitochondria

Animal cells.

A generalised animal cell is meant to represent all animal cells. This means the chosen cell can’t have specialisations (eg. axons in nerve cells). A liver cell is often used to represent a generalised animal cell. A liver cell does have large amounts of mitochondria (to fuel metabolic processes like de-toxifying poisons), and Rough Endoplasmic Reticulum (to make enzymes for the metabolic processes).

image credit: tech woman.co

image credit: tech woman.co

 

The function of these organelles can be understood through analogy. I would recommend viewing a cell as a city.

Cell City idea:

http://www.open.edu/openlearn/nature-environment/natural-history/cells-are-cities-simple-version

 

Summary: Unique features found only in animal cells: Lysosomes, Centrioles. The extra-cellular matrix is a collection of molecules including collagen (protein) and polysaccharides (carbohydrate) which are secreted externally to the cell, which also help to support the cell structurally.

image credit: khan academy

image credit: khan academy

Plant cell

The general features of a plant cell are often represented using a palisade mesophyll cell. These contain a large number of chloroplasts for photosynthesis, and are located on near the upper surface of a leaf to maximise exposure to light (light usually comes from above, and this also avoids shading by other tissues).

image credit: bioninja

image credit: bioninja

 

Plant cells have a lot of features in common with animal cells. They have a regular shape, are often larger, and have some unique organelles. The cell wall is an extra-cellular component.

 

Lesson four: Stem cell therapy

Objectives: understand how stems cells can be used to treat certain conditions. Categorise stem cells

Keywords:

  • Stem cell: An undifferentiated cell eg. embryonic cell
  • Totipotent, Pluripotent, and Multipotent: decreasing degrees of potency, respectively; can become any cell, can become most cells, can become only two or three types of cell.
  • Embryonic Stem Cell Therapy: Therapy which replaces damaged cells with cells from an embryo.
  • Therapeutic cloning: a process of creating an artificial embryonic cell with the nucleus of an adult cell, to avoid the problem of tissue rejection. 
  • Adult Stem Cell therapy: therapy which replaces damaged cells with cells from adult stem cell tissue such as bone marrow.

Stem cells are cells which are undifferentiated. This means they have not yet specialised to form particular cells. The term potency, refers to their ability to form different kinds of cells.

Early embryonic cells (fewer than four divisions) are totipotent. They can become any cell. Older embryonic cell care pluripotent (they can become any kind of cell except placental cells). Adult stem cells tend to be mutipotent (they can become only a few kinds of cells).

Stem cell therapy involves using stem cells to replace damaged or poorly functioning cells in a patient. So far, the most progress has been made with adult stem cell therapy. However, the potential exists to use embryonic stem cell therapy (ESC), but the ethical implications of using human embryos has tended to hinder this research.

One of the diseases which has been treated using embryonic stem cell theory, is Statgard’s disease; a disease which involves progressive loss of vision (through degeneration of the retinal cells). Vision is restored by surgically placing a patch of correctly functioning retinal cells behind the retina. The retinal cells are grown from embryonic stem cells.

Task, read the link below and discuss.

https://www.theguardian.com/science/2015/sep/29/first-uk-patient-receives-stem-cell-treatment-to-cure-sight-loss

The problem of tissue rejection

One of the problems with using Embryonic Stem Cells, is that the surface membrane proteins of the retinal cells may not match the proteins of the recipient. This will cause the immune system to reject the transplanted cells.

This can be avoided by using therapeutic cloning. In therapeutic cloning, an artificial embryonic cell is created by replacing the true nucleus of an embryonic cell, with the nucleus of an adult cell from the recipient.

thera_diagram

Stem cells may also be taken from the umbilical cord blood of a new-born baby, maintained in tissue culture, as a reserve of cells that could replace faulty cells eg. in the case of leukaemia. This would not be effective in preventing genetic diseases, as these cells would carry the same faulty genes.

 

1.3 Cell Membrane structure

Lesson one

Objectives: Understand what is meant by the ampiphatic phospholipid bi-layer. Understand the role of membrane proteins and cholesterol. Understand that the Singer-Nicholson model for membrane structure has replaced the Davson-Danielli model.

Keywords:

  • Ampiphatic: having a hydrophilic (water-loving) and a hydrophobic end (water-hating)
  • Phospholipid: the backbone molecule of the cell membrane. Made from a phosphate group and two fatty acid chains, joined through glycerol.
  • Integral proteins: proteins which span the cell membrane
  • Peripheral proteins: proteins which are embedded in the surface of a cell membrane

Cell membranes surround all cells, as explained in cell theory. Cell membranes also enclose many eukaryotic organelles, e.g. lysosomes. Some organelles have a double membrane eg. chloroplast, mitochondria, nucleus. Perhaps surprisingly, they all have much the same structure.

image credit: cronodon

image credit: cronodon

  • A: Phospholipid A1 phosphate, A2 fatty acid chains
  • B: Glycolipids
  • C: Glycoproteins
  • D: Carbohydrate group
  • E: Cholesterol
  • F: Peripheral protein
  • G: Integral protein

 

 

 

 

 

Follow slides Slides 1-7 in the powerpoint below

 

[slideshare id=52257087&doc=c-150831160046-lva1-app6891]

Task: Model the cell membrane with plasticine. This is an example from an IB Biology class at the Lincoln school. Can you interpret it?

IMG_0031

Task: Draw the cell membrane, using the Singer-Nicolson fluid mosaic model.

[slideshare id=52022804&doc=c-150824214449-lva1-app6891]

 

Task: The cell membrane story. Review the history of the evidence that led to the falsification of the Davson-Danielli cell membrane model and the acceptance of the Singer-Nicolson cell membrane model

Task: Draw the cell membrane from memory. Be careful to use sharp, unbroken lines to show outlines. Label clearly, and indicate the size of the cell membrane (7.5nm thick)

Just for fun: A class challenge! image



Crossing the membrane: Helpful video links

 

1.4 Membrane transport in cells:

use the rest of the powerpoint slides 8-22.

 

 

Memory Trigger Osmosis (with thanks to Seniors 3 class).

 

 

Lab: Osmotic potential of Potato tissue

First of all, consider the effect of differing osmotic potential on cells

 osmotic potential and cells

You can download the instructions for your lab here:

IB Biology Lab Potato Tissue

In class we have been analysing excel graphs to make two kinds of graphs: bar charts (comparing two contrasting sets of data), and a scatter graph (looking for a correlation).

I have uploaded the demo file we were using

drawing graphs and tables

 

How to draw a bar graph in excel (brief notes)

  • Prepare your table, according to the IA student guide.
  • Select the data that you wish to plot (you can select discrete columns using the control and command keys together)
  • Go to insert graph, 2-d clustered column.
  • If excel has plotted your x axis as a series, you will need to adjust this by clicking on your graph using control click (on the graph), and then select data.
  • You can remove the unwanted series (it will usually be series one), and then select it as an x axis label.
  • You should use the chart layout tab to edit the title, axese labels, gridlines (choose major and minor), and error bars.
  • For error bars we may use uncertainty (for individual data readings), or standard deviation (if we are plotting means which represent sets of data)
  • Prepare an error bar column, insert error bars, custom, specify value, and then highlight your error bar column in your table twice (for positive and negative)
  • If x axis bars are produced, delete them.
  • If your error bars are too small, they may not show up (ie if you have a small uncertainty relative to your data).

 How to draw a scatter graph in excel (brief notes)

  • Prepare your table, according to the IA student guide
  • Select the data that you wish to plot (you can select discrete columns using the control and command keys together)
  • Go to insert scatter graph, with markers
  • If excel has plotted your x axis as a series, you will need to adjust this by clicking on your graph using control click (on the graph), and then select data.
  • You can remove the unwanted series (it will usually be series one), and then select it as an x axis label.
  • You should use the chart layout tab to edit the title, axese labels, gridlines (choose major and minor), and error bars.
  • You should also add trendline, choose linear, and in option find R2 value (display it). The closer that is to 1, the better is your line of fit and the more meaningful is the relationship shown.
  • For error bars we may use uncertainty (for individual data readings), or standard deviation (if we are plotting means which represent sets of data)
  • Prepare an error bar column, insert error bars, custom, specify value, and then highlight your error bar column in your table twice (for positive and negative)
  • If x axis bars are produced, delete them.
  • If your error bars are too small, they may not show up (ie if you have a small uncertainty relative to your data).

[slideshare id=592619&doc=01-statistical-analysis-1221114089218264-9]

 Task: Prepare a graph and table using the data on hummingbird length

Task: Find out if the differences between the hummingbird bill lengths are significant

Task: Choose two investigate one measurement in the classroom, and dividing the class into two groups, use the t-test to see if the differences are significant (eg. is there a significant difference in the heights between boys and girls in this class).

we will need to use the formula pasted below

Our null hypothesis will be that there is no significant difference between the hummingbird length in these two birds.

Option 1: Do the t test, without using the t test automatic function.

1) Paste the data for one humming bird type on its own, making the start of a new table

2) Add a column next to it, where each cell represents the mean of that data set =average(select values)

3) Enter a formula in the next column, for the differences between each value,= value-average

4) Add a new column, to square all these differences =value^2 (this is on the keyboard)

5) Add a cell at the bottom with the total of the squared differences = sum( squared differences)

6) You can now apply the formula to get the standard deviation. (note of course you can skip all this by selecting =STDEV(values), but it is good to know how it is done!

7) You need to repeat this for the other hummingbird bill sizes.

8) Now you should apply the t test formula to get the calculated t test value. Note you will not be expected to remember either of these formulas by the IB, but you should be able to use them.

9) Find out the degrees of freedom (total number of hummingbirds – 2).

10) Calculate the value of t from the table below, then look up the critical value of t from the table (its on slide number)

11) If it is bigger, we reject the null hypothesis that there is no significant difference.

 

standard deviation formulat-test-formula

Option 2 relies on excel to do most of the work for us. It only gives us a P value (probability), and if it is less than 0.05 we reject the null hypothesis. We don’t need to look at the critical t test value if we use the excel function.

1) In a blank cell, type = t test

2) Brackets will appear, to guide you in what to enter =T Test(array1, array2, tails, type)

3)For array 1 select all of one type of hummingbird, for array 2 select all the other type of hummingbird.

4) For tails, enter 2 (this means we don’t know which is bigger).

5) For type, enter 3 (this means we don’t know if they have the same standard deviation).

Optional investigation: Find out, is there a significant difference between reaction times between boys and girls in our class? Use this site to measure reaction time  https://faculty.washington.edu/chudler/java/redgreen.html

Mitosis the Mystery – Unmasked. A PBL element

Mitosis is a difficult concept to understand as it involves tiny cellular structures moving in a continuous way to facilitate cell division. In order to clarify the process, biologists have divided mitosis into discrete steps, and clarified the behaviour of DNA in each stage. The other elements of the cell that aid in this type of cell division are also described. By isolating specific stages a complex process is rendered in a digestible way. Your task in this project will be to present mitosis to a specific audience in a way that will successfully deliver understanding and the context. Focus on innovation and clarity.

The links for suggested resources are repeated here:

Oxford IB Diploma txtbk pages 53-54

Khan academy phases of mitosis

BIo ninja – Mitosis and cell replication

Teaching medicine in schools the link between mitosis and cancer

10 rules for making an effective oral presentation

You can download the document here: Mitosis the Mystery – unmasked!

1.5 The Origin of life

Lesson One: Objectives: Cells can only come from other cells. The first cell must have come from inorganic compounds, made outside of cells. Eukaryotic cells absorbed some prokaryotes to form specific organelles, i.e. mitochondria and chloroplasts

Keywords:

Important links used in class below

1.6 Mitosis

Lesson objectives: What is mitosis, what are the different stages, how to calculate mitotic index. Is there a link with cancer?

Keywords:

  • Cell division: when cells divide to form new cells. Mitosis, Meiosis, and Binary fission are forms of cell division.
  • Mitosis: a kind of cell division in eukaryotic cells, that creates two identical somatic cells with a diploid chromosome number 
  • Somatic cells: body cells eg. cheek cells
  • Diploid number: the same number of chromosomes as in a body cell eg. 46 chromosomes in humans
  • Chromosome: a highly condensed structure made from super-coiled DNA and histone proteins
  • Sister chromatid: a word used to describe two identical strands of coiled DNA joined together by a centromere (i.e. a chromosome). 
  • Mitotic index: the ratio between the number of cells in mitosis, and the total number of cells. This is used to understand how fast cells are dividing eg. in a tumour (high mitotic index represents fast division)
  • Interphase: the stage in between mitosis, which is highly metabolically active (divided into G1,S,G2)
  • Tumour: an abnormal growth in the body, resulting from cells carrying out mitosis in an uncontrolled way (may be benign or malignant. Malignant means cancerous).
  • Cyclins: proteins which are released to trigger each stage of mitosis eg. there is a cyclin for prophase, which peaks during prophase.
  • Oncogene: genes which control cyclins. Mutations to oncogenes, are thought to cause cancer.

 Additional help with MTOC, Centrosome and Centrioles:

  • Centrioles, Centrosome, and Microtubule Organizing centres: these are all related terms to the part of a cell that generates microtubules.
  • Microtubule organizing centre: an area of a cell that makes any kind of microtubules (including cilia or flagella, not just spindle fibres
  • Centrosome: A MTOC that makes spindle fibres
  • Centrioles: An additional structure in a centrosome, that is only found in animal cells. Consists of two bundles of microtubules, each made from 9 pairs of microtubules, arranged at right angles to each other.

image credit: study.com

image credit: study.com

 Essential questions: Why do cells need to divide. Why can’t we keep the same number of cells, and just let each cell grow bigger?

What is mitosis? 

Mitosis is a kind of cell division, which occurs in eukaryotic cells.  Cells divide to form two somatic  cells, with a diploid chromosome number. Mitosis is associated with growth, repair of cells, and asexual reproduction.

Mitosis in action: If you scratch the surface of your skin, the cells of the malpighian layer will be replaced by new cells formed by mitosis. The  basement layer is making new cells approximately every 24 hours. The fastest human tissue is a recently fertilised human embryo, (1-8 cell stage), which can go through a mitotic cycle in only 30 minutes!! (this misses out G1, and G2 of interphase, so the cells are minute). Cells in the liver divide only once a year (so take care of your liver, it is slow to recover eg. from alcohol poisoning).

The overall function of Mitosis is two divide duplicated DNA neatly to form two identical nuclei. Sister chromatids carry identical DNA sequences, conveniently joined by a centromere (two sister chromatids + centromere = chromosome).The mitotic spindles separate these (see image)

 

CegBB_FW8AApbay

Q) When was the DNA duplicated to form the sister chromatids?

Q) What else needs to be duplicated?

answers found below:

Interphase:

Interphase is the stage in between mitosis. Interphase, Mitosis and Cytokinesis complete the cell cycle ) below. The DNA occurs as chromatin, and not in chromosomes. Interphase was once wrongfully thought of as a ‘resting stage’. It is now recognised as being highly metabolically active.

image credit: university of Leicester

Interphase can be divided into:

  • G1: Replication of organelles
  • S: replication of DNA
  • G2: Expansion of the cell and more replication of non-DNA materials.

Stages of mitosis:

A visual summary of mitosis in an animal cell is shown below:

image credit: everythngscience.com

image credit: everythngscience.com

 

Watch the video to help consolidate this information

Mitosis Tasks

Task A: Summarise in a table the changes that occur in P,M,A,T in the nuclear membrane, DNA, centrosome

Task B Try to Identify the stage of mitosis in they cycle https://www.classzone.com/books/ml_science_share/vis_sim/chm05_pg71_celldiv/chm05_pg71_celldiv.html

 

Mitotic index:

This mathematical formula  represents the ratio of cells during mitosis, to the total number of cells.

An example is shown below

image credit: bioninja.au

image credit: bioninja.au

This is useful in that the mitotic index is a function of how fast cells are dividing. Cells with a high mitotic index are dividing more frequently, and are therefore growing faster. This could be bad news in a malignant tumour.

slide_8

Cyclins and controlling the Cell Cycle

Cyclins are proteins which control the stages of the cell cycle. There are four main types of cyclins in human cells, and they activate each other with the help of enzymes to perform their tasks in succession, like a relay team.

It works like this:

  1. A cyclin is released
  2. The cyclin binds to an enzyme called cyclin-dependent kinase
  3. The enzyme causes phosphate to be attached to other proteins in the cell
  4. The phosphate activates the proteins, triggering them to carry out tasks such as assembling the mitotic spindle

 

In this way, mitosis can be controlled and cells only divide when they are needed.

The control of the cell cycle

http://highered.mheducation.com/sites/0072495855/student_view0/chapter2/animation__control_of_the_cell_cycle.html

Sir Tim Hunt discovered the cyclins in 2001 quite by accident alone in his lab in London. Watch this interview to listen to his story.

Discussion points:

-what was Sir Tim trying to find out in his experiment?

-what anomaly did he notice in his data?

-do serendipity and accidents have a place in science?

-what attitude should we take to strange results that we find in our own experiments?

 

The link between Mitosis and Cancer

Mitosis is usually regulated by the  body, and new cells are only produced when needed. We know that this is due to the effect of cyclins, and also due to special genes called oncogenes which help regulate cell division.

Mutations are changes in DNA. These are caused by mutagens (DNA -changing agents, also called carcinogens). If the mutagen causes a mutation in an oncogene, then they can cause a cell to begin dividing irregularly, as oncogenes will not do their job properly. This can lead to the formation of a tumour.

 

Ch10D8

A tumour is a group of abnormal cells that develop due to abnormal cell division. Benign tumours stay in one place in the body, and these do not cause cancer – they may be removed through surgery.

Sometimes the tumour may be classified as malignant. Cancer is the presence of malignant tumours in the body. Malignant tumours spread abnormal groups of cells around the body and may set up secondary tumours. The mechanism for this is called metastasis.

 

The mechanism behind metastasis is explained in this video, although you are not required to know about the role of chemicals (eg. MMP), in the process.

 

Smoking and Cancer:

 

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