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391 Cards in this Set
- Front
- Back
- 3rd side (hint)
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An Organism |
A life form, a living entity made up of one or more cells |
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Characteristics Shared by organisms |
Cells Replication Information Energy Evolution |
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Cells |
Organisms consist of membrane bound units called cells. The membrane of a cellregulates the passage of materials between exterior and interior spaces |
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Replication |
One of the great biologists of the twentieth century, Francois Jacob, said that the“dream of bacterium is to become two bacteria”. Almost everything an organism does contributesto one goal: replicating itself. |
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Information |
Organisms process heredity, or genetic, information encoded in units called genes.Organisms also respond to information from the environment and adjust to maintain stable internalconditions. Right now, cells throughout your body are using information stored in your genes tomake the substances, or molecules that keep you alive; your eyes and brain are decodinginformation on this page that will help you learn some biology, and if your room is too hot you mightbe sweating to cool off. |
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Energy |
To stay alive and reproduce, organisms have to acquire and use energy. To give just twoexamples: plants absorb sunlight; animals ingest food. |
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Evolution |
Organisms are the products of evolution, and their populations continue to evolvetoday |
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Three greatest unifying idea in all of science |
The cell Theory The chromosome Theory of inheritance The theory of evolution |
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Theory |
An explantion for a very broad class of observed phenomena that is supported by a wide body of evidence. Note that this definition contrastssharply with everyday usage of the word “theory” which often carries meanings such as“speculation” or “guess |
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Robert Hooke |
In 1665 the Englishman Robert Hooke devised a crude microscope to examine the structure of cork(a bark tissue) from an oak tree. The instrument magnified the objects to just 30 x (30 times) theirnormal size, but it allowed Hooke to see something extraordinary. In the cork he observed small,empty looking compartments that were invisible to the naked eye. Hooke coined the term “cells” forthese structures because he though they resembled the cells inhabited by monks in a monastery. |
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Anton van Leeuwenhoek |
developedmuch more powerful microscopes, some capable of magnifications up to 300x. With theseinstruments, van Leeuwenhoek inspected samples of pond water and made the first observation ofa dazzling collection of single celled organisms that he called “animalcules |
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Rudolph Virchow |
In 1858 a, German scientist named Rudolph Virchow proposed that all cells arise from cells alreadyin existence. The complete Cell Theory builds on this concept: All organisms are made of cells, andall cells come from preexisting cells |
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Cell Theory |
All organisms are made of cells, andall cells come from preexisting cells. |
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Hypothesis |
a testable statement to explain a set of observations |
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Thoery vs Hypothesis |
Biologists typically use the word “theory” to refer to proposed explanation for broad patterns innature and “hypothesis” when referring to explanation for more tightly focused questions. A theoryserves as a framework for developing new hypotheses. |
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Louis Pasteur |
Pasteur wanted to determine whether organisms could arise spontaneously in a nutrient broth orwhether they appear only when a broth is exposed to a source of preexisting cells. To address thequestion he created two treatment groups that were identical in every aspect but one: the factorbeing tested—in this case, a broths exposure to preexisting cells.Both treatments used glass flasks filled with the same amount of the same nutrient broth. Bothflasks were boiled for the same amount of time to kill any existing organisms. After sterilization byboiling however, any bacteria and fungi cling to dust particles in the air could drop into the broth inthe flask shown in Figure 1.2a because the neck of the flask was straight.
In contrast, in the flask with the long swan neck, water would condense in the crook of the swanneck anger boiling and this pool of water would trap any bacteria or fungi that entered on dustparticles. Thus, the contents of the swan-necked flask were isolated from any source of preexistingcells even though they were still open to the air. The spontaneous generation hypothesis predictedthat cells would appear in both treatment groups. The all cells from cells hypothesis predicted thatcells would appear only in the treatment exposed to a source of preexisting cells. The broth in the straight necked flask exposed to preexisting cells quicklyfilled with bacteria and fungi. This observation was important because it showed that thesterilization step had not altered the nutrient broths capacity to support growth. The broth in theswan necked flask remained sterile, however. Even when the flask was let standing for months, noorganisms appeared in it. This result was inconsistent with the hypothesis of spontaneousgeneration. |
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experiment |
powerful scientific tool because they allow researchers to test the effect of a single, well defined factor on aparticular phenomenon. |
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prediction |
An experimental prediction describes a measure or observable result thatmust be correct if a hypothesis is valid |
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Chemical Evolution |
the formation of complex organic molecules (see also organic molecule) from simpler inorganic molecules through chemical reactions in the oceans during the early history of the Earth; the first step in the development of life on this planet. The period of chemical evolution lasted less than a billion years |
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Walter Sutton and Theodor Boveri in 1902–provided the foundation for |
provided the foundation for he chromosome theory ofinheritance |
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The chromosome theory of inheritance |
Inside cells, hereditary or genetic information is encoded in units called genes that are located on chromosomes. |
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Chromosome |
consists of a molecule ofdeoxyribonucleic acid, or DNA |
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Genes |
consists of specific segments of DNA that code for products in the cell. |
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1953 James Watsonand Francis Crick |
proposed that DNA is a double stranded helix |
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Rosalind Franklin in Maurice Wilkins |
work led to the proposal that DNA is a double stranded helix |
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DNA |
Each strand of the double helix is made up of varying sequences of four molecular building blocks,each containing a different kind of base. In terms of structure, on each strand of the double helix thebuilding blocks of DNA are connected one to another linearly. In terms of function, they are likeletters of the alphabet, the four different kinds of bases in the building blocks are symbolized by theletters A,T,C, and G. A sequence of this letter code is like the sequence of letters in a word, it hasmeaning. In this way DNA carries, or encodes, the information required for an organism's growth and reproduction The two strands of the double helix are joined by interactions between pairs of bases. Base pairingoccurs only between certain letters: A always pairs with T and C always pairs with G. THe pairs arearranged much like the rungs on a ladder, with the backbones of the strands acting as the sides ofthe ladder. Base pairing is key: it permits DNA to be copied and faithfully preserves the informationencoded within the DNA. |
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The Central Dogma |
The central dogma first articulated byCrick describes the flow of information in cells. In this context, the term “dogma” means a frameworkfor understanding. Put simply, DNA codes for RNA, which codes for proteins. Genetic information flows from DNA to RNA to proteins. Differences in proteins encoded by differentDNA sequences may lead to different physical traits. |
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The Flow of Genetic Information |
Genetic information flows from DNA to RNA to proteins. Differences in proteins encoded by differentDNA sequences may lead to different physical traits. |
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Ribonucleic Acid RNA |
Molecular machinery in cells makes a copy of a particular genes information in the form of a closelyrelated molecule called ribonucleic acid, or RNA. RNA molecules carry out a number of specializedfunctions in cells. For example, molecular machinery reads a messenger RNA molecule todetermine what molecular building blocks to use to make a protein. Proteins are crucial to mosttasks required for a cell to exist, from forming structural components to promoting the chemicalreactions that sustain life. |
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What happens when a mistake is made |
Differences in DNA sequences lead to differences in the sequence of the building block in proteins.The implications are profound: The outward appearance of an organism is a product of the proteinsproduced by its molecular machinery, so differences in DNA sequences might lead to a difference,for example, in finch beak size and shape, or in the length of a giraffe’s neck. Changes is sequencelead to the heritable variations that underlie the diversity of life. |
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Life Requires Energy |
The chemical reactions that sustain life in all its diversity take place inside cells. Transmitting geneticinformation, and the other work carried out by cells, requires energy. Organisms, whether singlecelled or multicellular are capable of living in a wide array of environments because they vary in cellstructure and how they acquire and use energy. |
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Two fundamental Nutritional Needs |
Organisms have two fundamental nutritional needs, chemical energy in the form of the moleculeATP ( or adenosine triphosphate) and molecules that can be used as building blocks for thesynthesis of DNA, RNA, proteins, the cell membrane, and other large, complex compounds requiredby the cell |
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Charles Darwain andAlfred Russel Wallace |
all diverse species all distinct, identifiable types of organisms, areconnected by common ancestry. |
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Darwin and Wallace’s theory of Evolution |
Darwin and Wallace’s theory made two important claims concerning patterns that exist in the naturalworld.1) Species are related by common ancestry. This idea contrasted with the prevailing view inscience at the time, which was that species represent independent entities createdseparately by a divine being.2) The Characteristics of species can be modified from generation to generation. Darwin calledthis process descent with modification. This claim argued against the popular view at thetime that species do not change. To put it anotherway, species are related to one another and can change through time |
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Evolution |
a change in the characteristics of a population over time |
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population |
a group of individuals of the same species living in the same area at the same time. |
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Natural Selection |
a process that explained how evolution occurs. If certain heritable traits lead to increased success in producing offspring, then those traits becomemore common in the population over time. In this way, the populations characteristics change as aresult of natural selection acting on individuals. This is a key insight: Natural selection acts onindividuals, but evolutionary change occurs in populations. |
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Two Conditions Of Natural Selection |
Natural Selection occurs whenever two conditions are met. 1) Individuals within a population vary in characteristics that are heritable meaning, traits thatcan be passed onto offspring.2) In a particular environment, certain versions of these heritable traits help individuals survivebetter and reproduce more than do other versions. |
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speciation |
divergence process in which populations of one species to diverge and form new species. Research on speciation has two important implications: All species come from preexisting species,and all species, past and present, trace their ancestry back to a single common ancestor. |
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fitness |
an individual's ability to produce viable offspring relative to that ability inother individuals in the population. Individuals with high fitness produce manysurviving offspring. |
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adaptation |
a heritable trait thatincreases the fitness of an individual in a particular environment relative toindividuals lacking that trait |
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Tree of life |
The theory of evolution by natural selection predicts that biologists should be able to construct a treeof life, a family tree of organisms. If life on Earth arose just once, then such a diagram woulddescribe the genealogical relationships between species with a single, ancestral species at its base. |
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Carl Woese |
One of the great breakthroughs in research on the tree of life occurred when American biologist CarlWoese (pronounced woze) and colleagues began analyzing the molecular components oforganisms as a way to understand their evolutionary relationships. Their goal was to understand thephylogeny of all organisms, their actual genealogical relationships. Translated literally, “phylogeny”means “tribe-source”. Before Woese’s work and follow up studies, biologists thought that the most fundamentaldivision among organisms was between prokaryotes and eukaryotes. The Archaea werevirtually unknown, much less recognized as a major and highly distinctive branch on the treeof life Fungi were thought to be closely related to plants. Instead, they are much more closelyrelated to animals. |
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phylogeny |
actual genealogical relationships |
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importance of DNA and RNA |
Because the sequence of building blocks in DNA is a trait that can change during the course ofevolution. Although a gene may code for an RNA or protein molecule that performs the samefunction in all organisms, the corresponding DNA sequence is not identical among species.
Recall that the building blocks in DNA are symbolized bythe letters A, T, C,and G.Biologists use this letter code to describe DNA sequences. In land plants,for example, a section of DNA might start with the sequence A-T-A-T-C-G-A-G. In green algae,which are closely related to land plants, the same section of the molecule might containA-T-A-T-G-G-A-G. But in brown algae, which are not closely related to green algae or to land plants,the same part of the molecule might consist of A-A-A-T-G-G-A-C. |
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DNA Sequences |
In models focused on the information content in DNA, structural details can be left out and thedouble stranded DNA double helix simplified to show the letter code on one strand only. Sequencescan then be compared for similarities and differences |
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phylogenetic tree |
depicts evolutionary history
Just as afamily tree shows the relationships between individuals, a phylogenetic tree shows relationshipsbetween species. On a phylogenetic tree, branches that share a recent common ancestor that is, anancestral population, represents species that are closely related; branches that don’t share recentcommon ancestors represent species that are more distantly related. |
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The Tree of life |
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Three Domains of Life |
Bacteria
Archaea
Eukarya |
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LUCA |
“last universal common ancestor” of cells,
Researchers who study the origin of life propose that the tree’s root extends allthe way back to a “last universal common ancestor” of cells, or LUCA. |
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Eukaryotes |
have a prominent component called the nucleus
eukaryotes are multicellular (“many-celled”)
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Eukaryotes |
have a prominent component called the nucleus
eukaryotes are multicellular (“many-celled”)
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prokaryotes |
Cells that lack a nucleus,
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Eukaryotes vs Prokaryotes |
Eukaryotic Cells Have a membrane bound nucleus
Prokaryotic cells do not have a membrane boud neculeus |
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Traditional Approaches |
Traditional approaches for classifying organisms, including the system of five kingdomsdivided into various classes, orders, and families that you may have learned in high school,are inaccurate in many cases, because they do not reflect the actual evolutionary history ofthe organisms involved. |
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taxonomy |
the effort to name and classify organisms |
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taxon |
Any named group at anylevel of classification system |
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domain |
Based on the tree of life, Woese proposed a new taxonomic category called the domain. He designatedvthe Bacteria, Archaea, and Eukarya as the three domains of life. |
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phylum |
major lineages within each domain. each phylum is considered a major branchon the tree of life biologists currently name 30-35phyla each of them distinguished by distinctive aspects of body structure as well as by distinctivegene sequences |
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Scientific (Latin Names) |
Each type of organism is assigned a two-part name.
Genus
and
Species |
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Carolus Linnaeus |
In 1735, a Swedish botanist named Carolus Linnaeus established a system for naming species that is still in use today |
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Genus |
The first part of the two part name indicates the organisms genus (plural:genera). Agenus is made up of a closely related group of species. For example, Linnaeus put humansin the genus Homo. Although humans are the only living species in this genus, at least sixextinct organisms, all of which walked upright and made extensive use of tools, were lateralso assigned to Homo |
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Species |
The second term in the name identifies the organisms species. Linnaeusgave humans the species name sapiens. A species name is always preceded by its genus. |
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scientific name |
An organism's genus and species designation is called its scientific name, or Latin name. Scientificnames are always italicized. Genus names are always capitalized, but species names are not, as inHomo sapiens. Linnaeus maintained that different types of organisms should not be given the samegenus and species names |
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Robert Simmons and Lue Scheepers |
In the mid 1990s assembled data suggesting thatthe food competition hypothesis is only part of the story. Their analysis of observational datasupports an alternative hypothesis: Long necks allow giraffes to use their heads as effectiveweapons for battering their opponents, and longer necked giraffes have a competitive advantage infights. |
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hypothesis testing |
two step process: Step 1: state the hypothesis as precisely as possible and list the predictions it makes Step 2 Design an observational or experimental study that is capable of testing thosepredictions |
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null hypothesis |
latter possibility, specifies what should be observed when the hypothesis being tested isn't correct. |
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Important Characteristics of Good Experimental Design |
control experimental conditions must be as constant or equivalent as possible Repeating |
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control |
It is critical to include a control. A control checks for factors, other than the one being tested,that might influence the experiments outcome. In this case,there were two controls. Includinga normal, unmanipulated individual controlled for the possibility that switching the individualsto a new channel altered their behavior. The researchers also had to control for thepossibility that the manipulation itself, and not the change in leg length affected the behaviorof the stilts and stumps ants. This is why they did the second test, where the ants didoutbound and return runs with the same legs. |
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The experimental conditions must be as constant or equivalent as possible |
The experimental conditions must be as constant or equivalent as possible. Theinvestigators used ants of the same species, from the same nest, at the same time of day,under the same humidity and temperature conditions, at the same feeders, in the samechannels. Controlling all the variables except one, leg length is this case, is crucial becauseit eliminates alternative explanation for the results |
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Repeating |
Repeating the test is essential. It is almost universally true that larger sample sizes inexperiments are better. By testing many individuals, researchers can reduce the amount ofdistortion or “noise” in the data caused by unusual individuals or circumstances |
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theory of chemical evolution |
leading scientific explanation for life’s origin The theorymaintains that the formation of increasingly complex carbon containing substances culminated in amolecule that could replicate itself. At this point, there was a switch from chemical evolution tobiological evolution. As the original molecule multiplied, the process of evolution by natural selection took order.Eventually a descendent of the original molecule became metabolically active and acquired amembrane. When this occurred, the five characteristics of life were fulfilled. Life had begun. |
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Atomic Structure and Subatomic Particles |
Atom Structure: Protons and neutrons in the nucleus very small dense central core |
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Protons Neutrons Electrons |
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atomic mass unit |
1/12 the mass of a single carbon atom containing 6 protons and 6 neutrons |
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Atomic Number (Z) |
The number of protons in the nucleus. also known as the nuclear charge . This number identitfies the element. |
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Mass Number (A) |
The total number of neutrons and protons in the nucleus of the atom. |
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finding the number of neutrons |
A-Z= # neutrons |
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an atom has no charge |
nuber of electrons = number of protons |
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Isotopes |
atoms that have the same atomic number but different mass number atoms that have the same number of protons but different number of neutrons |
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Isotope Symbols |
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Hydrogens Isotopes |
1H is hydrogen 2H is deuterium 3H is tritium |
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Ions |
a charged species formed from a neutral atom or molecule when electrons are gained or lost. |
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Cation |
positive charged ion
formed by loosing electrons |
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Anion |
negative charged ion
formed by electrons being gained |
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electrons |
have wave nature have a particle nature |
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orbitals |
regions in space with high electron density |
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energy levels get closer together as you move further away form the nucleus |
energy levels get closer together as you move further away form the nucleus |
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orbital diagram |
shows what subshells (orbitals) are occupied by electrons |
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Ground state |
lowest energy state of all electrons |
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procedure for writing the electron configuration |
1) find the nearest noble gas which comes before the element
2) Place the noble gas symbol in square brackets This is called the noble gas core
3) Now use the breakdown of the periodic table that you learned to add electonns in until you have reached the element of interest |
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Navigating the Periodic Table |
# of valence electrons |
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valence electrons |
The electrons written after the noble gas core
These valence electrons are the ones involved in chemical bondin |
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Electron Configurations of Cations and Anions |
anions are usually formed from non metals
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for Anions |
Place additonal electrons in the next available orbital according to the rules you already know.
anions are usually formed from non metals
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For Cations |
Always write the configuration of the neurtral element (usually a metal) and then take the electrons from the subshell with the highest n. And then p before s. |
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Isoelctronic |
Atoms and ions which have the same electron configuration |
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Ionization Energy |
The minimum energy required to remove an electron from a gaseous atom in its ground state endothermic process always positive value This is a measure of how tightly the electrons are held in the atom |
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atomic radius |
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shielding |
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Ionic Radius |
The radius of an anion or cation
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Electron Affinity |
The negative of the energy change that occurs when an electron is accepted by an atom in the gaseous state to form an anion. |
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Trend of Electron Affinity |
Increase in the tendency to accept electrons from left to right across the periodic table
This shows up as larger positive for EA for halogens
EA's are generally lower for metals than those of nonmetals
metals dont accept electrons they donate electrons
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Hydrogen |
Gains electron when bonded to a metal becoming (hydride) H-
Loses electron when bonded to non metal becoming H+
non-metal |
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Group 1A Elements Alkali Metals |
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Group 2A Elements Alkaline Earth Metals |
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Chemical bonds |
Compounds are made of atoms held together by bonds bonds are forces of attraction between atoms Results from attractions between protons and electrons |
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Formulas for Ionic Compounds |
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Ionic Compounds |
Formed from the combination of a cation and an anion.
Electrically neutral
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Nomenclature |
Systematic method for naming compounds
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organic compound |
compounds containing primarily carbon and hydrogen |
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Inorganic Compounds |
Everything else |
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sssssssssssssssss |
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Molecular Compounds |
Commonly called covalent compounds
Contain descrete molecular units
Usaully composed of non metallic elements
Most are binary compounds (contain two elements) |
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Naming Binary Acids |
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Molar Mass |
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Solubility |
Maximum amount of solute that will dissolve in a given quantity of a solvent at a specific temperature
Soluble: Majority of the solute dissolves Insoluble: Solute does not dissolve
All ionic compounds are electrolytes but not all electrolytes are soluble |
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Oxidation number |
Number of charges the atom would have in a molecule ( or ionic compound) IF electrons were transferred completely. |
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d |
d |
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Lewis Dot Symbols |
Symbol of an element and one dot for each valence electron Electron configurations shows all electrons, Lewis dot symbols shows valence electrons |
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energy |
the capacity to do work |
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work |
directed energy change resulting from a process |
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forms of energy |
kinetic potential |
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kinetic energy |
the energy produced by a moving object |
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potential energy |
energy available by virtue of an objects position |
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chemical energy |
energy stored within the structural units of chemicl substances |
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Thermal Energy |
the energy associated with the random motion of atoms and molecules |
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Radiant energy |
solar energy, that is enrgy that comes from the sun |
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Heat |
The transfer of thermal energy between two bodies that are at different temperatures |
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thermochemistry |
the study of heat change in chemical reactions |
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Heat Exchange |
occurs between The system and The surroundings |
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Exothermic process |
transfer of thermal energy to the surroudings (gives off heat) |
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Endothermic Process |
heat is supplied to the system (heat is absorbed) |
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atom |
the smallest identifiable unit of matter. |
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Acids |
Sour Taste
Can Dissolve many metals
Neutralize bases |
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Bases |
Bitter
Slippery
Neutralize Acids |
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theory of chemical evolution |
the formation of increasingly complex carbon containing substances culminated in amolecule that could replicate itself. At this point, there was a switch from chemical evolution tobiological evolution. |
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atom |
the smallest identifiable unit of matter |
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electrons |
extremely small particles called electrons orbit an atomic nucleus made up of larger particles called protons and neutrons |
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diagram of atoms |
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Protons |
have a positve electric charge +1 |
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neutrons |
electrically neutral |
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electrons |
negative electric charge -1 |
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neutral atom |
When the number of protons and electrons are the same |
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atomic number |
number of protons in an atom |
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mass number |
the sum of the protons and neutrons in a atom |
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Dalton Da |
Although the masses of protons, neutrons, and electrons can be measured in grams, the numbersinvolved are so small that biologists prefer to use a special unit called the dalton (Da). This unit ofmeasure was named after John Dalton, who was responsible for formulating modern atomic theoryin the seventeenth century. The masses of protons and neutrons are virtually identical and areroutinely rounded to 1 Da each. The mass of an electron is so small that it is normally ignored. So,the mass of an atom is equal to its mass number |
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isotopes |
froms of an element with different numbers of neutrons |
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atomi weight |
The atomic weight of an element is an average of all the masses of the naturallyoccurring isotopes based on their abundance in nature. This is why the atomic weight of an elementis often slightly different from its mass number. For example, carbon's atomic weight is 12.01 ratherthan 12, which reflects that while the most abundant isotope of carbon has 6 neutrons and a mass of12 daltons (12C) there are also less abundant isotopes with greater atomic weights. |
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radioactive isotope |
unstable isotope e. Its nucleus will eventually decay and release energy (in the form ofradiation). When 14C decays, one of its neutrons changes into a proton, converting 14C to thestable 14N isotope of nitrogen, wit 7protons and 7 neutrons. Timing of decay is specific to eachradioactive isotope, a fact that has been very useful in estimating the dates of key events in Earth’shistory. |
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Most abudant elements in organisms are highlighted in bliue |
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Orbitals |
Electrons move around atomic nuclei in specific regions called orbitals. Each orbital canhold up to two electrons.● Orbitals are grouped into levels called electron shells.● Electron shells are numbered 1,2,3, and so on, to indicate their relative distance from thenucleus. Smaller numbers are closer to the nucleus.● Each electron shell contains a specific number of orbitals. Each orbital in a shell is loadedwith one electron before any orbital is filled with a second, paired electron.● The electrons of an atom fill the innermost shellsfirst, before filling outer shells. |
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valence shell. |
outermost shell of each element |
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valence electrons |
The electronsfound in the outermost shell of each element. |
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Valence |
The number of unpaired electrons found in atoms valence shell is referred toas its valence. Carbon’s valence is four, oxygen is two. |
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Stability |
an atom is most stable when its valence shell isfilled. |
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Filling of valence shells |
One way that valence shells can be filled is through the formation of chemical bondsattractions that bind atoms together |
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covalent bond |
When two atoms share electrons, the chemical bond is called acovalent bond, and the connected atoms are termed a molecule. |
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compounds |
different elements are bonded together |
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electronegativity |
the strength at which an atom pulls shared electrons toward the nucleus |
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electronegativtiy |
What is responsible for an atom’s electronegativity? It’s a combination of two things, the number ofprotons in the nucleus and the distance between the nucleus and the valence shell.
If you return tothe periodic table in Figure 2.3 and move your finger along a full row from left to right, you willmoving toward elements that increase in number of protons and in electronegativity (ignoring thosewith full outer shells in the far right column). Each row in the table represents a shell of electrons. Asyour finger moves down the table, it passes over elements with more shells and lesselectronegativity. In Figure 2.3, fluorine would have the highest electronegativity and sodium wouldhave the lowest. |
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trend in electronegativity |
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non polar covalent bond |
A bond that invlolves equally shared electrons |
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polar covalent bond |
asymmetric sharing of electrons |
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ionic bonds |
the electrons in ionic bonds are completely transferred from one atom to the other.
The electron transfer occurs becuase it gives teach of the two resutling atoms a full valence shell.
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ion |
An atom or molecule that carries a full charge, rather than the partial charges that arise from polarcovalent bond |
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a |
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linear structures |
Nitrogen (N2) and carbon dioxide (CO2) have linear structures (see Figure 2.8).There are only two atoms in N2, so the molecule can only be linear. The three atomsin CO2 are linear because the electrons in the two C=O bonds repel one anotherand are thus 180 degrees apart, which maximizes the distance between them. |
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tetrahedral structures |
Methane (CH4) has a tetrahedral structure (Figure 2.9a). The tetrahedron formsbecause the repulsive forces between electrons push the four C-H bonds as farapart as they can get, such that each bond to the central carbon atom is 109.5degrees away from its neighboring bonds. |
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bent planar structures |
Water (H2O) has a planar (flat) structure,with a bond geometry that is bent ratherthan linear (Figure 2.9b). Why? The electrons in the four orbitals of oxygens valenceshell repulse each other, just like the electrons in the C-H bonds in methane do. Butin water, two of the orbitals in the central oxygen atom are filled with unsharedelectron pairs, which push the O-H bond closer together than what is observed inmethanes C-H bonds. The result is a flat, V-shaped molecule with O-H bonds thatare 104.5 degrees apart. |
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Molecular Formulas |
are compact, but don’t contain a great deal of information theyindicate only the numbers and types of atoms in a molecule. |
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Structural Formulas |
indicate which atoms in a molecule are bonded together Single, double, and triple bonds are represented by single, double, and triple dashes,respectively. Structural formulas also indicate geometry in two dimensions. Thismethod is useful for planar molecules such as water and CO2. |
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Ball-and-stick models |
s take up more space than structural formulas, but provideinformation on the three dimensional shape of molecules and often indicate therelative sizes of the atoms involved. |
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Space Filling models |
are more difficult to read than ball than stick models but moreaccurately depict the relative sizes of atoms and their spatial relationships. (Figure2.10d) |
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aqueous |
water based |
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Two environments for chemical evolution |
1. The atmosphere, which in the early Earth was probably dominated by gases ejectedfrom volcanoes. Water vapor, carbon dioxide (CO2), and nitrogen (N2) are thedominant gases ejected by volcanoes today; a small amount of molecular hydrogen(H2) and carbon monoxide (CO) may also be present.2. Deep sea hydrothermal vents, where extremely hot rocks contact deep cracks in theseafloor. In addition to gases such as CO2 and H2, certain deep sea vents are richin minerals containing reactive metals such as nickel and iron. |
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The most common reaction in the mix of gases that emerges from volcanoes results in theproduction of carbonic acid, which can be precipitated in rain water |
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system |
A system is defined as just those substances you want to focus attention on, thesurrounding are ignored, except for their effect on the system. |
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the mass of the reactants is alwaysequal to the mass of products |
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law ofconservation of mass, |
mass cannot be created or destroyed but it may be rearranged throughchemical reactions. |
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endothermic |
thermal energy is absorbed by the system during the process |
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exothermic |
releases thermal energy to the environment |
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Energy |
the capacity to do work or supply heat. This capacity exists in one of twoways, as a stored potential or as an active motion. |
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thermalenergy |
The kinetic energy of molecular motion |
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heat |
When two objects with different temperatures come into contact, thermal energy istransferred between them |
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first law of thermodynamics, |
energy is conserved itcannot be created or destroyed, but only transferred and transformed. |
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spontaneous |
Chemicalreactions are spontaneous if they are able to proceed on their own, without any continuous externalinfluence such as added energy |
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Two factors determine if a reaction will proceed spontaneously: |
Reactions tend to be spontaneous if the products have lower potential energy thanthe reactants, that is, when the shared electrons in the reaction products are heldmore tightly than those in the reactants. For example, when hydrogen and oxygengases react, water is produced spontaneously.
The electrons involved in the O-H bonds of water are held much more tightly by themore electronegative oxygen atom than when they were shared equally in the O-Hand O=O bonds of H2 and O2. As a result, the products have much lower potentialenergy than the reactants. |
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two |
Reactions tend to be spontaneous when the product molecules are less orderedthan the reactant molecules. For example glucose is a single, highly orderedmolecule. But when glucose burns in air, it breaks up into gaseous carbon dioxideand water vapor. These product molecules are much less ordered than the reactantglucose molecules. The amount of disorder in a system (or the surroundingenvironment) is called entropy. Entropy increases in the system when the productsof a chemical reaction are less ordered than the reactant molecules. |
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entropy |
The amount of disorder in a system (or the surroundingenvironment) is called entropy
Entropy increases in the system when the productsof a chemical reaction are less ordered than the reactant molecules. |
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spontaneous reactions |
Reactions tend to be spontaneous when the product molecules are less orderedthan the reactant molecules.
For example glucose is a single, highly orderedmolecule. But when glucose burns in air, it breaks up into gaseous carbon dioxideand water vapor. These product molecules are much less ordered than the reactantglucose molecules |
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s |
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second law of thermodynamics |
states that in all spontaneous reactions, entropy, alwaysincreases when both the system and its environment are taken into account. |
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When the shared electrons are far from the atomic nuclei, the bond is long andweak. If the electrons are shifted closer to one or both of the atoms, the bond becomes shorter andstronger. Atoms bound together with weak bonds have a greater capacity to be broken apart toreform into new, stronger bonds during a reaction than do atoms held together by strong bonds. Amolecules potential to form stronger bonds is a type of potential energy called chemical energy. |
When the shared electrons are far from the atomic nuclei, the bond is long andweak. If the electrons are shifted closer to one or both of the atoms, the bond becomes shorter andstronger. Atoms bound together with weak bonds have a greater capacity to be broken apart toreform into new, stronger bonds during a reaction than do atoms held together by strong bonds. Amolecules potential to form stronger bonds is a type of potential energy called chemical energy. |
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miller spark discharge experiment |
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organic compounds |
Many molecules that contain carbonbonded to other elements, such as hydrogen |
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Functional Groups |
Functional Groups |
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Amino Group |
Acts as a base tends to attract a proton to form |
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Carboxyl |
Acts as an acid - tends to lose a proton in solution to form: |
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Carbonyl |
Aldehydes, especially, react with certain compounds to produce larger molecules to form |
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Hydroxyl |
highly polar so makes compounds more soluble through hydrogen bonding with water; may also act as a weak acid and drop a ptoton |
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Phosphate |
Molecules with more than one ponsphate linked together store large amounts of chemical energy |
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Sulfhydryl |
When present in proteins, can form disulfide (S-S) bonds that contribute to protein structure. |
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Amino and Carboxyl |
functional groups tend to attract or release a hydrogen ion (proton),respectively, when in solution. Amino groups function as bases; carboxyl groups act asacids. During chemical evolution and in organisms today, the most important types of aminoand carboxyl containing molecules are the amino acids. Amino acids contain both an aminogroup and a carboxyl group. Amino acids can be linked together by covalent bonds that formbetween amino and carboxyl groups. In addition bot of these functional groups participate inhydrogen bonding.s |
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Carbonyl |
groups are found on molecules such as acetaldehyde and acetone. Thisfunctional group is the sire of reactions that link these molecules into larger, more complexorganic compounds |
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Hydroxyl |
groups are important because they act as weak acids. In many cases the protonsinvolved in acid-base reactions that occur in cells come from hydroxyl groups on organiccompounds. Because hydroxyl groups are polar molecules containing hydroxyl groups willform hydrogen bonds and tend to be soluble in water. |
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Phosphate |
groups carry negative charges on two of their oxygen atoms. When phosphategroups transferred from one organic compound to another, the change in charge oftendramatically affects the structure of the recipient molecule. In addition, phosphate groupsthat are bonded together store chemical energy that can be used in chemical reaction. |
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Sulfhydryl |
groups consist of a sulfur atom bonded to a hydrogen atom. They are importantbecause sulfhydryl groups can link to one another via disulfide (O-H) bonds. |
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macromolecules |
arge molecules made up ofsmaller molecular subunits joined together |
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monomer |
a molecularsubunit used to build a macromolecule |
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polymer |
When a large number of monomers are bonded together |
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polymerization |
The process of linking monomers together |
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hydrogen bonding |
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Four types of macromolecules that were key to evoluton |
proteins nucleic acids carbohydrates lipids |
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carbohydrate (sugar) |
encompasses the monomers called monosaccharides, smallpolymers called oligosaccharides and the large polymers called polysaccharides. The name“carbohydrate” is logical because the molecular formula of many of these molecules is (CH2O)n,where the n indicates the number of “carbon-hydrate” groups ( the word hydrate refers to water). they are made up of a carbonyl group (C=O),several hydroxyl groups (-OH), along with multiple carbon hydrogen bonds (C-H). Furthermore, notall CH2O compounds are carbohydrates |
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Monosaccharides (simple sugars) |
Monosaccharides or simple sugars are the monomers of carbohydrates. |
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carbon count |
Three carbon sugars,such as those in Figure 5.1 are called trioses. Ribose, which acts as a building block fornucleotides, has five carbons and is called a pentose; the glucose that coursing through ourbloodstream right now is a six carbon sugar or a hexose. |
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ring structures |
Although Figure 5.2 shows monosaccharides as linear chains, it’s actually rare for sugars consistingof five or more carbons to exist in this form. In aqueous solution, they spontaneously form ringstructures when the carbonyl group reacts with a hydroxyl group of another carbon. An example ofthis process is shown in Figure 5.3. When glucose (a six carbon aldose) forms a ring, the C-1carbon ( the first carbon in the linear chain) forms a bond with the oxygen atom of the C-5 hydroxyl.In this reaction, a hydrogen atom is removed from the C-5 hydroxyl and a hydrogen is added to theC-1 carbonyl to generate a new hydroxyl group. This balanced exchange preserves the number ofatoms and hydroxyls between the ring and linear forms. |
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alpha and beta glucose |
When sugars form a ring structure, the position of the newly formed hydroxyl group (e.g. at C-1 inglucose) will be fixed in one of two possible orientations: below or above the plane of the ring. THearrangement of the other hydroxyl groups remains the same, so there are two possible forms ofglucose: alpha-glucose and beta-glucose. The two forms exist in equilibrium, but the beta-glucose ismore common because it is slightly more stable than alpha-glucose. The significance of these twopossible forms becomes apparent when they are linked together, which is the subjet of the nextsection |
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complex carbohydrates |
Simple sugars covalently link to form chains of varying lengths called complex carbohydrates. Thesechains range in size from short oligosaccharides to long polysaccharides. |
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disaccharide |
When just two sugars link together |
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polymerization (condensation) |
Monosaccharides polymerize when a condensation reaction occurs between two hydroxyl groupsresulting in a covalent connection (-O-) called a glycosidic linkage, or glycosidic bond. Theinverse reaction, hydrolysis,cleaves these linkages. |
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Cleavage ( hydrolysis) |
hydroysis cleaves glycosidic linkages |
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geometry of glycosidic linkages |
Because glycosidic linkages form between hydroxyl groups, and because every monosaccharidecontains at least two hydroxyls, the location and geometry of glycosidic linkages can vary widelyamong different oligosaccharides and polysaccharides. |
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Alpha and Beta Glycosidic linkage |
Maltose and lactose illustrate two of the most common glycosidic linkages, called thealpha-1,4-glycosidic linkage and the Beta-1,4-glycosidic linkage. The numbers refer to the carbonson either side of the linkage, indicating that the linkages are between the C-1 and C-4 carbons. Theirgeometry, however, is different: alpha and beta refer to the contrasting orientations of the C-1hydroxyls on opposite sides of the plane of the glucose rings |
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the most common polysaccharides found in organisms today |
starch Glycogen Cellulose Chitin Petptidoglycan |
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starch |
In plant cells, some monosaccharides are polymerized and stored for later use in the form of starch.Starch consists entirely of alpha-glucose joined by glycosidic linkages. Most of these linkages arebetween C1 and C4 carbons, and the angle of these bonds causes the chain of glucose residues tocoil into a helix. starch is made up of two types of polymers. One is anunbranched molecule called amylose, which contain only alpha-1,4-glycosidic linkages. The other isa branched molecule called amylopectin. Branching occurs when a glycosidic linkage formsbetween a C1 carbon and a C6 carbon (and alpha-1,6-linkage). In amylopectin, branching occurs atabout one out of every 30 glucose residues. |
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Glycogen |
Glycogen performs the same storage role in animals as starch does in plants. In humans, forexample, glycogen is stored in the cells of liver and muscle tissues. When you start exercising,enzymes begin breaking glycogen into glucose monomers, which are then processed in musclecells to supply energy.Glycogen is a helical polymer of alpha-glucose and is nearly identical to the branched form of starch.However, instead of and alpha-1,6-glycosidic linkage occurring in about 1 out of every 30 residues inamylopectin , a branch occurs in about 1 out of every 10 glucose subunits. The branches providemore ends for enzymes to release glucose when your body needs it. |
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Cellulose |
All cells are enclosed by a membrane and the cells of many organisms are also surrounded by aprotective layer of material called a cell wall. Polysaccharides are the primary building materials formost of these cell walls, including those plants, fungi, and bacteria.In plants, the major component of the cell wall is cellulose. Cellulose is a polymer made fromBeta-glucose monomers joined by Beta-1,4-glycosidic linkages. As Table 5.1 shows, the geometryof the linkage is such that each glucose residue in the chain is flipped in relation to the adjacentresidue. The flipped orientation is important because (1) it generates a linear molecule, rather thanthe helix seen in starch; and (2) it permits multiple hydrogen bonds to form between adjacent,parallel strands of cellulose. As a result, cellulose forms strong fibers consisting of multiple parallelstrands joined by hydrogen bonds. Interacting cellulose fiber give plant cells structural support. |
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Chitin |
Chitin is a polysaccharide that stiffens the cell walls of fungi. It’s also found in a few types of protistsand in many animals. It is, for example, the important component of the external skeletons of insectsand crustaceans.Chitin is similar to cellulose, but instead of consisting of glucose residues, the monosaccharideinvolved in one called N-acetylglucosamine (abbreviated as NAG). These NAG monomers arejoined by Beta-1,4-glycosidic linkages. As in cellulose, the geometry of these bonds results in everyother residue being flipped in orientation. The NAG subunits in chitin also form hydrogen bondsbetween adjacent strands to produce a stiff protective armor. |
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Peptidoglycan |
Most bacteria, like all plants and fungi, have cell walls. The primary structural component of bacterialcell walls consists of a polysaccharide called peptidoglycan.Peptidoglycan is the most complex of the polysaccharides discussed so far. It has a long backboneformed by NAG and N-acetylmuramic acid (NAM) that alternate with each other and are linked byBeta-1,4-glycosidic linkages. In addition, a short chain of amino acids is attached at the C-3 carbonof NAM. When molecules of peptidoglycan align, peptide bonds link the amino acid chains onadjacent strands. These links servet the same purpose as the hydrogen bonds between the parallelstrands of cellulose and chitin in the cell walls of other organisms.While there is no evidence to suggest polysaccharides played a significant role in chemicalevolution, they became enormously important once cellular life evolved. So in the next section let'slook closely at how they function in today's cells. |
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carbohydrate functions |
besides serving as precursors to other moleculesthey (1) provide fibrous structural materials (2) mark cell identity and (3) store chemical energy. Let’s look at each of these functions in turn. |
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Structural carbohydrates |
celluose
chitin
peptidoglycan
To appreciate why cellulose, chitin, and peptidoglycan are effective structural molecules, recall thatthey form long strands and that bonds can form between adjacent strands. In the Cell walls of plantsfor example, a collection of about 80 cellulose molecules are cross linked by hydrogen bonding toproduce a fiber. These cellulose fibers, in turn, crisscross to form a tough sheet that is able towithstand pulling and pushing forces, what an engineer would call tension and compression.Structural carbohydrates are not just tough, but durable. Almost all organisms produce enzymes that only few organisms haveenzymes capable of digesting cellulose, chitin, or peptidoglycan. These fibers tend to be insolublethanks to the strong interaction between strands consisting of Beta-1,4-glycosidic linkages. Theexclusion of water within these fibers makes them more difficult to hydrolyze, so they are resistant todegradation and decay |
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almost all organisms |
produce eenzyes that cleave alpha glycosidic linkages |
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Cell identity |
polysaccharides act as an identification badge on the outer surface of the plasmamembrane that surrounds a cell |
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glycolipid |
A glycolipid is a lipid that has been glycosylated, meaning it has one ormore covalently attached carbohydrates |
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glycoprotein |
A glycoprotein is a protein that is similarly linked tocarbohydrates. The carbohydrates attached to glycolipids and glycoproteins are usually short,branched oligosaccharides. |
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cell cell signaling |
cell-cell signaling. Each cell in your body has carbohydrates on its surface that identify it as part ofyour body. For example, your blood type (A,B,AB,or O) is determined by the type of markeroligosaccharides presented on the surface of your blood cells. The A, B, and O markers arise fromdifferent modification of the carbohydrates in glycolipids. In addition, each distinct type of cell in amulticellular organism for example, the nerve cells and muscle cells in your body- displays adifferent set of glycoproteins on its surface. Ths identification information helps cells recognize andcommunicate with each other. |
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carbohydrates |
carbohydrates are also used in cell identity, as astructural material, and a source of carbon atoms for the synthesis of other complex molecules. |
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photosynthesis |
plants harvest the energy in sunlight andstore it in the bonds of carbohydrates by the process known as photosynthesis |
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photosynthesis |
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Carbon dioxide has low potential energy because the electrons involved in covalent bondsare held tightly by oxygen atoms. (b) Carbohydrates such as the sugar shown here havehigh potential energy because many of the covalent bonds are weak and the electrons areheld equally between C and H atoms |
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starch and glycogen as efficient energy storage moleucles |
Starch and glycogen are efficient energy storage molecules because they polymerize viaalpha-glycosidic linkages instead of the beta-glycosidic linkages in the structural polysaccharides.The alpha-linkages in storage polysaccharides are readily hydrolyzed to release glucose, while thestructural polysaccharides resist enzymatic degradation. |
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phosphorylase |
The most important enzyme involved in catalyzing the hydrolysis of alpha-glycosidic linkages |
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amylases |
The enzymes involved in breakingthe alpha-glycosidic linkages in starch |
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Glucose makes ATP |
When a cell needs energy, reactions break down glucose and capture some of the released energythrough synthesis of the nucleotide adenosine triphosphate (ATP). More specifically the energythat's released when sugars are processed is used the synthesize ATP from a precursor calledadenosine diphosphate (ADP) plus free inorganic phosphate (Pi) molecule. The overall reaction canbe written as follows: |
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To put this in terms of bonds, some of the chemical energy stored in the C-H and C-C bonds ofcarbohydrate [(CH2O)n] is released as new C=O bonds are formed in CO2. This energy is thentransferred to a new bond linking a third phosphate group to ADP to form ATP. |
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Lipid |
is a catchall term for carbon containing compounds that are characterized by a physicalproperty, their insolubility in water |
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lipid insolubility in water |
This insolubility results from a high proportion of non polar C-Cand C-H bonds relative to polar functional groups. Lipids do dissolve, however in organic solventconsisting of nonpolar compounds like benzene (C6H6). To understand why lipids are insoluble in water, examine the five carbon compounds, calledisoprene,illustrated in Figure 6.1a. Note that isoprene consists entirely of carbon atoms bonded tohydrogen atoms. Molecules that contain only carbon and hydrogen are known as hydrocarbons.Hydrocarbons are nonpolar because electrons are shared equally in C-H bonds owing to the similarelectronegativities of carbon and hydrogen. Since C-H bonds form no partial charges, hydrocarbonsdo not dissolve in water. Lipids therefore, are mostly hydrophobic because they have a significanthydrocarbon component. |
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isoprenoids |
long branched hydrocarbon chains |
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fatty acid |
a simple lipid consisting of a hydrocarbonchain bonded to a polar carboxyl functional group (-COOH). |
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saturated |
Hydrocarbon chains that consist of only single bonds between the carbons |
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unsaturated |
Ifone or more double bonds exist |
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polyunsaturated |
contain lipids with many double bonds |
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waxes |
Saturated lipids have extremely long hydrocarbon tails |
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melting points of lipids |
If the lipidsare composed of straight chains, many of these interactions will form along the chain and allow thelipids to pack together tightly to form a solid. If they hydrocarbons are bent, like the unsaturated fattyacid on the right side of Figure 6.1b,they will have fewer interactions, move freely, and form a liquid Highly saturated lipids, such as in butter, have relatively high melting points and are solid at roomtemperature (20-22 degrees celsius). Saturated lipids have extremely long hydrocarbon tails, likewaxes, form particularly stiff solids at room temperature. Highly unsaturated lipids are liquid at roomtemperature and called oils. Unsaturated lipids may be converted to saturated lipids by breakingdouble bonds and adding hydrogen atoms via the process of hydrogenation. |
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Butter consists primarily of saturated lipids (b) waxes are lipids with extremely long saturatedhydrocarbon chains (c ) oils are dominated by “polyunsaturates” lipids with hydrocarbonchains that contain multiple C=C double bonds. (d) The product Crisco is made byconverting polyunsaturates into saturated lipids by hydrogenation. |
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Three types of lipids found in cells |
Steroids fats phospholipids |
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Steroids are a family of lipids distinguished by the bulky, four ring structure highlighted in orange inFigure 6.3. The various steroids differ from one another by the functional groups or side groupsattached to different carbons in those hydrophobic rings. Steroids such as estrogens andtestosterone are known for their role as hormones in cell signaling. The steroid shown in the figure ischolesterol, which has a polar hydrophilic hydroxyl group attached to the top ring and nonpolarisoprenoid “tail” attached at the bottom |
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Fats |
Fats are nonpolar molecules composed of three fatty acids that are linked to a three carbonmolecule called glycerol. Because of this structure, fats are also called triacylglycerols ortriglycerides. Thanks to all of these bonds, fats can store about twice as much chemical energy per gram ascarbohydrates. |
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carbs vs fats |
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formation of fats |
fats form when a dehydration reaction occurs between a hydroxyl group ofglycerol and the carboxyl group of a free fatty acid (when fatty acids are not attached to othermolecules, they are referred to as free fatty acids). The glycerol and fatty acid molecules becomejoined by what is called an ester linkage. An ester linkage occurs when two atom s (one of themcarrying a double bonded oxygen, often a carbonyl group) are linked together by an oxygen. Butnotice that since fatty acids are not linked into chains, they are not considered monomers, and thusfats are not polymers. In this way, the structure of fats differs from the polymers that are formedwhen amino acids, nucleotides, and monosaccharides link together. |
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) Fats form when dehydration reaction connect glycerol to three fatty acids and produce esterlinkages. (b) Most phospholipids consist of glycerol linked to only two fatty acid or isoprenoidchains. Unlike fats, the third hydroxyl in glycerol is attached to a phosphate group and asmall polar or charged organic molecule ( in this example, choline). |
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phospholipid |
Phospholipids consist of a glycerol that is linked to a phosphate group and two hydrocarbon chainsof either isoprenoids or fatty |
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phospholipids with fatty acid tails |
found in the domains Bacteria and Eukarya |
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phospholipids with isprenoid tails |
found in the domain Archaea |
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phospholipids |
are crucial componetns of the plams membrane The branched isoprenoid chains in archaeal phospholipidsprovide greater membrane stability and protection in the extreme environments inhabited by certainarchaea. |
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phospholipids |
Besides the nonpolar, hydrophobic region that defines lipids, membrane forming lipids have polar,hydrophilic region. To better understand this structure, take another look at the phospholipidillustrated in Figure 6.5b. Notice that the molecule has a “head” region containing a negativelycharged phosphate group attached to a polar group. The charges and polar covalent bond in thehead region interact with water molecules when a phospholipid is placed in solution. In contrast, thelong hydrocarbon tails of a phospholipid are nonpolar and hydrophobic. Water molecules cannotform hydrogen bonds with hydrocarbon tail, so they do not interact extensively with this part of themolecule. |
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amphipathic |
Substances that contain both hydrophilic and hydrophobic regions Phospholipids are amphipathic. As figure 6.3 shows, cholesterol is also amphipathicbecause it has a hydrophilic hydroxyl functional group attached to its hydrophobic rings. |
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amphipathic lipids in water |
Amphipathic lipids do not dissolve when they are placed in water. Their hydrophilic heads interactwith water, but their hydrophobic tails do not. Instead of dissolving in water, amphipathic lipidsassume one of two types of structures: micelles or lipid bilayers. |
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Micelles |
are tiny spherical aggregates created when thehydrophilic heads of a set of lipids face outward and interact with the water, while thehydrophilic tails interact with each other in the interior, away from the water Micelles tend to form from free fatty acids or other simple amphipathic lipids with single hydrocarbonchains |
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lipid bilayer |
created when lipid molecules align in paired sheets. As Figure 6.6bon page 126 shows, the hydrophilic heads in each layer face the surroundingsolution while the hydrophobic tails face one another inside the bilayer. In this way,the hydrophilic heads interact with water while the hydrophobic tails interact with oneanother. Phospholipids, which have bulkier nonpolar regions consisting of two hydrocarbon tails, tendto form bilayers |
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Micelles and phospholipid bilayers form spontaneously |
Micelles and phospholipid bilayers form spontaneously in water, no input of energy is required. Thisfact may come as a surprise because at the level of lipid organization, entropy seemingly decreases,the lipids become less disordered as micelles and phospholipid bilayers form. (Recall that entropy isa measure of the randomness or disorder in a system; see Ch.2 Section 2.3) How can this beexplained if spontaneous processes tend to increase entropy? The answer involves understandinghow amphipathic lipids aggregate. First you must consider the organization of water molecules. Recall that hydrophobic interactionsoccur when nonpolar structure become surrounded by a “cage” of highly organized water molecules.When amphipathic lipids are dispersed in an aqueous solution, cages of water form around each ofthe nonpolar tails. If the tails aggregate to form micelles and bilayers, then only the hydrophilicregions of the lipids are exposed and the water cages will melt. This decrease in water moleculeorganization results in an overall increase in the entropy of the system. |
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vesicles |
small bubble like strucutres consisting of lipid bilayers surrouding a small amount of aqueous solution. |
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liposomes |
artificialy genrated membrane bound vesicles |
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The construction of a planar bilayer across a hole in a wall separating two water filledcompartments (b) A wide variety of experiments are possible with planar bilayers; just a fewexperimental questions are suggested here. |
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permeability |
The permeability of a structure is its tendency to allow a given substance to pass throughit. |
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selective permeability of lipid bilayers |
lipid bilayers are highly slective |
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selective permeability |
means that some substances cross a membrane more easily than othersubstances do. This difference in membrane permeability is a critical issue because controlling whatpasses between the exterior and interior environments is a key characteristic of cells small nonpolar molecules such as oxygen (O2) move acrossbilayers quickly. If the small molecules are polar but uncharged, such as water (H2O) the rate oftransport decreases. Larger polar molecules cross the membrane even slower. |
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Only certain substances cross lipid bilayers readily. The polarity, size, and charge of solutes affecttheir rate of diffusion across a membrane. |
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pattern of permeability |
charged substances and polar molecules above a certain size are more stable dissolved in water, apolar environment, than they would be in the nonpolar interior of membranes. The length and saturation state of the hydrocarbon tails, in addition to the presence ofcholesterol molecules, profoundly influences the physical properties of a membrane and itspermeability |
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Bond Saturation and Hydrocarbon Chain Length Affect Membrane Permeability |
A phosphlipid’s degree of saturation, along with the length of its hydrocarbon tails, affects keysaspects of its behavior in a membrane.● When unsaturated hydrocarbon tails are packed into a lipid bilayer, kinks created bydouble bonds produce spaces among the tails. These spaces reduce the number ofvan der Waals interactions that help hold the hydrophobic tails together, weakeningthe barrier to solutes.● Packed saturated hydrocarbon tails have fewer spaces and more van der Waalsinteractions. As the length of saturated hydrocarbon tails increases, the forces thathold them together also increase, making the membrane even denser. |
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In general, phospholipids containing unsaturated hydrocarbon tails form bilayers that have moregaps and are more permeable than bilayers formed from phospholipids with saturated hydrocarbontails. |
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Cholesterol Affects Membrane Permeability |
Researchers have found that addingcholesterol molecules to artificial membranes dramatically reduces their permeability. |
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a |
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s |
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Temperature and permeability |
, lowtemperatures can make membranes impervious to molecules that would cross them readily at moremoderate temperatures. Put your finger at 0 degrees celsius on the x-axis of the graph (just aboutthe freezing point of water), and note that membranes that lack cholesterol are almost completelyimpermeable to glycerol. But if you trace any of the three data lines in the same figure to the right(increasing temperature), you will see that permeability increases |
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