Exploring the world of the cell

Cells and Viruses

In 1676, van Leeuwenhoek used his microscopes to look into a drop of lake water and discovered small tiny creatures living in it. He laid the foundations of cell biology and microbiology

A Cell is defined as the membrane-bound structure that forms the basic unit of life. The cytoplasm of the cell is surrounded by a lipid bilayer (cell membrane) that controls the entry and exit of substances. Prokaryotic cells and plant cells have a cell wall that is rigid and which protects and offers support. The cell cytoplasm contains organelles that have specific functions inside the cell.

On the cellular level

• Atoms – Organelles – Cells – Tissues – Organs – Organ system – organism
• Bacteria can cause infections and can as well prevent you from getting infections. Bacteria that live inside our gut are called normal flora

The sub-atomic particles are protons, neutrons, and electrons (protons and neutrons are found within the nucleus while electrons are located on the outer shell). Atom is defined as the smallest thing which determines the properties of an element. The chemical properties of an element are specifically defined by the electrons of an atom.

Atoms make molecules such as proteins, carbohydrates, lipids, and nucleic acids. Molecules make organelles that function like organs inside the cell e.g nucleus, chloroplast. Organelles build a cell that can be an individual organism, especially for the single-celled organisms. Cells group together to form tissues that are specific and differentiated to perform a specific function. Tissues group to form organs which in turn make an organ system. Organ system e.g the nervous system, cardiovascular system group to make up an organism.

The cell theory states that (i) all living things are composed of cells, (ii) cells form the basic unit of function in living things, and (iii) existing cells are used to produce new cells that differentiate to form specific functions.

Normal flora or human microbiota

There are 10^13 humans cells and 10^14 bacterial cells in the body. Most of the bacteria that live in the body are beneficial rather than harmful. These beneficial bacteria are called normal flora or human microbiota. They are mainly located in the urogenital tract, skin, GI tract, and respiratory tract. Normal flora variation may be caused by three main factors which are age, diet, environment

Normal flora provides nutrition by breaking down the complex carbohydrates to produce useful metabolites for the body such as vitamin K. They are playing a key role in offering protection by competing with pathogenic bacteria and by preventing their access to essential docking sites, and bacteriocins which inhibit the growth of pathogenic strains.

How cells get what they need

The source of energy for the cell is food. Cells carry out cellular respiration to break down nutrients in food, to form ATP (energy currency for the cell). Mitochondria uses glucose and oxygen to form carbon dioxide, water, and energy which is used by cells in physiological functions. The cell eliminates the byproducts of such process by excretion e,g carbon dioxide. Cells ingest nutrients through various mechanisms. Plants, algae, and some bacteria carry out photosynthesis which uses carbon dioxide and water to form oxygen, water, and glucose.

DNA to protein

• The synthesis of protein begins within the nucleus of the cell
• DNA is a double helix nucleic acid molecule that stores genetic information
• The whole process of protein synthesis is referred to as the central dogma of life
• DNA is transcribed to RNA through transcription process, then ribosomes use RNA to synthesize proteins through transcription

A nucleotide consists of sugar, a nitrogenous base, and a phosphate group. If the nucleotide has a single sugar ring, it is categorized as a pyrimidine (cytosine, thymine, and uracil). If the nucleotide has two sugar rings, it is categorized as a purine (Guanine and Adenine). The double helix is a model by Watson and Crick that describes DNA as a twisted ladder, the sugar and phosphate forming the backbone of the ladder while the nitrogen bases form the rungs.

The two strands in DNA double helix are anti-parallel (one running from 5′-3′ and the other from 3’5), which is why they are described as complementary.

The central dogma is the idea that information flows in one direction i.e, from DNA to proteins and not vice versa. DNA is transcribed in the nucleus by RNA polymerase, translated in the ribosomes to form amino acids, which are then joined together to form a protein polypeptide of interest. During translation, mRNA carries the codons, rRNA forms part of the ribosome that translates mRNA, and tRNA brings amino acids that are added to the codons.

Every three nucleotides on the RNA form a codon, which encodes a particular amino acid. The gene has start codon and stop codon. The start codon signals the beginning of the translation while the stop codon signals the end of translation. The genome has a promoter sequence that allows transcription of downstream genes, and the operator sequence which turns the gene on or off to regulate gene expression. Genes also have noncoding regions that are removed to make mature mRNA; these regions are called exons, and regions that code for amino acids; these are called introns.

Terms

• Bioinformatics – Science that combines the use of biology, information technology, and computing to organize and analyze genetic information

Computer databases are used in bioinformatics to store, retrieve and assist the understanding of biological information. Bioinformatics is applied in medicine to treat diseases, forming databases for genetic diseases, forming genetic maps that can analyze heritable genes, in designing primers for PCR processes that amplify genes, and in agriculture to develop resistant crops.

In forensics, bioinformatics is used to store the offender’s genome (DNA profiles) which can be used to identify subsequent crimes committed by the same individual. The three major nucleotide databases in this field are the European Molecular Bio Lab (EMBL), the DNA data bank of Japan, and the GenBank. Four major protein sequence databases are the Swiss-prot, PIR, UniProt, and ExPASY.

• Genomics – This is the study of an organism’s entire genome

The study of how genome components interact with each to form an organism’s traits is functional genomics. Mapping is used to determine the location of each gene on an organism’s chromosome and if the location can be viewed microscopically, the process is called cytogenic mapping.

If the frequency of the genetic recombination is used to determine the location on a chromosome, this is called linkage mapping. If DNA cloning techniques are applied to determine the location, this is described as physical mapping. The location of a gene on the chromosome is termed as the locus.

• Proteomics – The study of proteins in a cell and their interaction with each other

The entire set of proteins that are expressed by the genome at a particular time is called the proteome (the study of proteomes is proteomics). All mRNA molecules in the cell are the transcriptome. There is a need to study proteomics independent of genomics because the genome does not provide any information about the proteomics.

Concept or Term	Definition or Description
Cells and Viruses	Van Leeuwenhoek discovered cells in lake water, laying the foundations of cell biology and microbiology.
Cell	Membrane-bound structure that forms the basic unit of life. Contains cytoplasm, surrounded by a lipid bilayer (cell membrane). Organelles perform specific functions within the cell.
Atom	Smallest unit determining properties of an element. Composed of protons, neutrons, and electrons.
Molecules	Combinations of atoms, such as proteins, carbohydrates, lipids, and nucleic acids.
Organelles	Structures within a cell that function like organs. Examples: nucleus, chloroplast.
Tissues	Groups of cells with specialized functions that work together.
Organs	Composed of tissues and perform specific functions.
Organ system	Group of organs working together. Example: nervous system, cardiovascular system.
Organism	A complete living individual made up of organ systems.
Cell Theory	(i) All living things are composed of cells. (ii) Cells form the basic unit of function. (iii) Existing cells produce new cells.
Normal Flora or Human Microbiota	Beneficial bacteria living in the body, found in the urogenital tract, skin, GI tract, and respiratory tract.
Source of Energy for Cells	Cells obtain energy from food through cellular respiration, using glucose and oxygen to produce ATP.
DNA	Double helix nucleic acid molecule storing genetic information.
Protein Synthesis	Process of transcribing DNA to RNA and using ribosomes to synthesize proteins.
Nucleotide	Building block of DNA or RNA, composed of sugar, nitrogenous base, and phosphate group.
DNA Double Helix	Model describing DNA as a twisted ladder, with sugar and phosphate forming the backbone and nitrogen bases as the rungs.
Central Dogma of Life	Information flows from DNA to proteins. DNA transcribed to RNA, then translated to synthesize proteins.
Codon	A sequence of three nucleotides on RNA that encodes a particular amino acid.
Genome	All the genetic material of an organism.
Bioinformatics	Science combining biology, information technology, and computing to analyze genetic information.
Genomics	Study of an organism’s entire genome.
Proteomics	Study of proteins in a cell and their interactions.

Levels of Organization	Atom, molecule, cell, tissue, organ, organ system, organism, population, community, ecosystem, and biosphere
Metabolism	All the chemical reactions that occur within a cell
Homeostasis	The ability of a cell or an organism to maintain an internal environment that operates under specific conditions
Examples of Homeostasis	Digestive system, cardiovascular system, respiratory system, urinary system, nervous and endocrine systems
DNA	Deoxyribonucleic acid, contains the genetic information for all life
Genes	Short sequences of hereditary material that specify the instructions for a specific trait
Reproduction	The process of producing offspring; passing on genetic information
Growth	Increase in size and number of cells; part of development
Mutation	Minor variations in genetic material; basis of evolutionary changes
Evolution	The process by which a population changes over time
Natural Selection	Mechanism by which evolution occurs
Adaptation	Traits that allow an organism to better survive in its environment
Photosynthesis	Process by which plants, algae, and bacteria convert sunlight into energy
Biodiversity	Variety of life on Earth; affected by human activities
Three Domains	Bacteria, Archaea, Eukarya
Prokaryotes	One-celled organisms that lack a nucleus; found in Bacteria and Archaea domains
Eukaryotes	Organisms with cells containing a nucleus; found in Eukarya domain
Kingdoms in Eukarya	Plantae, Fungi, Animalia, Protista
Invertebrates	Animals without a backbone
Vertebrates	Animals with a backbone
Mammals	Vertebrates with hair/fur and mammary glands
Humans	Distinguished by highly developed brains, upright stance, language, tool use
Culture	Human activities and products passed on outside of biological inheritance
Language	Unique to humans, allows symbolic communication
Biosphere	Living network spanning Earth’s surface, atmosphere, soil, and sea
Microorganisms	Decompose and clean up pollutants, play important roles in ecosystems
Freshwater Ecosystems	Rivers and lakes, provide water and food
Forests	Prevent flooding
Science	A way of knowing about the natural world
Scientific Method	Observation, hypothesis, prediction, experiment, data analysis, conclusion
Control Group	Group not exposed to experimental variable
Test Group	Group exposed to experimental variable
Placebo	Inactive substance given to the control group
Double-blind Study	Neither patient nor administering person has information
Scientific Journals	Reliable sources for scientific studies
Anecdotal Data	Testimonials, not considered reliable
Abstract	Synopsis of a scientific paper
Methodology	Explanation of how the study was conducted
Results	Facts or data discovered
Conclusion	Interpretation of the data
Graphs	Visual representation summarizing data
Statistical Data	Use of statistics to evaluate data
Standard Error	Measure of uncertainty for a particular value
Statistical Significance	Results not due to chance alone
Probability Value (p)	Indicates the likelihood of results due to chance alone
Challenges in Science	Technology, bioethics, biodiversity, human influences, emerging diseases, climate change, global warming