Ch 1: 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

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.

Quick Revision on Cell

Biology
they study of living organisms and their environments

Basic characteristics common to all living things
they are organized, they acquire materials and energy, they are homeostatic, they respond to stimuli, they reproduce and grow, and they have an evolutionary history

They are organized – Levels of Organization
Atom, molecule, cell, tissue, organ, organ system, organism, population, community, ecosystem, and biosphere

Atom
smallest unit of an element composed of electrons, protons, and neutrons

molecule
union of two or more atoms of the same or different elements

cell
the structural and functional unit of all living things

tissue
a group of cells with a common structure and function

organ
composed of tissues functioning together for a specific purpose

organ system
composed of several organs working together

organism
an individual; complex individuals contain organ systems

population
organisms of the same species in a particular area

community
interaction populations in a particular area

ecosystem
a community plus the physical environment

biosphere
regions of the Earth’s crust, waters, and atmosphere inhabited by living organisms

Organisms acquire materials and energy
humans and animals acquire food for energy.

Metabolism
describes all the chemical reactions that occur within a cell

Organisms Maintain Homeostasis
which is the ability of a cell or an organism to maintain an internal environment that operates under specific conditions. An example is the human body does this with temperature and the various organ systems work together to do this.

Examples of homeostasis
Digestive system takes in the nutrients, the cardiovascular system distributes the nutrients and oxygen to cells, the respiratory system exchanges gases with the environment, the urinary system excretes the metabolic waste of cells, and the nervous and endocrine systems coordinate functions of the other systems

Organisms Respond to stimuli
without the body’s ability to respond to stimuli there would be no homeostasis. Examples are the hand on the stove jerking away, the startling effect of a loud noise and how the heartbeat increases, blood pressure rises, the vessels dilate to restore normal blood pressure. Another example is moving toward or away from food. Some behaviors help us acquire food and reproduce.

Organisms Reproduce and Grow
Reproduction is a fundamental characteristic of life, cells only come into being from preexisting cells – All living organisms have parents. Organisms reproduce and pass on genetic information tot he next generation.

Growth
recognized by an increase in size and often in then umber of cells – part of development – used to indicate all the changes that occur from the time of they egg is fertilized until death. Also includes repair after an injury.

DNA or deoxyribonucleic acid
contains the genetic information for all life, contains the hereditary information that directs not only the structure of each cell, but also its function. This is contained within the genes.

Genes
short sequences of hereditary material that specify the instructions for a specific trait.

DNA is replicated before reproduction
so that an exact copy of each gene may be passed on to offspring.

Mutations
cause minor variations with the potential to make an organism better suited for the environment. This is what is used for the basis of evolutionary changes.

Organisms Have An Evolutionary History
evolution is the process by which a population changes over time.

Natural selection
is the mechanism by which evolution occurs.

Adaptation
each successive generation will include more members with the new variation that allows member of population to capture more resources and have more offspring than unchanged members. Example is the people that live in mountains in Tibetan Plateau with low oxygen and they have a lower amount of hemoglobin.

Sun
the ultimate source of energy for life on earth

Plants, algae, bacteria all harvest energy from the sun and convert it into energy
this process is called photosynthesis

Biodiversity
Humans are related to other animals

All life belongs to
one of three domains

The three domains are
bacteria, archaea, and eukarya

Domain Bacteria and domain archaea
both contain prokaryotes which are one celled organisms that lack a nucleus

Domain Eukarya
all of the cells contain a nucleus

Domain Eukarya has four kingdoms which are
plantae that consists of plants, fungi that consists of fungi, animalia that consists of animals, and protista that consists of protists

Most organisms in Animalia kingdom are
invertebrates. Examples are earthworms, insects, mollusks, and sponges

Vertebrates
are animals with a nerve cord protected by vertebral column. Examples are fish, reptiles, amphibians, and birds.

mammals
are vertebrates with hair or fur that also have mammary glands. Examples are humans, raccoons, seals, and meercats.

Humans are distinguished from apes by our
highly developed brains, we have a completely upright stance, we have a creative language and our ability to a wide variety of tools.

Humans have a cultural heritage
as well as a biological heritage.

Culture
encompasses human activities and products passed on from one generation to the next outside of direct biological inheritance.

Only humans have
language that allows us to communicate information and experiences symbolically

Humans are members of the biosphere
which is the living network that spans the surface of the Earth, into the atmosphere, and into the soil and sea.

We rely on microorganisms that decompose
some clean up pollutants like heavy metals and pesticides.

Fresh water ecosystems include rivers and lakes
they give water, fish, and food from crops

Forests
prevent flooding

Science As A Process
science is a way of knowing about the natural world.

Objective observations
are factual information

The Scientific Method Has Steps
The scientific method is on the basis of new and/ or previous observations.

The first step is an
observation

The second step is developing a hypothesis by inductive reasoning
which is a possible explanation for a natural event

Next a prediction is made and experiments are performed
which are a series of procedures designed to test a specific hypothesis

The experimental design
is the manner that is chosen to conduct an experiment; a good one ensures that the scientist is testing what they want to test and their results will be meaningful

A prediction
is made of what the experiment results will be

All conditions are to be kept constant
except for an experimental variable because it is deliberately changes.

Test Groups
of one or more are exposed to the experimental variable

Control group
is the other group and it is NOT exposed to the experimental variable.

If both both the test group or groups and the control group show the same result
then the hypothesis is not supported. Hypothesis must be changed and repeat the previous steps until the results are supported.

Model organisms and model systems
are used to test hypothesis.

Collect and analyze data
which is the results of the experiment.

Correlation
does not mean causation

Develop a conclusion
in which scientists use data to determine whether a hypothesis is supported.

Experiments and observations
must be repeatable

Scientific Theory
the ultimate goal of science to understand the natural world in terms of Scientific theories

Scientific theories are
accepted explanations for how the world works

Basic theories of Biology
cell theory, gene theory, theory of evolution which is considered the unifying concept of biology and also known as the Principle of Evolution

Controlled Study
control group, test group or groups, placebo and sometimes you have a double-blind study where neither patient of administering person don’t have any information

Observation, hypothesis, results, and a conclusion
which sometimes go on to further study and then the publication of scientific studies which are reviewed by experts.

Scientific Journals versus other sources of information
more reliable sources include websites that end in .edu, .gov and .org

Anecdotal Data
consists of testimonials by individuals rather than results from a controlled, clinical study. Never considered reliable.

Look for an abstract
which is a synopsis

look for methodology
which tells how the scientist conducted their study

look for results
which tell us what facts or data were discovered

look for a conclusion
which is the interpretation of the data by the author of the paper

graphs
shows relationship between two quantities; they summarize data in a clear and simplified manner

statistical data
most authors publishing articles use statistics to help evaluate their data

standard error
tells how uncertain a particular value is; it tells how far off the average could be

statistical significance
there is always the chance that the results were due to chance or some other factor other than the experimental variable.

To take this into account scientists calculate the
probability value of p that their results were due to change alone

If the value of p is low
they describe the results as statistically significant

Probability value of p
less than five percent is acceptable

Challenges facing science
science is a systematic way of acquiring knowledge about the natural world

technology
is the application of scientific knowledge to the interest of humans and the basis is scientific investigations. Examples are new lighter cell phones or a new drug

Bioethics
is a branch of ethics concerned with the development and consequences of biological technology. An example is genetic engineering like modified foods or GMOs

Biodiversity is the single most
significant bioethical issue we face today.

Human Influences on Ecosystems
we clear forests, grasslands, dump waste in the water supply, and pollutants. This affects ecosystems and they level of biodiversity

extinction
is the death of a species or a larger taxonomic group. Humans have increased this rate by a factor of 100 to 1000.

Emerging diseases
H5N1 is the avian flu and was a mutation from birds to humans. SARS came from people eating the exotic cat called a civet. Legionnaires emerged in 1976 from a contaminated air conditioner in a hotel where the bacteria thrived in the cooling tower.

globalization
results in the transport of diseases all over the world.

climate change
changes in the normal cycle of the Earth’s climate that may be caused by humans. It is due to an imbalance in chemical cycling of the element carbon

global warming
increased carbon dioxide in the atmosphere causing climate change through excessive greenhouse gases and affects ecosystems