IB DP Biology Topic 1: Cell biology 1.1 Introduction to cells Study Notes

​Both living and non-living things are composed of molecules made from chemical elements such as Carbon, Hydrogen, Oxygen, and Nitrogen. The organization of these molecules into cells is one feature that distinguishes living things from all other matter. The cell is the smallest unit of matter that can carry on all the processes of life.

In the Introduction to Cells unit students learn about the evidence for cell theory, unicellular organisms, microscopy, cell size, and stem cells.

​There are ethical issues involved in stem cell research, whether humans or other animals are used. Use of embryonic stem cells involves the death of early-stage embryos, but if therapeutic cloning is successfully developed the suffering of patients with a wide variety of conditions could be reduced.

​The unit is planned to take 2 school days

• Looking for trends and discrepancies—although most organisms conform to cell theory, there are exceptions. (3.1)
  • Define “trend” and “discrepancy.”
  • Explain why “trends and discrepancies” are useful in scientific study.
  • List features of cells that would be considered a “trend”.
  • List examples of cell types or organisms that are “discrepancies” to the cell theory
• Ethical implications of research—research involving stem cells is growing in importance and raises ethical issues. (4.5)
  • Explain why biological research must take ethical issues into consideration.

1.1.U.1 According to the cell theory, living organisms are composed of cells.(Oxford Biology Course Companion page 2).

• State the three parts of the cell theory.
• Outline evidence that supports the cell theory.
• Compare the use of the word theory in daily language and scientific language.

All organisms contain one or more cells which are capable of carrying on the life activities needed by the organism. This idea is often referred to as the cell theory. The cell theory is a scientific theory which describes the properties of cells. These cells are the basic unit of structure in all organisms and also the basic unit of reproduction.

• All living organisms are composed of cells. Multicellular organisms (example: humans) are composed of many cells while unicellular organisms (example: bacteria) are composed of only one cell. Cells are the basic unit of structure in all organisms.
• Cells are the smallest unit of life. They are the smallest structures capable of surviving on their own.
• Cells come from preexisting cells and cannot be created from nonliving material. For example, new cells arise from cell division and a zygote (the very first cell formed when an organism is produced) arises from the fusion of an egg cell and a sperm cell.

1.1.U.2 Organisms consisting of only one cell carry out all functions of life in that cell.  (Oxford Biology Course Companion page 8). [Students are expected to be able to name and briefly explain these functions of life: nutrition, metabolism, growth, response, excretion, homeostasis and reproduction.]

• Outline eight functions of life

​All living things are composed of one or more cells, each capable of carrying out the life functions. The organelles present in single-celled organisms often act in the same manner as the tissues and systems found in many celled organisms. Single-celled organisms perform all of the life processes needed to maintain homeostasis, by using specialized cell organelles.

• Metabolism – the web of all enzymes-catalyzed reactions in a cell or organism (respiration)
• Response – living things can respond to and interact with the environment
• Homeostasis – the maintenance and regulation of internal cell conditions (temperature, water, etc)
• Growth – living things can grow or change size/shape
• Reproduction – living things produce offspring either sexually or asexually
• Excretion – the removal of metabolic waste
• ​Nutrition – feeding by either the synthesis of organic molecules (photosynthesis) or absorption of organic molecules

1.1.U.3 Surface area to volume ratio is important in the limitation of cell size. (Oxford Biology Course Companion page 9).​

• Outline the activities occurring in the volume and at the surface of the cell.
• Calculate the surface area, volume and SA:V ratio of a cube.
• Explain the benefits and limitations of using cubes to model the surface area and volume of a cell.
• Describe the relationship between cell size and the SA:V ratio of the cell.
• Explain why cells are often limited in size by the SA:V ratio.
• List three adaptations of cells that  maximize the SA: volume ratio.

The rate of metabolism of a cell is a function of its mass / volume  (larger cells need more energy to sustain essential functions)
The rate of material exchange is a function of its surface area  (large membrane surface equates to more material movement). The greater the SA/volume ratio is, the faster the cell can remove waste and heat, and absorb oxygen and nutrients essential for the cell to function properly.

As a cell grows bigger, its internal volume enlarges and the cell membrane expands. Unfortunately, the volume increases more rapidly than does the surface area, and so the relative amount of surface area available to pass materials to a unit volume of the cell steadily decreases. the surface area to the volume ratio gets smaller as the cell gets larger.

​If the cell grows beyond a certain limit, not enough material will be able to cross the membrane fast enough to accommodate the increased cellular volume. When this happens, the cell must divide into smaller cells with favorable surface area/volume ratios, or cease to function.

As a cell grows, volume increases faster than surface area, leading to a decreased SA:Vol ratio

• If metabolic rate exceeds the rate of exchange of vital materials and wastes (low SA:Vol ratio), the cell will eventually die
• Hence growing cells tend to divide and remain small in order to maintain a high SA:Vol ratio suitable for survival

Cells and tissues that are specialized for gas or material exchanges will increase their surface area to optimize material transfer

​1.1.U.4 Multicellular organisms have properties that emerge from the interaction of their cellular components. 

• Define and provide an example of unicellular and multicellular organism.
• Define and give examples of emergent properties.

Living things have different levels of organization. Smaller parts combine to make increasingly complex systems. An emergent property is a characteristic an entity gains when it becomes part of a bigger system. Emergent properties help living organisms better adapt to their environments and increase their chances of survival.

Emergence in science and system theories is defined as how complex systems and patterns arise out of a multiplicity of relatively simple interactions. Basically, complex life systems involve millions of small simple interactions that work together to allow the complex system to function properly.

The emergence properties arise from the interaction of components. The whole is greater than the sum of its parts. Multicelluar organisms are capability of completing functions that individuals cells can’t

In multicellular organisms:

• Cells may be grouped together to form tissues
• Organs are then formed from the functional grouping of multiple tissues
• Organs that interact may form organ systems capable of carrying out specific body functions
• Organ systems collectively carry out the life functions of the complete organism

1.1.U.5 Specialized tissues can develop by cell differentiation in multicellular organisms. 

• ​Define tissue
• Outline the benefits of cell specialization in a multicellular organism.
• Define differentiation.

Every cell in a multicellular organism contains all genes of that organism. However, not all of those genes are activated in every cell or at the same time. When the gene is activated, the gene will encode for specific proteins. These proteins will affect the structure and function of cells.

​By activating certain genes and not others, the cells are able to differentiate and form specialized tissues. ​Differentiation depends on gene expression which is regulated mostly during transcription. It is an advantage for multicellular organisms as cells can differentiate to be more efficient unlike unicellular organisms who have to carry out all of the functions within one cell.

In development after the zygote divides to form the blastocyst ( around 120-130 cells), and then the gastrula, which is differentiated into several dermal layers of cells (mesoderm, endoderm, ectoderm, and germ cells) that form into specific specialized cells.

​1.1.U.6 Differentiation involves the expression of some genes and not others in a cell’s genome. 

• Describe the relationship between cell differentiation and gene expression.

Differentiation is the process during development whereby newly formed cells become more specialised and distinct from one another as they mature. All cells of an organism share an identical genome – each cell contains the entire set of genetic instructions for that organism. The activation of genes within a given cell by chemical signals will cause it to differentiate.

Within the nucleus of a eukaryotic cell, DNA is packaged with proteins to form chromatin. Active genes are usually packaged in an expanded form called euchromatin that is accessible to transcriptional machinery. Inactive genes are typically packaged in a more condensed form called heterochromatin (saves space, not transcribed). Differentiated cells will have different regions of DNA packaged as euchromatin and heterochromatin according to their specific function

​1.1.U.7 The capacity of stem cells to divide and differentiate along different pathways is necessary in embryonic development and also makes stem cells suitable for therapeutic uses. 

• Define zygote and embryo.
• List 2 key properties of stem cells that have made them on the active areas of research in biology and medicine today.
• Explain why stem cells are most prevalent in the early embryonic development of a multicellular organism.
• Contrast the characteristics of embryonic, umbilical cord and adult somatic stem cells.
• Define totipotent, multipotent and pluripotent.

​Stem cells are cells that are not fully differentiated but have the ability to divide and differentiate into different types of cells (e.g. one stem cell can differentiate into a blood cell, a liver cell or a kidney cell). Stem cells are necessary in embryonic development as all the cells in the adult organism stem from the embryonic stem cells.

Stem cells can divide many times and into many types of cells. Early stage embryos are made up of stem cells that make up all future cells. As the embryonic cells divide they gradually become committed and therefore are no longer stem cells. Some stem cells remain in the adult organism (e.g. bone marrow, skin and liver). These adult stem cells are pluripotent but not totipotent (i.e. can differentiate into many different cells but not all types of cells). Adult stem cells are vital for repair and regeneration of damaged tissue. Stem cells are ideal for therapeutic use in tissue repair and degenerative diseases

When a cell differentiates and becomes specialized, it loses its capacity to form alternative cell types

Stem cells are unspecified cells that have two key qualities:

• Self Renewal – They can continuously divide and replicate
• Potency – They have the capacity to differentiate into specialized cell types

There are four main types of stem cells present at various stages of human development:

• Totipotent – Can form any cell type, as well as extra-embryonic (placental) tissue (e.g. zygote)
• Pluripotent – Can form any cell type (e.g. embryonic stem cells)
• Multipotent – Can differentiate into a number of closely related cell types (e.g. haematopoeitic adult stem cells)
• Unipotent – Can not differentiate, but are capable of self renewal (e.g. progenitor cells, muscle stem cells)

​1.1.A.1 Questioning the cell theory using atypical examples, including striated muscle, giant algae and aseptate fungal hyphae.

• Describe features of striated muscle fibers that make them an atypical example cell.
• Describe features of aseptate fungal hyphae  that make them an atypical example cell.​
• Describe features of giant algae that make them an atypical example cell.

Striated muscle fibres:

• Muscle cells fuse to form fibres that may be very long (>300mm)
• Consequently, they have multiple nuclei despite being surrounded by a single, continuous plasma membrane
• Challenges the idea that cells always function as autonomous units

Aseptate fungal hyphae:

• Fungi may have filamentous structures called hyphae, which are separated into cells by internal walls called septa
• Some fungi are not partitioned by septa and hence have a continuous cytoplasm along the length of the hyphae
• Challenges the idea that living structures are composed of discrete cells

Giant Algae

• Certain species of unicellular algae may grow to very large sizes (e.g. Acetabularia may exceed 7 cm in length)
• Challenges the idea that larger organisms are always made of many microscopic cells

Other exceptions to the rule

• Virus don’t reproduce
• Red blood cells have no nucleus
• Mitochondria reproduce inside cell

​1.1.A.2  Investigation of functions of life in Paramecium and one named photosynthetic unicellular organism. 

• Describe characteristics of Paramecium that enable it to perform the functions of life.
• Describe characteristics of Chlamydomonas that enable it to perform the functions of life.

​Unicellular organisms are composed of a single cell. These cells must be able to carry out all the life functions

How unicellular organisms fulfill these basic functions may differ according to structure and habitat

1. Paramecium  (heterotroph)

• Paramecia are surrounded by small hairs called cilia which allow it to move (responsiveness)
• Paramecia engulf food via a specialised membranous feeding groove called a cytostome (nutrition)
• Food particles are enclosed within small vacuoles that contain enzymes for digestion (metabolism)
• Solid wastes are removed via an anal pore, while liquid wastes are pumped out via contractile vacoules (excretion)
• Essential gases enter (e.g. O2) and exit (e.g. CO2) the cell via diffusion (homeostasis)
• Paramecia divide asexually (fission) although horizontal gene transfer can occur via conjugation (reproduction)

2. Scenedesmus  (autotroph)

• Scenedesmus exchange gases and other essential materials via diffusion (nutrition / excretion)
• Chlorophyll pigments allow organic molecules to be produced via photosynthesis (metabolism)
• Daughter cells form as non-motile autospores via the internal asexual division of the parent cell (reproduction)
• Scenedesmus may exist as unicells or form colonies for protection (responsiveness)

​1.1.A.3 Use of stem cells to treat Stargardt’s disease and one other named condition. ​

• Outline the cause and symptoms of Stargardt’s disease.
• Explain how stem cells are used in the treatment of Stargardt’s disease.
• Outline the cause and symptoms of leukemia.
• Explain how stem cells are used in the treatment of leukemia.

Stem cells can be used to replace damaged or diseased cells with healthy, functioning ones

This process requires:

• The use of biochemical solutions to trigger the differentiation of stem cells into the desired cell type
• Surgical implantation of cells into the patient’s own tissue
• Suppression of host immune system to prevent rejection of cells (if stem cells are from foreign source)
• Careful monitoring of new cells to ensure they do not become cancerous

Examples of Stem Cell Therapy

1.  Stargardt’s Disease

An inherited form of juvenile macular degeneration that causes progressive vision loss to the point of blindness. This is caused by a gene mutation that impairs energy transport in retinal photoreceptor cells, causing them to degenerate
The disease is treated by replacing dead cells in the retina with functioning ones derived from stem cells.

2.  Parkinson’s Disease

A degenerative disorder of the central nervous system caused by the death of dopamine-secreting cells in the mid-brain. Dopamine is a neurotransmitter responsible for transmitting signals involved in the production of smooth, purposeful movements. Individuals with Parkinson’s disease typically exhibit tremors, rigidity, slowness of movement and postural instability. Treatment is by replacing dead nerve cells with living, dopamine-producing ones.

3.  Other Therapeutic Examples

• Leukemia:  Bone marrow transplants for cancer patients who are immunocompromised as a result of chemotherapy
• Paraplegia:  Repair damage caused by spinal injuries to enable paralyzed victims to regain movement
• Diabetes:  Replace non-functioning islet cells with those capable of producing insulin in type I diabetics
• Burn victims:  Graft new skin cells to replace damaged tissue

​1.1.A.4 Ethics of the therapeutic use of stem cells from specially created embryos, from the umbilical cord blood of a new-born baby and from an adult’s own tissues. 

• List the source and mechanism of obtaining stem cells.
• Discuss the benefits and drawbacks in using embryonic, cord blood and adult stem cells.

Stem cells can be derived from one of three sources:

• Embryonic stem cells – fertilize egg with sperm, fusion forms a zygote, the cell will now divide by mitosis till it is about 12-16 cells. These are all embryonic stem cells. They can differentiate into any cell type but have a higher risk of becoming tumor cells. There is also less chance that the cells have genetic damage as they are very new and don’t have time to accumulate mutations like adult stem cells.
• Umbilical Cord Stem Cells – stem cells obtained from the cord, can be frozen and used later on in life. These are easily obtained and stored after birth.
• Adult Stem Cells – obtained from some adult tissue such as bone marrow. They are difficult to obtain and have less growth potential and limited capacity to differentiate when compared to embryonic stem cells; however, they are fully compatible with adult’s tissue (no rejection) and there is less chance for a malignant tumor to occur.

The ethical considerations associated with the therapeutic use of stem cells will depend on the source. Using multipotent adult tissue may be effective for certain conditions, but is limited in its scope of application. Stem cells derived from umbilical cord blood need to be stored and preserved at cost, raising issues of availability and access.  The greatest yield of pluripotent stem cells comes from embryos, but requires the destruction of a potential living organism.

Stem cells can be artificially generated via nuclear transfer or nuclear reprogramming, with distinct benefits and disadvantages.

Somatic cell nuclear transfer (SCNT):

• Involves the creation of embryonic clones by fusing a diploid nucleus with an enucleated egg cell (therapeutic cloning)
• More embryos are created by this process than needed, raising ethical concerns about the exigency of excess embryos

Nuclear reprogramming:

• Induce a change in the gene expression profile of a cell in order to transform it into a different cell type (transdifferentiation)
• Involves the use of oncogenic retroviruses and transgenes, increasing the risk of health consequences (i.e. cancer)

​1.1.S.1 Use of a light microscope to investigate the structure of cells and tissues, with drawing of cells.  

• Label the names of parts of the microscope.
• Given the magnification of the ocular and objective lenses, calculate the total microscope magnification.
• Measure the field of view diameter of a microscope under low power.
• Calculate the field of view diameter of a microscope under medium or high power.
• Estimate the size of a sample in the microscope field of view.
• Demonstrate how to focus the microscope on  a sample.
• Demonstrate how to make a temporary “wet mount” on a microscope slide.

​Microscopes are scientific instruments that are used to observe objects that are too small to see with the naked eye

There are two main types of microscope: optical (light) microscopes and electron microscopes

Light Microscopes

• Use lenses to bend light and magnify images by a factor of roughly 100-fold
• Can be used to view living specimens in natural color
• Chemical dyes and fluorescent labeling may be applied to resolve specific structures

Electron Microscopes

• Use electromagnets to focus electrons resulting in significantly greater magnifications and resolutions
• Can be used to view dead specimens in monochrome (although false colour rendering may be applied)
• Transmission electron microscopes (TEM) pass electrons through specimen to generate a cross-section
• Scanning electron microscopes (SEM) scatter electrons over a surface to differentiate depth and map in 3D

Living specimens can be viewed in their natural color using light microscopes, although stains are usually applied to enhance specific structures

When attempting to draw microscopic structures, the following conventions should be followed:

• A title should be included to identify the specimen (e.g. name of organism, tissue or cell)
• A magnification or scale should be included to indicate relative size
• Identifiable structures should be clearly labelled (drawings should only reflect what is seen, not idealised versions)

1.1.S2  ​Drawing of cell structures as seen with the light microscope. 

• Demonstrate how to draw cell structures seen with a microscope using sharp, carefully joined lines and straight edge lines for labels.​     

1.1.S3  ​Calculation of the magnification of drawings and the actual size of structures and ultrastructures shown in drawings or micrographs. (Practical 1) (Oxford Biology Course Companion page 6).​

• Define micrograph.
• State why the magnification of a drawing or micrograph is not the same as the magnification of the microscope.
• Use a formula to calculate the magnification of a micrograph or drawing.
• If given the magnification of a micrograph or drawing, use a formula to calculate the actual size of a specimen.​

​Magnification = Image size (with ruler) ÷ Actual size (according to scale bar)

​​Calculation of Actual Size:

To calculate the actual size of a magnified specimen, the equation is simply rearranged:

Actual Size = Image size (with ruler) ÷ Magnification

Relative Sizes of Biological Materials

• Eukaryotic cell (plant) = ~100 μm
• Eukaryotic cell (animal) = ~10 – 50 μm
• Organelle (e.g. mitochondrion) = ~1 – 10 μm
• Prokaryotic cell (bacteria) = ~1 – 5 μm
• Virus = ~100 nm
• Plasma membrane = ~7.5 nm
• Molecules (e.g. glucose) = ~1 nm
• Atoms = ~100 pm