Biology 311C Book

Section 1.1

THEME: New properties emerge at each level in the biological hierarchy

emergent properties - new properties that arise with each step upward in the hierarchy of life, owing to the arrangement and interactions of parts as complexity increases

ex: although photosynthesis occurs in an intact chloroplast, it will not take place in a disorganized test-tube mixture of chlorophyll and other chloroplast molecules. Because photosynthesis requires a specific organization of these molecules in the chlroplast

ex: if a blow to the head disrupts the intricate architecture of a human brain, the mind may cease to function properly even though all the brain tissues are still present. Our thoughts and memories are emergent properties of a complex network of nerve cells

reductionism - the approach of reducing complex systems to simpler components that are more manageable to study

ex: by studying the molecular structure of DNA that had been extracted from cells, James Watson and Francis Crick inferred, in 1953, how this molecule could serve as the chemical basis of inheritance

systems biology - approach that attempts to model the dynamic behavior of whole biological systems based on a study of the interactions among the system's parts.

a combination of components that function together

ex: ground level on a street corner, where you can observe local traffic, to a helicopter high above a city, from which you can see how variables such as time of day, accidents, etc. affect traffic throughout the city

[1-10. 1 = Largest, 10 = Smallest]

1) Biosphere - all life on earth and all the places where life exists

2) Ecosystems - all living things in a particular area, along with all the nonliving components of the environment with which life interacts

3) Communities - entire array of organisms inhabiting a particular ecosystem

4) Populations - all the indibiduals of a species living within the bounds of a specified area

5) Organisms - individual living things

6) Organs and Organ Systems - organs are body parts that carries out a particular funtion in the body. Organ systems are a team of organs that cooperate in a larger function

7) Tissues - a group of cells that work together, performing a specialized function

8) Cells -life's fundamental unit of structure and function. Single cell performs all functions of life. Multi-cellular divides labor among spcialized cells

9) Organelles - the various functional components present in cells

10) Molecules - chemical structure consisting of two or more small chemical units called atoms

THEME: Organisms Interact with Other Organisms and Physical Environment

ex: leaves absorb light energy from the sun

ex: leaves fall to the ground and are decomposed by organisms that return minerals to the soil

ex: water and minerals in the soil are taken up by the tree through its roots

ex: animals eat leaves and fruit from the tree

ex: leaves take in carbon dioxide from the air and release oxygen

global climate change - increase in temperature and change in weather patterns all around the planet, due mostly to increasing atmospheric CO2 levels from the burning fossil fuels. The increase in temperature, called global warming, is a major aspect of global climate change

THEME: Life requires energy transfer and transformation

Similar to the examples under theme to the left. All are related and dependent on one another, forming an ecosystem

a fundamental characteristic of living organisms is their use of energy to carry out ife's activities

THEME: Structure and Function Are Correlated at All Levels of Biological Organization

ex: a leaf; its thin, flat shape maximizes the amount of sunlight that can be captured by its chloroplasts. Analyzing a iological structure gives us clues about what it does and how it works. Conversely, knowing the function of something provides insight into its construction

THEME: The Cell is An Organism's Basic Unit of Structure and Function

Cell has a special place as the lowest level of organization that can perform all activities required for life

eukaryotic cell - a cell subdivided by internal membranes into various membrane-enclosed organelles

largest organelle is nucleus

The other organelles are located in the cytoplasm, the entire region between the nucleus and outer membrane of the cell

prokaryotic cell - a cell where the DNA is not separated from the rest of the cell by enclosure in a membrane-bounded nucleus

lack the other kinds of membrane-enclosed organelles that characterize eukaryotic cells

THEME: The Continuity of Life is Based on Heritable Information in hte Form of DNA

genes - the units of inheritance that transmit information from parents to offspring

DNA - deoxyribonucleis acid; chromosomes that have almost all of the cell's genetic material

the molecular structure of DNA accounts for its ability to store information. Each DNA molecule is made up of two long chains, called strands, arranged in a double helix

DNA provides the blueprints for making proteins, and proteins are the main players in building and maintaining the cell and carrying out its activities

Other human proteins include proteins in a muscle cell that drive contraction and the defensive proteins called antibodies. Enzymes, which catalyze (speed up) specific chemical reactions, are mostly proteins and are crucial to all cells

gene expression - the procee in which a sequence of nucleotides along a gene is transcribed into RNA, which is then translated into a specific protein with a unique shape and function. The information in a gene directs the production of a cellular product

a particular sequence of nucleotides says the same thing in one organism as it does in another

differences between organisms reflect differences between their nucleotide sequences rather than between their genetic codes

genome - the entire "library" of genetic instructions that an organism inherits

genomics - the science of studying whole sets of genes of a species as well as comparing genomes between species

bioinformatics - the use of computational tools to store, organize, and analyze the huge volume of data that result from high-throughput methods

THEME: Feedback Mechanisms Regulate Biological Systems

Just as a coodrinated control of traffic flow is necessary for a city to function smoothly, regulation of biological processes is crucial to the operation of living systems. The key is the ability of many biological processes to self-regulate by a mechanism called feedback

negative feedback - accumulation of an end product of a process slows that process

most common form of regulation in living systems

ex: the cell's breakdown of sugar generates chemical energy in the form of a substance called ATP. When a cell makes more ATP than it can use, the excess ATP "feeds back" and inhibits an enzyme near the beginning of the pathway

positive feedback - an end product speeds up its own production

ex: the clotting of your blood in response to injury. When a blood vessel is damages, structures in the blood called platelets begin to aggregate at the site. Positive feedback occurs as chemicals released by the platelets attract more platelets. The platelet pileup then initiates a complex process that seals the qound with a clot

Section 1.2

CORE THEME: Evolution accounts for the unity and diversity of life

THEME: Classifying the Diversity of Life

Three domains of life:

Bacteria

all prokaryotic

Chapter 27 explains differences

bacteria are the most diverse and widespread prokaryotices and are now classified into multiple kingdoms

Archaea

all prokaryotic

Many of the prokaryotes knowns as archaea live in the Earth's extreme environments, such as salty lakes and boiling hot springs. Domain Archaea includes multiple kingdoms

Eukarya

Includes three kingdoms of multicellular eukaryotes:

Plantae

produce their own sugars and other food molecules by photosynthesis

Fungi

absorb dissolved nutrients from their surroundings; many decompose dead organisms and organic wastes and obsorb nutrients from these sources

Animalia

animals obtain food by ingestion, which is hte eating and digesting of other organisms

THEME: Charles Darwin and the Theory of Natural Selection

"The Origin of Species" articulated two main points:

1st) that contemporary species arose from a succession of ancestors, an idea that Darwin supported with large amount of evidence

Darwin called this evolutionary history of species "descent of modification"

2nd) a proposed mechanism for descent with modification, called "natural selection"

natural selection - when the natural environment "selects" for hte propagation of certain traits among naturally occurring variant traits in the population

Darwin propsed that natural selection, by its cumulative effects over long periods of time, could cause an ancestral species to give rise to two or more descendant species. This could occur, for example, if one population fragmented into several subpopulations isolated in different environments. In these separate arenas of natural selection, one species could gradually radiate into multiple species as the geographically isolated populations adapted over many generations to different sets of environmental factos

Section 1.3

CORE THEME: In studying nature, scientists make observations and then form and test hypotheses

science - a way of knowing, an approach to understanding the natural world

inquiry - the heart of science; a search for information and explanation, often focusing on specific questions

THEME: Making Observations

observation - use of the senses to gather information, either directly or indirectly with the help of tools such as microscopes that extend our senses

data - recorded observations

qualitative data - data in the form of recorded descriptions rather than numerical measurements

quantitative data - data generally recorded as measurements

inductive reasoning - logic of collecting and analyzing observations hopefully leading to important conclusions

Through induction, we derive generalizations from a large number of specific observations. "The sun always rises in the east" is an example. And so is "All organisms are made of cells"

THEME: Forming and Testing Hypotheses

hypothesis - a tentative answer to a well-framed question; an explanation on trial. It is usually a rational accounting for a set of observations, based on the available data and guided by inductive reasing

example of scientific thought process:

Observations

Question

Hypothesis 1: Dead batteries

Prediction: Replacing batteries will fix problem

Test of prediction

Test falsifies hypothesis

Hypothesis 2: Burnt-out bulb

Prediction: Replacing bulb will fix problem

Test of prediction

Test does not fasify hypothesis

deductive reasoning - generally used after the hypothesis has been developed and involves logic that flows in the opposite direction, from the general to the specific

ex: From general premises we extrapolate to the specific results we should expect if hte premises are true:

Premise 1: all organisms are made up of cells

Premise 2: humans are organisms

Conclusion from deductive reasoning = humans are composed of cells

THEME: The Flexibility of the Scientific Method

controlled experiment - an experiment that is designed to compare an experimental group with a control group

researchers usually "control" unwanted variables not by eliminating them through environmental regulations, but by canceling out their effects by using control groups

theory - an explanation that is broader in scope than a hypothesis, generates new hypothesis, and is supported by a large body of evidence

a theory is general enough to spin off many new, specific hypotheses that can be tested

compared to any one hypothesis, a theory is generally supported by a much greader body of evidence

Section 1.4

CORE THEME: Science benefits from a cooperative approach and diverse viewpoints

THEME: Building on the work of others

model organism - a species that is easy to grow in the lab and lends itself particularly well to the questions being investigated

because all organisms are evolutionarily related, lessons learned from a model organism are often widely applicable

THEME: Science, Technology, and Society

technology - applies scientific knowledge for some specific purpose

science - the goal of science is to understand natural phenomena

Section 2.1

THEME: Matter consists of chemical elements in pure form and in combinations called compounds

matter - anything that takes us space and has mass

element - substance that cannot be broken down to other substances by chemical reactions. Matter is made up of elements

compound - a substance consisting of two or more different elements combined in a fixed ratio

essential elements - elements that an organism needs to live a healthy life and reproduce

trace elements - elements required by an organism in only minute quantities

Section 2.2

THEME: An element's properties depend on the structure of its atoms

atom - the smallest unit of matter that still retains the properties of an element

Subatomic particles

neutrons

protons

electrons

electron shells - electrons found here. Each shell has a characteristic average distance and energy level

first shell closest to nucleus and has lowest potential energy

the chemical behavior of an atom is determined by the distribution of electrons in the atom's electron shells

valence electrons - the electrons on the outermost shell. The chemical behavior of an atom depends mostly on these

valence shell - the outmost electron shell

orbital - the three-dimensional space where an electron is found 90% of the time

dalton - the unit of measurement for atoms and subatomic particles

Isotopes - when an atom takes on a different atomic form that has more neutrons than other atoms of the same element

radioactive isotope - an isotope in which the nucleus decays spontaneously, giving off particles and energy

energy - defined as the cpaacity to cause change

potential energy - energy that matter possesses because of its location or structure

Section 2.3

THEME: The formation and function of molecules depnd on chemical bonding between atoms

chemical bonds - when atoms stay close together, held by attractions. Atoms with incomplete valence shells can interact with certain other atoms in such a way that each partner completes its valence shell: the atoms either share or transfer valence electrons

covalent bond - the sharing of a pair of valence electron by two atoms

two or more atoms held together by covalent bonds constitute a molecule

single bond - H-H or H:H, a pair of shared electrons

double bond - sharing two pairs of valence electrons O=O

valence - the number of unpaired electrons required to complete the atom's outermost shell

electronegativity - the attraction of a particular atom for the electrons of a covalent bond. The more electronegative an atom is, the more strongly it pulls shared electrons toward itself

nonpolar covalent bond - a type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity

polar covalent bond - a covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive

ionic bond - the attraction of cations and anions forming a bond

ion - a charged atom or molecule

cation - when the charge is postitive

anion - when the charge is negative

ionic compounds/salts - compounds formed by ionic bonds

Hydrogen bonds - the noncovalent attraction between a hydrogen and an elctronegative atom

the partial positive charge on a hydrogen atom allows the hydrogen to be attracted to a different electronegative atom nearby

van der Waals interactions - weak attractions between molecules or parts of molecules that result from transient local partial charges

many small positive and negative attractions that, when put together, are strong

ex: each gecko toe has hundreds of thousands of tiny hairs, with multiple projections at each hair's tip that increase surface area. The van der Waals interactions between the hair tip molecules and the molecules of the wall's surface are so numerous htat despite their individual weakenss, together they can support the gecko's body weight

Section 2.4

THEME: Chemical reactions make and break chemical bonds

chemical reactions - the making and breaking of chemical bonds, leading to changes ni the composition of matter

Stoichiometry

reactants - starting materials

products - ending materials

chemical equilibrium - the point at which the reactions exactly offset one another

Section 3.1

THEME: Polar covalent bonds in water molecules result in hydrogen bonding

polar covalent bond - a covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive

ex: [Polar covalent bonds in a water molecule] because oxygen is more electronegative than hydrogen, shared electrons are pulled more toward oxygen. This results in a partial negative charge on the oxygen and a partial positive charge on hte hydrogens

polar molecule - a molecule (such as water) with an uneven distribution of charges in different regions of the molecule

Section 3.2

THEME: Four emergent properties of water contribute to Earth's suitability for life

Cohesion of water molecules

cohesion - the linking together of like molecules by hydrogen bonds

surface tension - a measure of how difficult it is to stretch or break the surface of a liquid

water has a greater surface tension than most other liquids. At the interface between water and air is an ordered arrangement of water molecules, hydrogen-bonded to one another and to the water below

adhesion - the clinging of one substance to another

Moderation of temperature by water

kinetic energy - the energy of motion

for a given body of matter, the amount of heat is a measure of the matter's total kinetic energy due to the motion of its molecules; thus, heat depends in part on the matter's volume

temperature - measure of heat intensity that represents the average kinetic energy of the molecules, regardless of volume

calorie - the amount of heat it takes to raise the temperature by 1 g of water by 1 * C (degrees celcius)

temperature is the average kinetic energy of molecules

specific heat - the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1 * C (degrees celcius)

we can trace water's high specific heat, like many of its other properties, to hydrogen bonding. Heat must be absorbed in order to break hydrogen bonds; by the same token, heat is released when hydrogen bonds form

heat of vaporization - the quantity of heat a liquid must absorb for 1 g of it to be converted from the liquid to the gaseous state

water's high heat of vaporization is another emergent property resulting from the strength of its hydrogen bonds, which must be broken before the molecules make their exodus from the liquid

evaporative cooling - as a liquid evaporates, the surface of the liquid that remains behind cools down

Water: the solvent of life

solution - a liquid that is a completely homogeneous mixture of two or more substances

solvent - the dissolving agnet of a solution

solute - substance that is dissolved

An aqueous solution is one in which water is the solvent

hydration shell - the sphere of water molecules around each dissolved ion

ex: we have a spoonful of table salt, the ionic compound sodium chloride (NaCl). Placed in water. Surface of each grain, or crystal, of salt, the sodium and chloride ions are exposed to the solvent. These ions and the water molecules have a mutual affinity owing to the attraction between opposite charges. The oxygen regions of the water molecules are negatively charged and are attracted to sodium cations. The hydrogen regions are positively charged and are attracted to chloride anions. As a result, water molecules surround the individual sodium and chloride ions, seperating and shielding them from one another

Working inward from the surface of each salt crystal, water eventually dissolved all ions. The result is a solution of two solutes, sodium cations and chloride anions, homogeneously mixed with water, the solvent

hydrophillic - an substance that has an affinity to water

substances can be hydrophilic without actually dissolving

ex: some molecules in cells are so large that they do not dissolve. Instead they remain suspended in the aqueous liquid of the cell

colloid - a stable suspension of fine particles in a liquid

hydrophobic - a substance that can repel water

cannot form hydrogen bonds

ex: vegetable oil

Section 3.3

Acidic and basic conditions affect living organisms

hydrogen ion - H+, a single proton with a charge of 1+

Occasionally, a hydrogen atom participating in a hydrogen bond between two water molecules shifts from one molecule to the other. When this happens, the hydrogen atom leaves its electron behind, and what is actually transferred is a hydrogen ion

The water molecule that lost a proton is now a hydroxide ion (OH-), which has a charge of 1-

The proton binds to the other water molecule, making that molecule a hydronium ion (H3O+)

chem reaction: 2 H2O => H3O+ + OH-

double arrows means reversible reaction that reaches a state of dynamic equilibrium

Acids and Bases

acid - a substance tht increases the hydrogen ion concentration of a solution

ex: HCl -> H+ + Cl-

this source of H+ (dissociation of water is the other source) results in an acidic solution - one having more H+ than OH-

base - a substance that reduces the hydrogen ion concentration of a solution

ex: NH3 + H+ <=> NH4+

the base reduces the H+ concentration. Solutions with a higher concentration of OH- than H+ are known as basic solutions

a solution in which the H+ and OH- concentrations are equal is said to be neutral

pH declines as H+ concentration increases

a solution of pH 3 is not twice as acidic as a soution of pH 6, but a thousand times more acidic

Buffers

buffer - a substance that minimizes changes in hte conentrations of H+ and OH- in a solution

it does so by accepting hydrogen ions from the solution when they are in excess and donating hydrogen ions to the solution when they have been depleted

There are several buffers that contribute to pH stability in human blood and many other biological solutions. One of these is carbonic acid (H2CO3), formed when CO2 reacts with water in blood plasma. Carbonic acid dissociates to yield a bicarbonate ion (HCO3-) and a hydrogen ion (H+):

H2CO3 <=> HCO3- + H+

the chemical equilibrium between carbonic acid and bicarbonate acts as a pH regulator, the reaction shifting left or right as other processes in the solution add or remove hydrogen ions

If the H+ concentration in blood begins to fall (that is, if pH rises), hte reaction proceeds to the right and more carbonic acid dissociates, replenishing hydrogen ions

But when H+ concentration in blood begins to rise (when pH drops), the reaction proceeds to the left, with HCO3- (the base) removing the hydrogen ions from the solution and forming H2CO3

the carbonic acid-bicarbonate buffering system consists of an acid and a base in equilibrium with each other. Most other buffers are acid-base pairs

Section 4.1

THEME: Organic chemistry is the study of carbon compounds

Organic compounds range from simple molecules, such as methane (CH4), to colossal ones, such as proteins, with thousands of atoms. Most organic compounds contain hydrogen atoms in addition to carbon atoms

Section 4.2

THEME: Carbon atoms can form diverse molecules by bonding to four other atoms

hydrocarbons - organic molecules consisting of only carbon and hydrogen

atoms of hydrogen are attached to the carbon skeleton wherever electrons are available for covalent bonding

isomers - compounds that have the same numbers of atoms of the same elements but different structures and hence different properties

structural isomers - isomers that differ in the covalent arrangments of their atoms

cis-trans isomers (geometric isomers) - carbons that have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds

Single bonds allow the atoms they join to rotate freely about hte bond axis without changing the compound

In contrast, double bonds do not permit such rotation

Notice CIS is on the left and TRANS is on the right

cis isomer: the two X's are on the same side

trans isomer: the two X's are on opposite sides

enantiomers - isomers that are mirror images of each other and that differ in shape due to the presence of an asymmetric carbon, one that is attached to four different atoms or groups of atoms

the "L" in "L-alanine" means left

the "D" in "D-alanine" means right

Section 4.3

THEME: A few chemical groups are key to the functioning of biological molecules

functional groups - chemical groups that affect molecular function by being directly involved in chemical reactions

7 chemical groups most important in biological processes:

hydroxyl - (---OH), a hydrogen atom is bonded to na oxygen atom, which is turn is bonded to a carbon skeleton of the organic molecule

compounds: alcohols (their specific names usually end in -ol)

functional properties: is polar as a result of the electrons spending more time near the electronegative oxygen atom. Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars

carbonyl group - (C=O) consists of a carbon atom joined to an oxygen atom by a double bond

compounds: ketones - if hte carbonyl group is within a carbon skeleton. Aldehydes - if the carbonyl group is at the end of the carbon skeleton

functional properties: a ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups)

carboxyl group - (---COOH) when an oxygen atom is double-bonded to a carbon atom that is also bonded to an ---OH group

compounds: carboxlic acids (organic acids)

functional properties: acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is so polar. Found in cells in hte ionized form with a charge of 1- and called a carboxylate ion

amino group - (---NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton

compounds: amines. Glycine, a compound that is both an amine and a carboxylic acid because it has both an amino group and a carboxyl group; compounds with both groups are called amino acids

functional properties: acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms). Found in cells in the ionized form with a charge of 1+

sulfhydryl group - (---SH) consists of a sulfur atom bonded to an atom of hydrogegn; it resembles a hydroxyl group in shape

compounds: thiols. Cysteine, an important sulfer-containing amino acid

functional properties: two sulfhydryl groups can react, forming a covalent bond. This "cross-linking" helps stabilize protein structure. Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be "permanently" curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds

phosphate group - (---OPO3^2-) a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges

compounds: organic phosphates. Glycerol phosphate, which takes part in many important chemical reaction in cells; glycerol phosphate also provides hte backbone for phospholipids, the most prevalent molecules in cell membranes

functional properties: contributes negative charge to the molecule which it is a part. Molecules containing phosphate groups have the potential to react with water, releasing energy

methyl group - (---CH3) consists of a carbon bonded to three hydrogen atoms. The carbon of a methyl group may be attached to a carbon or to a different atom

compounds: methylated compounds. 5-Mythyl cytosine, a component of DNA that has been modified by addition of a methyl group

functional properties: addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function

adenosine triphosphate - (ATP) consists of an organic molecule called adenosine attached to a string of three phosphate groups

Although ATP is sometimes said to store energy, it is more accurate to think of it as storing the potential to react with water

OVERVIEW: The Molecules of Life

macromolecules - a giant molecule formed by the joining of small molecules, usually by a dehydration reaction. Polysaccharides, proteins, and nucleic acids are macromolecules

Section 5.1

THEME: Macromolecules are polymers, built from monomers

polymer - a long molecule consisting of many similar or identical building blocks linked by covalent bonds, much as a train consists of a chain of cars

monomers - the repeating units that serve as the building blocks of a polymer

monomers are connected by dehydration reactions

The Synthesis and Breakdown of Polymers

enzymes - specialized macromolecules that speed up chemical reactions

dehydration reaction - a reaction in which two molecules are covalently bonded to each other, with the loss of a water molecule

hydrolysis - a process that is essentially the reverse of the dehydration reaction. Polymers are disassembled to monomers by this

Section 5.2

THEME: Carbohydrates serve as fuel and building material

carbohydrates - both sugars and polymers of sugars

monosaccharide - the simplest carbohydrate, active alone or serving as a monomer for disaccharides and polysaccharides. Also known as simple sugars, monosaccharides have molecular formulas that are generally some multiple o CH2O

Subtopic

Section 25.1

Conditions on early Earth made the origin of life possible

Scientists hypothesize that chemical and physical processes on early Earth, aided by the emerging force of natural selection, could have produced very simple cells through a sequence of four main stages:

1) The abiotic (nonliving) synthesis of small organic molecules, such as amino acids and nitrogenous bases

2) The joining of these small molecules into macromolecules, such as proteins and nucleic acids

3) The packaging of these molecules into protocells, droplets with membranes that maintained an internal chemistry different from that of their surroundings

4) The origin of self-replicating molecules that eventually made inheritance possible

Miller and Urey experiment - tested the Oparin-Haldane hypothesis by creating laboratory conditions comparable to those that scientists at the time thought existed on early earth

His apparatus yielded a variety of amino acids found in organisms today, along with other organic compounds. Many laboratories have since repeated Miller's classic experiment using different recipes for the atmosphere, some of which also produced organic compounds

Section 27.1

Structural and functional adaptations contribute to prokaryotic success

most prokaryotes are unicellular, although the cells of some species remain attached to each other after cell division

most likely the first organism to inhabit earth (prokaryotes)

Subtopic

Cell-surface stuctures

a key feature of nearly all prokaryotic cells is the cell wall, which maintains cell shape, protects the cell, and prevents it from bursting in a hypotonic environment

in a hypertonic environment, most prokaryotes lose water and shrink away from their wall (plasmolyze), like other walled cells

such water losses can inhibit cell reproduction

Thus, salt can be used to preserve foods because it causes prokaryotes to lose water, preventing them from rapidly multiplying

the cell walls of prokaryotes differ in structure from those of eukaryotes. In eukaryotes that have cell walls, such as plants and fungi, the walls are usually made of cellulose or chitin

In contrast, most bacterial cell walls contain peptidoglycan, which is a polymer composed of modified sugars cross-linked by short polypeptides

Using a technique called the Gram stain, developed by the nineteenth-century Danish physician Hans Christian Gram, scientists can classify many bacterial species into two groups based on differences in cell wall composition

Samples are first stained with crystal violet dye and iodine, then rinsed in alcohol, and finally stained with a red dey such as safranin

The stucture of the bacterium's cell wall determines the straining response

Gram-positive bacteria have simpler walls with a relatively large amount of peptidoglycan

Gram negative bacteria have less peptidoglycan and are structurallly more complex, with an outer membrane that contains lipopolysaccharides (carbohydrates bonded to lipids)

The lipid portions of the lipopolysaccharides in the walls of many gram-negative bacteria are toxic, causing fever or shock

The outer membrane of a gram-negative bacterium helps protect it from the body's defenses

Gram-negative bacteria also tend to be more resistant than gram-positive species to antibiotics because the outer membrane impedes entry of hte drugs

The cell wall of many prokaryotes is surrounded by a sticky layer of polysaccharide or protein. This layer is called a capsule if it is dense and well-defined or a slime layer if it is less well organized

Both kinds of sticky outer layers enable prokaryotes to adhere to their substrate or to other individuals in a colony

Some prokaryotes stick to their substrate or to one another by means of hairlike appendages called fimbriae

Ex: the bacterium that causes gonorrhea uses fimbriae to fasten itslef to the mucous membranes of its host

fimbriae are usually shorter and more numerous than pili, appendages that pull two cells together prior to DNA transfer from one cell to the other; pili are sometimes referred to as sex pili

Motility

About half of all prokaryotes are capable of taxis, a directed movement toward or away from a stimulus

ex: prokaryotes that exhibit chemotaxis change their movement pattern in response to chemicals. They may move toward nutrients or oxygen (positive chemotaxis) or away from a toxic substance (negative chemotaxis)

Of the various structures that enable prokaryotes to move, the most common are flagella. Flagella may be scattered over the entire surface of the cell or concentrated at one or both ends

prokaryotic flagella differ greatly from eukaryotic flagella: they are one-tenth the wideth and are not covered by an extension of the plasma membrane

the flagella of prokaryotes are also very different in their molecular composition and their mechanism of propulsion

among prokaryotes, bacterial and archaeal flagella are similar in size and rotation mechanism, but the yare composed of different proteins

overall, these structural and molecular comparisons suggest that the flagella of bacteria, archaea, and eukaryotes arose independently

Since the flagella of organism in hte three domains perform similar functions but probably are not related by common descent, it is likely that they are analogous, not homologous, structures

Internal Organization and DNA

the cells of prokaryotes are simpler than those of eukaryotes in both their internal structure and the physical arrangement of their DNA

prokaryotic cells lack the complex compartmentalization found in eukaryotic cells. However, some prokaryotic cells do have specialized membranes that perform metabolic functions. These membranes are usually infoldings of the plasma membrane

the genome of a prokaryote is structurally different from a eukaryotic genome and in most cases has considerably less DNA

In the majority of prokaryotes, the genome consists of a circular chromosome with many fewer proteins than found in the linear chromosomes of eukaryotes

also, unlike eukaryotes, prokaryotes lack a membrane-bounded nucleus; their chromosome is located in the nucleoid, a region of cytoplasm that appears lighter than the surrounding cytoplasm in electron micrographs

in addition to its single chromosome, a typical prokaryotic cell may also have much smaller rings of independently replicating DNA molecules called plasmid, most carrying only a few genes

Reproduction and Adaptation

Prokaryotes are highly successful in part because of their potential to reproduce quickly in a favorable environment

by Binary Fission, a single prokaryotic cell divides into 2 cells, which then divide into 4, 8, 16, etc.

prokaryotic reproduction is limitied - the cells eventually exhaust their nutrient supply, poison themselves with metabolic wastes, face competition from other microorganism, or are consumed by other organisms

reproduction in prokaryotes draws attnetion to three key features of their biology

1) they are small

2) they reproduce by binary fission

as a result from these three features, prokaryotic populations can consist of many trillions of individuals - far more than populations of multicellular eukaryotes, such as plants and animals

3) they have short generation times

certain bacteria develop resistant cells called endospores when they lack an essential nutrient

the original cell produces a copy of its chromosome and surrounds it with a tough multilayered structure, forming the endospore

water is removed from the endospore, and its metabolism halts

the orginal cell then lyses, releasing the endospore

most endospores are so durable that they can survive in boiling water; killing them requires heating lab equipment to 121C under high pressure. In less hostile environments, endospores can remain dormant but viable for centuries, able to rehydrate and resume metabolism when their environment improves

Section 27.3

Diverse nutritional and metabolic adaptations have evolved in prokaryotes

the extensive genetic variation found in prokaryotic populations is reflected in the diverse nutritional adaptations of prokaryotes

Like all organisms, prokaryotes can be categorized by how they obtain energy and the carbon used in building the organic molecules that make up cells

Every type of nutrition observed in eukaryotes is represented among prokaryotes, along with some nutritional modes unique to porkaryotes

In fact, prokaryotes have an astounding range of metabolic adaptations, much broader than that found in eukaryotes

Organisms that obtain energy from light are called phototrophs

organism that obtain energy from chemicals are called chemotrpohs

organisms that need CO2 in some form as a carbon source are called autotrpohs

in contrast, heterotrophs require at least one organic nutrient, such as glucose, to make other organic compounds

the role of oxygen in metabolism

obligate erobes must use O2 for cellular respiration and cannot grow without it

obligate anaerobes, on the other hand, are poisoned by O2

some obligate anaerobes live exclusively by fermentation; others extract chemical energy by anaerobic respiration, in which substances other than O2, such as nitrate ions or sulfate ions, accept electrons at the "downhill" end of electron transport chains

facultative anaerobes use O2 if it is present but can also carry out fermentation or anaerobic respiration in an anaerobic environment

nitrogen metabolism

nitrogen is essential for the production of amino acids and nucleic acids in all organisms

whereas eukaryotes can obtain nitrogen from only a limited group of nitrogen compounds, prokaryotes can metabolize nitrogen in a wide variety of forms

for example, some cyanobacteria and some methanogens (a group of archaea) convert atmosphere nitrogen to ammonia, a process called nitrogen fixation

the cells can then incorporate this "fixed" nitrogen into amino acids and other organic molecules

in terms of their nutrition, nitrogen-fixing cyanobacteria are some of hte moset self-sufficient organisms, since they need only light, CO2, N2, water, and some minerals to grow

nitrogen fixation by prokaryotes has a large impact on other organisms

ex: nitrogen-fixing prokaryotes can increase the nitrogen available to plants, which cannot use atmospheric nitrogen but can use hte nitrogen compounds that the prokaryotes produce from ammonia

27.4

8.1

the totality of an organism's chemical reactions is called metabolism

metabolic pathways - a series of chemical reactions that eitehr builds a comoplex molecule (anabolic pathway) or breaks down a complex molecule to simpler molecules (catabolic pathway)

catabolic and anabolic pathways are the "downhill" and "uphill" avenues of hte metabolic landscape

energy released from the downhilll reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways

thermodynamics - the study of the energy transformation that occur in the collection of matter

first law - the energy of the universe is constant. "energy can be transferred and transformed, but it cannot be created or destroyed." The first law is also known as the "principle of conservation of energy."

second law - "every energy transfer or transformation increases the entropy of the universe."

a process that can occur without and input of energy is called a spontaneous process

"for a process to occur spontaneously, it must increase the entropy of the universe."

8.2

Gibbs free energy or just free energy - the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell

change in G = change in H - T*change in S

change in H = enthalpy / change in S = entropy / T = absolute temperature in kelvin

once we know the value of change in G for a process, we can use it to predict whether the process will be spontaneous

processes with a negative change in G are spontaneous

change in G = G final state - G initial state

chemical reactions can be classified as:

exergonic (energy outward)

occur spontaneously

endergonic (energy inward)

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