Nucleic Acids and so on....

Nucleic Acids

Nucleic acids form from polymers of nucleotides, molecules composed of a phosphate group, a five-carbon sugar, and a nitrogenous base. Five different nitrogenous bases exist:

Adenine
Guanine
Cytosine
Thymine ( only in DNA)
Uracil ( only in RNA)
DNA and RNA are nucleic acids that function in protein synthesis and the storage and transmission of genetic information.

Proteins

Proteins consist of one or more polypeptides, polymers of amino acids folded into complex three-dimensional shapes. An amino acid is a small molecule made up of a central carbon atom, an amino group, a carboxyl group, a hydrogen atom, and a functional group labeled “R.” Twenty different amino acids exist, each formed with a different R group. Polypeptides form when amino acids bond together in long chains. The twenty different amino acids can produce a diverse range of proteins, including enzymes, hormones, cell receptors, antibodies, transport proteins, storage proteins, motor proteins, and structural proteins, which perform a wide range of vital tasks in organisms.

All proteins have either three or four structural levels:

Primary structure refers to the sequence of amino acids that form the polypeptides.
Hydrogen bonds in single groups in a polypeptide chain result in a folded region referred to as the secondary structure. Secondary structures include helices (coils) and sheets (pleated folds).
The tertiary structure describes the folding of an entire polypeptide chain. Interactions between the R groups of the polypeptide chain determine the overall shape of the tertiary structure.
Interaction between two or more polypeptides forms the quaternary structure. Since some proteins consist of a single polypeptide, not all proteins exhibit quaternary structure


Protein Structure
Carbohydrates


Carbohydrates include both monosaccharides (also called simple sugars or simple carbohydrates) and polysaccharides (also called complex carbohydrates). Monosaccharides and polysaccharides perform different functions in organisms:

Monosaccharides, which include glucose, fructose, and lactose, provide cells with energy.
Polysaccharides, which include glycogen, starch, and cellulose, store energy and provide structural support to an organism.
Lipids

Unlike the other macromolecules, lipids are not composed of repeated monomers and therefore are not true polymers. Lipids exhibit a range of structural diversity, but all are nonpolar and therefore insoluble in water. Lipids include the following molecules:

Fats: store energy for future use in biological functions
Phospholipids: make up the cell membrane
Steroids: act as chemical messengers in an organism

Water/ H2O

Water is the most abundant molecule present in all living organisms. All chemical reactions within an organism take place in the presence of water. Several characteristics unique to water contribute to its vital importance in the processes of life, such as its properties as a solvent and tendency to form ions.

Water as a Solvent

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Solvents dissolve other molecules, called solutes, to form solutions, which are homogeneous mixtures of molecules. The hydrogen bonds that hold water molecules make water a versatile solvent that can form solutions with polar (hydrophilic) molecules. Water cannot form solutions with nonpolar (hydrophobic) molecules.


Water Ionization

Occasionally, water molecules spontaneously ionize, or break apart, into hydroxide ion (OH-) and hydrogen ion (H+), as illustrated in the following chemical equation.


The pH scale, which ranges from 0 to 14, expresses the relative concentrations of OH- and H+ in a solution. The pH value determines whether a solution is acidic, basic, or neutral:

Neutral solutions have equal concentrations of OH- and H+ and a pH of 7.
Acidic solutions have a greater concentration of H+ and a pH of less than 7.
Basic solutions have a greater concentration of OH- and a pH of greater than 7.
Acids lower the pH of solutions, while bases raise the pH. Buffers are substances that reduce the effect of acids and bases on the pH of a solution.

Calculating pH

The pH of a given solution expresses the negative logarithm of the hydrogen ion concentration, as represented in the following equation.

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pH = -log[H+]

For example, the [H+] of wine equals 10-3. Because the negative logarithm (represented by the exponent in this equation) is three, wine pH = 3 and is therefore acidic.

The scientific method

The Scientific Method

Biologists, like all scientists, conduct their research using the scientific method. The scientific method is a standardized way of making observations, gathering data, forming theories, testing predictions, and interpreting results.

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Researchers make observations to describe and measure biological states and behaviors. After observing certain events repeatedly, researchers come up with a theory that explains these observations. A theory is an explanation that organizes separate

pieces of information in a coherent way. Researchers generally develop a theory only after they have collected a great deal of evidence and make sure that their research results can be reproduced by others.

Biological research, like research in other fields, must meet certain criteria to be considered scientific. Research must be:

Replicable
Falsifiable
Precise
Parsimonious
Replicable

Research is replicable when others can repeat it and get the same results. When biologists report what they have found through their research, they also describe in detail how they made their discoveries. This way, other biologists can repeat the research to see if they can replicate the findings.

After biologists conduct their research and make sure it’s replicable, they develop a theory and translate the theory into a precise hypothesis. A hypothesis is a testable or observable prediction of what will happen given a certain set of conditions. If further tests or observations do not confirm the hypothesis, the biologist revises or rejects the original theory.

Falsifiable

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A good theory or hypothesis must also be falsifiable, which means that it must be stated in a way that makes it possible to reject it. In other words, other researchers have to be able to prove a theory or hypothesis wrong. Theories and hypotheses need to be falsifiable because all researchers can succumb to the confirmation bias. Researchers who display confirmation bias look for and accept evidence that supports what they want to believe and ignore or reject evidence that refutes their beliefs.

Precise

By stating hypotheses precisely, researchers ensure that they can replicate their own and others’ research. To make hypotheses more precise, researchers state exactly how their research has been conducted.

Parsimonious

The principle of parsimony, also called Occam’s razor, maintains that researchers should apply the simplest explanation possible to any set of observations. For instance, biologists try to explain results by using well-accepted theories instead of elaborate new hypotheses. Parsimony prevents researchers from inventing and pursuing outlandish theories.

Essential life functions

Transport: refers to processes which cause heat Energy, or particles, or something else, to flow out of the plasma and cease being confined. Diffusion partly determines the rate of transport. Energy losses from a plasma due to transport processes are a central problem in fusion energy research.
Excretion:
something excreted;esp:useless,superfluous,or harmful material(as urea)that is eliminated from the body and that differs from a secretion in not being produced to perform a useful function.
Regulation: how organisms control body processes- hormones, nervous system
Respiration: Respiration can occur with or without oxygen, aerobic ( with oxygen) and anaerobic ( without oxygen) respiration respectively.
Nutrition: how oranisms break down and absorb foods.
Synthesis: how organisms build neccessary molecules.
Reproduction: Sexual versus asexual, eggs, seeds, spores, placental, types of fertilization
Growth and Developement: metamorphosis, developement in egg or in uterus, growth from seed or spore.

Who lives on planet Earth?

What is an animal? evolved from colonial, flagelleted protist, starting in the precambrian sea.
Symmetry: There are two basic designs, radio symmetry and bilateral symmetry. Radio symmetry is like a starfish that has a single disk that radiates out into extra appendages. Bilateral symmetry is like a human where if you cut it down the middle it would be exactly the same on both sides.

Animals are multicellular, heterotrophic( does not make its own food), eukaryotes.
They ingest and have unique tissues
They lack cell walls that provide structual supports for plants and fungi.
Diploid stage usually dominates their life cycle.
All animals reproduce sexually and some can also reproduce asexually.
Phylum Chordata: must have gill slits, mucsles, notochord, adn a post anal tail

The mite

Phylum: Anthropods Class: Arachnida Kingdom: Animalia Domain: Eukarya

Spontaneous generation

In the natural sciences, abiogenesis, or origin of life, is the study of how life on Earth emerged from inanimate organic and inorganic molecules. Scientific research theorizes that abiogenesis occurred sometime between 4.4[1] and 3.5[2] billion years ago. By 2.4 billion years ago the ratio of stable isotopes of carbon (12C and 13C), iron (56Fe, 57Fe, and 58Fe) and sulfur (32S, 33S, 34S, and 36S) points to a biogenic origin of minerals and sediments[3][4] and molecular biomarkers indicate photosynthesis.[5][6]

Several hypotheses concerning early life have been proposed, most notably the iron-sulfur world theory (metabolism without genetics) and the RNA world hypothesis (RNA lifeforms).


In 1668, Francesco Redi, an Italian physician, did an experiment with flies and wide-mouth jars containing meat. This was a true scientific experiment — many people say this was the first real experiment — containing the following elements:

After this experiment, people were willing to acknowledge that “larger” organisms didn’t arise by spontaneous generation, but had to have parents. With the development and refinement of the microscope in the 1600s, people began seeing all sorts of new life forms such as yeast and other fungi, bacteria, and various protists. No one knew from where these organisms came, but people figured out they were associated with things like spoiled broth. This seemed to add new evidence to the idea of spontaneous generation — it seemed perfectly logical that these minute organisms should arise spontaneously. When Jean Baptiste Lamarck proposed his theory of evolution, to reconcile his ideas with Aristotle’s Scala naturae, he proposed that as creatures strive for greater perfection, thus move up the “ladder,” new organisms arise by spontaneous generation to fill the vacated places on the lower rungs.

In 1745 - 1748, John Needham, a Scottish clergyman and naturalist showed that microorganisms flourished in various soups that had been exposed to the air. He claimed that there was a “life force” present in the molecules of all inorganic matter, including air and the oxygen in it, that could cause spontaneous generation to occur, thus accounting for the presence of bacteria in his soups. He even briefly boiled some of his soup and poured it into “clean” flasks with cork lids, and microorganisms still grew there.

A few years later (1765 - 1767), Lazzaro Spallanzani, an Italian abbot and biologist, tried several variations on Needham’s soup experiments. First, he boiled soup for one hour, then sealed the glass flasks that contained it by melting the mouths of the flasks shut. Soup in those flasks stayed sterile. He then boiled another batch of soup for only a few minutes before sealing the flasks, and found that microorganisms grew in that soup. In a third batch, soup was boiled for an hour, but the flasks were sealed with real-cork corks (which, thus, were loose-fitting enough to let some air in), and microorganisms grew in that soup. Spallanzani concluded that while one hour of boiling would sterilize the soup, only a few minutes of boiling was not enough to kill any bacteria initially present, and the microorganisms in the flasks of spoiled soup had entered from the air.

This initiated a heated argument between Needham and Spallanzani over sterilization (boiled broth in closed vs. open containers) as a way of refuting spontaneous generation. Needham claimed that Spallanzani’s “over-extensive” boiling used to sterilize the containers had killed the “life force.” He felt that bacteria could not develop (by spontaneous generation) in the sealed containers because the life force could not get in, but in the open container, the broth rotted because it had access to fresh air, hence the life force inherent in its molecules, which contained and replenished the life force needed to trigger spontaneous generation. In the minimally-boiled flasks, he felt the boiling was not severe enough to destroy the life force, so bacteria were still able to develop.

By 1860, the debate had become so heated that the Paris Academy of Sciences offered a prize for any experiments that would help resolve this conflict. The prize was claimed in 1864 by Louis Pasteur, as he published the results of an experiment he did to disproved spontaneous generation in these microscopic organisms.

One very important point to note here is that Pasteur did not seek to find an answer to the broad question, “Has spontaneous generation ever occurred?” Rather, as any good scientist, he limited his scope to a very narrow piece of the picture: “Is it possible for spontaneous generation to occur given the specific conditions under which Needham (and others) claims it will occur,” i.e. the “life force?” Interestingly, in 1936, when Alexander Ivanovich Oparin, a Russian scientist, published The Origins of Life, in which he described hypothetical conditions which he felt would have been necessary for life to first come into existence on early Earth, some scientists found it difficult to acknowledge that under the very different conditions which Oparin was proposing for early Earth, some form of “spontaneous generation” might indeed have taken place.

One very important point to note here is that Pasteur did not seek to find an answer to the broad question, “Has spontaneous generation ever occurred?” Rather, as any good scientist, he limited his scope to a very narrow piece of the picture: “Is it possible for spontaneous generation to occur given the specific conditions under which Needham (and others) claims it will occur,” i.e. the “life force?” Interestingly, in 1936, when Alexander Ivanovich Oparin, a Russian scientist, published The Origins of Life, in which he described hypothetical conditions which he felt would have been necessary for life to first come into existence on early Earth, some scientists found it difficult to acknowledge that under the very different conditions which Oparin was proposing for early Earth, some form of “spontaneous generation” might indeed have taken place.

Homologous structures

Evidence from Living Organisms
By examining fossils and by determining their relative and absolute ages, scientists have collected evidence that supports the theory that species changed over time. Further evidence is derived from living organisms. In order to determine if species change scientists compare common ancestry, structure, biochemistry, and development of organisms alive today. As you read this section, study this evidence and critically evaluate whether it indicates that species may have arisen by descent and modification from ancestral species. Evidence of Common Ancestry
If species change over time, then scientists should be able to cite examples showing that a group of living species may have come from a common ancestor. Let us examine one of many cases for which this seems to be true. Gracing the islands of Hawaii is a family of birds commonly called the Hawaiian honeycreepers. All Hawaiian honeycreepers have similarities in skeletal and muscle structure that indicate they are closely related. However, each of the Hawaiian honeycreeper species has a bill specialized for eating certain foods. Scientists suggest that all 23 honeycreeper species apparently arose from a single species that migrated to Hawaii.


If a bat, a human, an alligator, and a penguin all evolved from a common ancestor, then they should share common anatomical traits. In fact, they do. Compare the forelimbs of the human, the bat, the penguin, and the alligator. Find the humerus, radius, ulna, and carpals in each forelimb. Though the limbs look strikingly different on the outside and though they vary in function, they are very similar in skeletal structure. More significantly, they are derived from the same structures in the embryo. Structures that are embryologically similar, but have different functions, are called homologous structures. Though these animals look different, a comparison of homologous structures indicates that they are quite similar. This suggests that these animals evolved from a common ancestor.

Speciation

Speciation is the evolutionary process by which new biological species arise. There are four modes of natural speciation, based on the extent to which speciating populations are geographically isolated from one another: allopatric, peripatric, parapatric, and sympatric. Speciation may also be induced artificially, through animal husbandry or laboratory experiments. Observed examples of each kind of speciation are provided throughout.
Defining a Species
A species is often defined as a group of individuals that actually or potentially interbreed in nature. In this sense, a species is the biggest gene pool possible under natural conditions.

For example, these happy face spiders look different, but since they can interbreed, they are considered the same species: Theridion grallator.



That definition of a species might seem cut and dried, but it is not—in nature, there are lots of places where it is difficult to apply this definition. For example, many bacteria reproduce mainly asexually. The bacterium shown at right is reproducing asexually, by binary fission. The definition of a species as a group of interbreeding individuals cannot be easily applied to organisms that reproduce only or mainly asexually.



Also, many plants, and some animals, form hybrids in nature. Hooded crows and carrion crows look different, and largely mate within their own groups—but in some areas, they hybridize. Should they be considered the same species or separate species?



If two lineages of oak look quite different, but occasionally form hybrids with each other, should we count them as different species? There are lots of other places where the boundary of a species is blurred. It’s not so surprising that these blurry places exist—after all, the idea of a species is something that we humans invented for our own convenience!

Classification of living things

Linnaean taxonomy is a method of classifying living things, originally devised by (and named for) Carolus Linnaeus, although it has changed considerably since his time. The greatest innovation of Linnaeus, and still the most important aspect of this system, is the general use of binomial nomenclature, the combination of a genus name and a single specific epithet to uniquely identify each species of organism. For example, the human species is uniquely identified by the binomial Homo sapiens. No other species of organism can have this binomial. Prior to Linnaean taxonomy, animals were classified according to their mode of movement.
All species are classified in a ranked hierarchy, originally starting with kingdoms although domains have since been added as a rank above the kingdoms. Kingdoms are divided into phyla (singular: phylum) — for animals; the term division, used for plants and fungi, is equivalent to the rank of phylum (and the current International Code of Botanical Nomenclature allows the use of either term). Phyla (or divisions) are divided into classes, and they, in turn, into orders, families, genera (singular: genus), and species (singular: species).
Though the Linnaean system has proven robust, expansion of knowledge has led to an expansion of the number of hierarchical levels within the system, increasing the administrative requirements of the system (see, for example, ICZN), though it remains the only extant working classification system at present that enjoys universal scientific acceptance. Among the later subdivisions that have arisen are such entities as phyla, superclasses, superorders, infraorders, families, superfamilies and tribes. Many of these extra hierarchical levels tend to arise in disciplines such as entomology, whose subject matter is replete with species requiring classification. Any biological field that is species rich, or which is subject to a revision of the state of current knowledge concerning those species and their relationships to each other, will inevitably make use of the additional hierarchical levels, particularly when fossil forms are integrated into classifications originally designed for extant living organisms, and when newer taxonomic tools such as cladistics and phylogenetic nomenclature are applied to facilitate this.
There are ranks below species: in zoology, subspecies and morph; in botany, variety (varietas) and form (forma). Many botanists now use "subspecies" instead of "variety" although the two are not, strictly speaking, of equivalent rank, and "form" has largely fallen out of use.
Groups of organisms at any of these ranks are called taxa (singular: taxon) or taxonomic groups.

How do genes work?

Most genes contain the information needed to make functional molecules called proteins. (A few genes produce other molecules that help the cell assemble proteins.) The journey from gene to protein is complex and tightly controlled within each cell. It consists of two major steps: transcription and translation. Together, transcription and translation are known as gene expression.
During the process of transcription, the information stored in a gene’s DNA is transferred to a similar molecule called RNA (ribonucleic acid) in the cell nucleus. Both RNA and DNA are made up of a chain of nucleotide bases, but they have slightly different chemical properties. The type of RNA that contains the information for making a protein is called messenger RNA (mRNA) because it carries the information, or message, from the DNA out of the nucleus into the cytoplasm.
Translation, the second step in getting from a gene to a protein, takes place in the cytoplasm. The mRNA interacts with a specialized complex called a ribosome, which “reads” the sequence of mRNA bases. Each sequence of three bases, called a codon, usually codes for one particular amino acid. (Amino acids are the building blocks of proteins.) A type of RNA called transfer RNA (tRNA) assembles the protein, one amino acid at a time. Protein assembly continues until the ribosome encounters a “stop” codon (a sequence of three bases that does not code for an amino acid).
The flow of information from DNA to RNA to proteins is one of the fundamental principles of molecular biology. It is so important that it is sometimes called the “central dogma.”

What is a gene?

A gene is an operational region of the chromosomal DNA, part of which can be transcribed into a functional RNA at the correct time and place during development. Thus, the gene is composed of the transcribed region and adjacent regulatory regions.We know that it is a chain of chemical makeup consisting of the letters A, T, C, and G. Genes are the information that tell your body how to look, and even control the way you laugh or smile. Every human and animal have genes inherited from their parents. A parent passes on traits to their children when they are born. Genes are lined up on chromosomes which are in pairs. Chromosomes and genes are made of deoxyribonucleic or DNA.
Chromosomes are found inside the nucleus of the cell. Although quite small a nucleus is like a very thick and specific dictionary. It just fits inside of a cell that of course requires a microscope to see. Humans are made up of 46 chromosomes and 23 chromosomal pairs. Half of these chromosomes come from one parent and half come from the other parent. In meiosis.
Each gene has a special job to do. It carries blueprints — the instructions — for making proteins in the cell. Proteins are the building blocks for everything in your body. Things like bones, mucsles, and skin are made of proteins. Those proteins help our bodies grow, work properly, and stay healthy. Scientists today estimate that each gene in the body may make as many as 10 different proteins.