Unit 1 - The Chemistry of Life

Evolution

A major aim of evolutionary biology is to understand the relationships among species, both living and extinct. For example, genome sequence comparisons have identified the hippopotamus as the land mammal sharing the most recent common ancestor with whales. (See Figure 22.20.

What other than carbon skeletons, do organic molecules depend on?

The properties of an organic molecule depend not only on the arrangement of its carbon skeleton but also on the various chemical groups attached to that skeleton.

Hydrophobic

"Water-fearing"; generally non polar or non ionic.

half-life

"parent" isotope decays into its "daughter" isotope at a fixed rate, expressed as the half-life of the isotope—the time it takes for 50% of the parent isotope to decay. Each radioactive isotope has a characteristic half-life that is not affected by temperature, pressure, or any other environmental variable

Are the nitrogenous bases a part of the backbone?

(Note that the nitrogenous bases are not part of the backbone.)

The synthesis and breakdown of polymers

(a) Dehydration reaction: synthesizing a polymer- Dehydration removes a water molecule, forming a new bond. (b) Hydrolysis: breaking down a polymer- Hydrolysis adds a water molecule, breaking a bond.

What happens If the H+ concentration in blood begins to fall (that is if pH starts to rise)?

, the reaction proceeds to the right and more carbonic acid dissociates, replenishing hydrogen ions

The pH of a solution is defined as

-log [H+]

What did the scientists believe about organic compounds?

. Artificial synthesis of the complex molecules extracted from living matter seemed impossible, however. Organic compounds were thought to arise only in living organisms, which were believed to contain a life force beyond the jurisdiction of physical and chemical laws

What happens at this equilibrium point?

. At this equilibrium point, the concentration of water molecules greatly exceeds the concentrations of H+ and OH- .

What do the measurements of CO2 levels in air bubbles trapped in ice?

. Based on measurements of CO2 levels in air bubbles trapped in ice over thousands of years, scientists calculate that the pH of the oceans is 0.1 pH unit lower now than at any time in the past 420,000 years. Recent studies predict that it will drop another 0.3-0.5 pH unit by the end of this century

Why does starch represent stored energy?

. Because glucose is a major cellular fuel, starch represents stored energy

What Determines Protein Structure?

. But what are the key factors determining protein structure? You already know most of the answer: A polypeptide chain of a given amino acid sequence can be arranged into a three-dimensional shape determined by the interactions responsible for secondary and tertiary structure. This folding normally occurs as the protein is being synthesized in the crowded environment within a cell, aided by other proteins.

Do large molecules such as protein dissolve in water?

. Even molecules as large as proteins can dissolve in water if they have ionic and polar regions on their surface

A molecular mimic

. Morphine affects pain perception and emotional state by mimicking the brain's natural endorphins

The role of hydrocarbons in fats.

1) Mammalian adipose cells stockpile fat molecules as a fuel reserve. This colorized micrograph shows part of a human adipose cell with many fat droplets, each containing a large number of fat molecules. 2) A fat molecule consists of a small, nonhydrocarbon component joined to three hydrocarbon tails that account for the hydrophobic behavior of fats. The tails can be broken down to provide energy.

Species that benefit from loss of ice

1) More light and warmer waters result in more phytoplankton, which are eaten by other organisms. 2)Bowhead whales, which feed on plankton they filter, are thriving 3)Some fish species, such as capelin, benefit from having more plankton to eat.

water soluble protein

1) This oxygen is attracted to a slight positive charge on the lysozyme molecule. 2)This hydrogen is attracted to a slight negative charge on the lysozyme molecule.

Secondary structure - Regions stabilized by hydrogen bonds between atoms of the polypeptide backbone

1)A region of α helix in transthyretin 2)A region of β pleated sheet in transthyretin 3)β strand, often shown as a folded or flat arrow pointing toward the carboxyl end

Species being harmed by loss of ice:

1)Loss of ice has reduced feeding opportunities for polar bears, who hunt from the ice. 2) The Pacific walrus depends on the ice to rest; its fate is uncertain. 3) Black guillemots in Alaska cannot fly from their nests on land to their fishing grounds at the edge of the ice, which is now too far from land; young birds are starving.

Double bond position

1-butene, 2- butene. The skeleton may have double bonds, which can vary in location.

What are the four emergent properties of water?

1. Cohesive behavior 2. Ability to moderate temperature 3. Expansion upon freezing 4. Versatility as a solvent

How many types of particles of atoms have been discovered by scientists using high energy collisions?

100

What are the bond angle in methane?

109.5 degrees. and they are roughly the same in any group of atoms where carbon has four single bonds

Atomic number for sodium & number of protons

11

The neutron & proton are almost identical in mass. What is their mass?

11.7 * 10 ^ -24 gram

Number of neutrons in sodium

12

How many forms of the C8H18 are there?

18 variants

Steps of the experiment:

1: The water mixture in the "sea" flask was heated; vapor entered the "atmosphere" flask 2: The "atmosphere" 2 contained a mixture of hydrogen gas (H2), methane (CH4), ammonia (NH3), and water vapor. 3. Sparks were discharged to mimic lightning. 4. A condenser cooled the atmosphere, raining water and dissolved molecules into the sea flask 5. As material cycled through the apparatus, Miller periodically collected samples for analysis.

Which orbital does the lone hydrogen electron occupy?

1s orbital

How many electrons can the first shell hold?

2 electrons

How many electrons can each orbital hold? The four orbitals of the second electron can hold?

2 electrons 8 electrons (2 in each)

How many atoms of hydrogen are needed to satisfy the valence of one oxygen atom?

2 hydrogen atoms

How many neutrons does helium have?

2 neutrons

How many protons & electrons does helium have?

2 protons & 2 electrons

Atomic mass of sodium

22.9898 daltons

Mass number for sodium

23

Possible structural isomers of C20H42

366319

What shape are molecules?

3d

half life of uranium 238

4.5 billion years. Uranium-238 was used to determine that moon rocks are approximately 4.5 billion years old, similar to the estimated age of Earth

How many electrons does carbon have?

6 electrons in total 1st shell - 2 electrons 2nd shell/valence shell - 4 electrons. A carbon atom usually completes its valence shell by sharing its 4 electrons with other atoms so that 8 electrons are present.Each pair of shared electrons constitutes a covalent bond

How many electrons does oxygen have in its second electron shell ?

6 valence electrons and hence needs to more to complete its valence shell.

How many electrons can the second shell hold?

8 electrons

How many naturally occurring elements do chemists recognise?

92 Examples: Gold, copper, carbon & oxygen

How does the cellulose in our food pass through the digestive tract?

; the cellulose in our food passes through the digestive tract and is eliminated with the feces

Within the backbone, the oxygen atoms have a partial negative charge, and the hydrogen atoms attached to the nitrogens have a partial positive charge

; therefore, hydrogen bonds can form between these atoms. Individually, these hydrogen bonds are weak, but because they are repeated many times over a relatively long region of the polypeptide chain, they can support a particular shape for that part of the protein

buffer

A buffer is a substance that minimizes changes in the concentrations of H+ and OH- in a solution.

asymmetric carbon

A carbon that is attached to four different atoms or four different groups of atoms. The four groups can be arranged in space around the asymmetric carbon in two different ways that are mirror images.

What do the rapidly moving electrons form around the nucleus?

A cloud of negative charge

Does a compound need to be ionic to dissolve in water?

A compound does not need to be ionic to dissolve in water; many compounds made up of nonionic polar molecules, such as the sugar in the sugar cube mentioned earlier, are also water-soluble. Such compounds dissolve when water molecules surround each of the solute molecules, forming hydrogen bonds with them.

Compound

A compound is a substance consisting of two or more different elements combined in a fixed ratio.

polar covalent bond

A covalent bond in which electrons are not shared equally

Covalent bond

A covalent bond is the sharing of a pair of valence electrons by two atoms

How does a cow harbour cellulose?

A cow harbours cellulose digesting prokaryotes and protists in its gut. These microbes hydrolyse the cellulose of hay and grass and convert the glucose to other compounds that nourish the cow

What may cause atherosclerosis?

A diet rich in saturated fats is one of several factors that may contribute to the cardiovascular disease known as atherosclerosis

How does RNA, the other type of nucleic acid, fit into gene expression, the flow of genetic information from DNA to proteins?

A given gene along a DNA molecule can direct synthesis of a type of RNA called messenger RNA (mRNA). The mRNA molecule interacts with the cell's protein-synthesizing machinery to direct production of a polypeptide, which folds into all or part of a protein.

A mole of ethyl alcohol

A mole of ethyl alcohol (C2H6O) also contains 6.02 * 1023 molecules, but its mass is only 46 g because the mass of a molecule of ethyl alcohol is less than that of a molecule of sucrose

anion

A negatively charged ion

Chemical groups are significant because __________.

A number of chemical groups can replace one or more hydrogens of the hydrocarbon. These groups may participate in chemical reactions or may contribute to function indirectly by their effects on molecular shape; they help give each molecule its unique properties.

single bond

A pair of shared electrons

A person with sickle cell disease :

A person with the disease has periodic "sickle cell crises" when the angular cells clog tiny blood vessels, impeding blood flow. The toll taken on such patients is a dramatic example of how a simple change in protein structure can have devastating effects on protein function.

The structure of a phospholipid.

A phospholipid has a hydrophilic (polar) head and two hydrophobic (nonpolar) tails. This particular phospholipid, called a phosphatidylcholine, has a choline attached to a phosphate group. the bilayer structure formed by self-assembly of phospholipids in an aqueous environment.

cation

A positively charged ion

What happens when the pH of a solution changes slightly?

A solution of pH 3 is not twice as acidic as a solution of pH 6, but 1,000 times (10 * 10 * 10) more acidic. When the pH of a solution changes slightly, the actual concentrations of H+ and OH- in the solution change substantially.

Table salt dissolving in water

A sphere of water molecules, called a hydration shell, surrounds each solute ion. Negative oxygen regions of polar water molecules are attracted to sodium cations (Na+). Positive hydrogen regions of water molecules are attracted to chloride anions (Cl-)

Solute

A substance that is dissolved in a solution.

base

A substance that reduces the hydrogen ion concentration of a solution is called a base.

What happens when a sugar cube is placed in water?

A sugar cube placed in a glass of water will dissolve with a little stirring. The glass will then contain a uniform mixture of sugar and water; the concentration of dissolved sugar will be the same everywhere in the mixture.

What is the dalton same as?

AMU Atomic mass unit

Acidic amino acids

Acidic amino acids have side chains that are generally negative in charge due to the presence of a carboxyl group, which is usually dissociated (ionized) at cellular pH.

Amino group (- NH2)

Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms). Compound name: Amine Glycine, an amino acid (note its carboxyl group) Ionized form of NH2, found in cells

Adhesion in plants

Adhesion of the water to cell walls by hydrogen bonds helps resist the downward pull of gravity.

Methyl group (-CH3)

Affects the expression of genes when on DNA or on proteins bound to DNA. Affects the shape and function of male and female sex hormones. Compound name: Methylated compound 5-Methylcytosine, a component of DNA that has been modified by addition of a methyl group

amino acid structure

All amino acids share a common structure. An amino acid is an organic molecule with both an amino group and a carboxyl group the small figure shows the general formula for an amino acid. At the center of the amino acid is an asymmetric carbon atom called the alpha (α) carbon. Its four different partners are an amino group, a carboxyl group, a hydrogen atom, and a variable group symbolized by R. The R group, also called the side chain, differs with each amino acid.

isotopes

All atoms of a given element have the same number of protons, but some atoms have more neutrons than other atoms of the same element and therefore have greater mass. These different atomic forms of the same element are called isotopes of the element. . In nature, an element may occur as a mixture of its isotopes

Atomic number

All atoms of a particular element have the same number of protons in their nuclei. This number of protons, which is unique to that element, is called the atomic number and is written as a subscript to the left of the symbol for the element

Starch: 1-4 linkage of α glucose monomers

All monomers are in the same orientation. Compare the positions of the OH groups highlighted in yellow with those in cellulose (c).

How does cellulose pass through the digestive tract?

Along the way, the cellulose abrades the wall of the digestive tract and stimulates the lining to secrete mucus, which aids in the smooth passage of food through the tract.

Fats

Although fats are not polymers, they are large molecules assembled from smaller molecules by dehydration reactions, like the dehydration reaction described for the polymerization of monomers

cohesion

Although the arrangement of molecules in a sample of liquid water is constantly changing, at any given moment many of the molecules are linked by multiple hydrogen bonds. These linkages make water more structured than most other liquids. Collectively, the hydrogen bonds hold the substance together, a phenomenon called cohesion.

Why are (H+) and OH- important?

Although the dissociation of water is reversible and statistically rare, it is exceedingly important in the chemistry of life. H+ and OH- are very reactive. Changes in their concentrations can drastically affect a cell's proteins and other complex molecules. As we have seen, the concentrations of H+ and OH- are equal in pure water, but adding certain kinds of solutes, called acids and bases, disrupts this balance.

Atomic nucleus

An atom's dense central core, containing protons and neutrons.

electron shell

An energy level representing the distance of an electron from the nucleus of an atom.

Example for hydrophobic

An example from the kitchen is vegetable oil, which, as you know, does not mix stably with water-based substances such as vinegar. The hydrophobic behavior of the oil molecules results from a prevalence of relatively nonpolar covalent bonds, in this case bonds between carbon and hydrogen, which share electrons almost equally. Hydrophobic molecules related to oils are major ingredients of cell membranes.

Glycogen

Animals store a polysaccharide called glycogen, a polymer of glucose that is like amylopectin but more extensively branched

How do animals carry their energy stores?

Animals, however, must carry their energy stores with them, so there is an advantage to having a more compact reservoir of fuel—fat. Humans and other mammals stock their long-term food reserves in adipose cells which swell and shrink as fat is deposited and withdrawn from storage.

What is another criterion for for classifying sugars?

Another criterion for classifying sugars is the size of the carbon skeleton, which ranges from three to seven carbons long. Glucose, fructose, and other sugars that have six carbons are called hexoses. Trioses (three-carbon sugars) and pentoses (five-carbon sugars) are also common.

Another example of trans isomers....

Another example involves trans fats, harmful fats formed during food processing that are discussed in Concept 5.3

For example, shown above is the complete globular transthyretin protein, made up of its four polypeptides.

Another example is collagen, which is a fibrous protein that has three identical helical polypeptides intertwined into a larger triple helix, giving the long fibers great strength.

kinetic energy

Anything that moves has kinetic energy, the energy of motion. Atoms and molecules have kinetic energy because they are always moving, although not necessarily in any particular direction. The faster a molecule moves, the greater its kinetic energy

Give an example for a natural occurring element that is toxic

Arsenic

evaporative cooling

As a liquid evaporates, the surface of the liquid that remains behind cools down (its temperature decreases). This evaporative cooling occurs because the "hottest" molecules, those with the greatest kinetic energy, are the most likely to leave as gas

what happens as the crystal collapses?

As the crystal collapses, the ice melts and molecules have fewer hydrogen bonds, allowing them to slip closer together. Water reaches its greatest density at 4°C and then begins to expand as the molecules move faster

What happens as the temperature falls from 4 degrees celsius to 0 degrees celsius?

As the temperature falls from 4°C to 0°C, water begins to freeze because more and more of its molecules are moving too slowly to break hydrogen bonds.

What happens at 0 degrees celsius?

At 0°C, the molecules become locked into a crystalline lattice, each water molecule hydrogen bonded to four partners

(a) Saturated fat

At room temperature, the molecules of a saturated fat, such as the fat in butter, are packed closely together, forming a solid. (b) Structural formula of a saturated fat molecule (Each hydrocarbon chain is represented as a zigzag line, where each bend represents a carbon atom; hydrogens are not shown.) Space-filling model of stearic acid, a saturated fatty acid (red = oxygen, black = carbon, gray = hydrogen)

How does water behave at temperatures above 4 degrees celsius?

At temperatures above 4°C, water behaves like other liquids, expanding as it warms and contracting as it cools.

basic amino acids

Basic amino acids have amino groups in their side chains that are generally positive in charge. (Notice that all amino acids have carboxyl groups and amino groups; the terms acidic and basic in this context refer only to groups in the side chains.) Because they are charged, acidic and basic side chains are also hydrophilic.

We are accustomed to thinking of shared traits, such as hair and milk production in mammals, as evidence of shared ancestry

Because DNA carries heritable information in the form of genes, sequences of genes and their protein products document the hereditary background of an organism. The linear sequences of nucleotides in DNA molecules are passed from parents to offspring; these sequences determine the amino acid sequences of proteins. As a result, siblings have greater similarity in their DNA and proteins than do unrelated individuals of the same species.

Why does an oxygen atom have two regions of partial negative charge?

Because electrons have a negative charge and are pulled toward oxygen in a water molecule, the oxygen atom has two regions of partial negative charge. Each hydrogen atom has one region of partial positive charge.

denatured protein

Because it is misshapen, the denatured protein is biologically inactive. Most proteins become denatured if they are transferred from an aqueous environment to a non polar solvent, such as ether or chloroform; the polypeptide chain refolds so that its hydrophobic regions face outward toward the solvent.

Why will water change its temperature lesser than other liquids when it absorbs or loses a given amount of heat?

Because of the high specific heat of water relative to other materials

ionic bond

Because of their opposite charges, cations and anions attract each other; this attraction is called an ionic bond. Note that the transfer of an electron is not, by itself, the formation of a bond; rather, it allows a bond to form because it results in two ions of opposite charge. Any two ions of opposite charge can form an ionic bond. The ions do not need to have acquired their charge by an electron transfer with each other.

Why is the second shell in sodium now the valence shell?

Because sodium no longer has an electron in the third shell, the second shell is now the valence shell.

Why do we measure substances in units called moles?

Because we can't weigh out small numbers of molecules, we usually measure substances in units called moles.

The sequence of amino acids determines the protein's shape—where an α helix can form, where β pleated sheets can exist, where disulfide bridges are located, where ionic bonds can form, and so on. But how does protein folding occur in the cell?

Biochemists now know the amino acid sequence for about 65 million proteins, with roughly 1.5 million added each month, and the three-dimensional shape for almost 35,000. Researchers have tried to correlate the primary structure of many proteins with their three-dimensional structure to discover the rules of protein folding. . Unfortunately, however, the protein-folding process is not that simple. Most proteins probably go through several intermediate structures on their way to a stable shape, and looking at the mature structure does not reveal the stages of folding required to achieve that form.

when two carbon atoms are joined by a double bond

But when two carbon atoms are joined by a double bond, as in ethene (C2H4), the bonds from both carbons are all in the same plane, so the atoms joined to those carbons are in the same plane as well (

How can we deduce the number of neutrons?

By subtracting the atomic number from the mass number

What are the elements that account for 3.7% of the living matter?

Calcium (1.5%), Phosphorous(1%) , potassium(0.4%) , Sulfur (0.3%), sodium(0..2%), chlorine (0.2%), magnesium (0.1%)

Polysaccharides

Carbohydrate macromolecules are polymers called polysaccharides, composed of many sugar building blocks.

Molecular Diversity Arising from Carbon Skeleton Variation

Carbon chains form the skeletons of most organic molecules.

How does carbon enter the biosphere?

Carbon enters the biosphere through the action of producers—plants and other photosynthetic organisms that use solar energy to transform atmospheric CO2 into the carbon-based molecules of life. These molecules are then taken up by consumers, which feed on other organisms.

Length

Carbon skeletons vary in length.. Ethane & propane

enzymes

Catalysts for chemical reactions in living things

Phospholipids

Cells as we know them could not exist without another type of lipid—phospholipids. Phospholipids are essential for cells because they are major constituents of cell membranes.

Cellulose

Cellulose microfibrils in a plant cell wall. Microfibril (bundle of about 80 cellulose molecules). Cellulose molecule (unbranched). Hydrogen bonds between parallel cellulose molecules hold them together.

How are certain starch molecules?

Certain starch molecules are largely helical, fitting their function of efficiently storing glucose units

Where is chitin also found?

Chitin is also found in fungi, which use this polysaccharide rather than cellulose as the building material for their cell walls

Chitin, a structural polysaccharide.

Chitin, embedded in proteins, forms the exoskeleton of arthropods. This emperor dragonfly (Anax imperator) is molting—shedding its old exoskeleton (brown) and emerging upside down in adult form.

Cholesterol, a steroid.

Cholesterol is the molecule from which other steroids, including the sex hormones, are synthesized. Steroids vary in the chemical groups attached to their four interconnected rings (shown in gold).

What is the mass of neutrons & protons?

Close to 1 dalton

atomic mass

Close to mass number

cohesion of water

Cohesion due to hydrogen bonds between water molecules helps hold together the column of water within the cells.

Ethyl alcohol specific heat.

Compared with most other substances, water has an unusually high specific heat. For example, ethyl alcohol, the type of alcohol in alcoholic beverages, has a specific heat of 0.6 cal/(g * °C); that is, only 0.6 cal is required to raise the temperature of 1 g of ethyl alcohol by 1°C.

H20 water

Compound consisting of the elements hydrogen & water in a 2 : 1 ratio.

cis isomer

Consider a simple molecule with two double-bonded carbons, each of which has an H and an X attached to it. The arrangement with both Xs on the same side of the double bond is called a cis isomer. The two Xs are on the same side.

Phosphate group ( --- OPO3 ^2-)

Contributes negative charge (1- when positioned inside a chain of phosphates; 2- when at the end). When attached, confers on a molecule the ability to react with water, releasing energy. Compound name: Organic phosphate Glycerol phosphate, which takes part in many important chemical reactions in cells

Coral reefs are sensitive ecosystems that act as havens for a great diversity of marine life.

Coral reefs are sensitive ecosystems that act as havens for a great diversity of marine life.The disappearance of coral reef ecosystems would be a tragic loss of biological diversity

Why doesn't cotton dissolve in water in spite of being hydrophilic?

Cotton consists of giant molecules of cellulose, a compound with numerous regions of partial positive and partial negative charges that can form hydrogen bonds with water. Water adheres to the cellulose fibers. Thus, a cotton towel does a great job of drying the body, yet it does not dissolve in the washing machine. Cellulose is also present in the walls of water-conducting cells in a plant; you read earlier how the adhesion of water to these hydrophilic walls helps water move up the plant against gravity.

disulfide bridges

Covalent bonds called disulfide bridges may further reinforce the shape of a protein. Disulfide bridges form where two cysteine monomers, which have sulfhydryl groups (—SH) on their side chains (see Figure 4.9), are brought close together by the folding of the protein. The sulfur of one cysteine bonds to the sulfur of the second, and the disulfide bridge (—S—S—) rivets parts of the protein together (see yellow lines in Figure 5.16 ribbon model). All of these different kinds of interactions can contribute to the tertiary structure of a protein, as shown here in a small part of a hypothetical protein:

Presence of rings

Cyclohexane and Benzene. Some carbon skeletons are arranged in rings. In the abbreviated structural formula for each compound (to its right), each corner represents a carbon and its attached hydrogens.

Denature can also result from ....

Denaturation can also result from excessive heat, which agitates the polypeptide chain enough to overpower the weak interactions that stabilize the structure.

What does a PET scan do?

Detects locations of intense chemical activity in the body.

lactose intolerance

Disaccharides must be broken down into monosaccharides to be used for energy by organisms.. Lactose intolerance is a common condition in humans who lack lactase, the enzyme that breaks down lactose

Why do enantiomers differ in shape?

Due to the presence of an asymmetric carbon

Chromosome

Each chromosome contains one long DNA molecule, usually carrying several hundred or more genes. When a cell reproduces itself by dividing, its DNA molecules are copied and passed along from one generation of cells to the next. The information that programs all the cell's activities is encoded in the structure of the DNA. The DNA, however, is not directly involved in running the operations of the cell, any more than computer software by itself can read the bar code on a box of cereal. Just as a scanner is needed to read a bar code, proteins are required to implement genetic programs

What does each electron shell contain?

Each electron shell contains electrons at a particular energy level, distributed among a specific number of orbitals of distinctive shapes and orientations.

Functional groupd

Each has certain properties, such as shape and charge, that cause it to participate in chemical reactions in a characteristic way

To understand the structure of a single nucleotide, let's first consider the nitrogenous bases

Each nitrogenous base has one or two rings that include nitrogen atoms. (They are called nitrogenous bases because the nitrogen atoms tend to take up H+ from solution, thus acting as bases.)

2)

Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions. sodium ion - cation, chlorine ion - anion

Sodium Chloride (NaCl)

Elements sodium & chlorine in a 1 : 1 ratio

Why are enzymes that digest starch by hydrolyzing its α linkages unable to hydrolyze the β linkages of cellulose?

Enzymes that digest starch by hydrolyzing its α linkages are unable to hydrolyze the β linkages of cellulose due to the different shapes of these two molecules.

evaporation

Evaporation from leaves pulls water upward from the roots through water-conducting cells.

What does evaporation of sweat from human skin do?

Evaporation of sweat from human skin dissipates body heat and helps prevent overheating on a hot day or when excess heat is generated by strenuous activity.

What does the evaporative cooling of water contribute to?

Evaporative cooling of water contributes to the stability of temperature in lakes and ponds and also provides a mechanism that prevents terrestrial organisms from overheating. For example, evaporation of water from the leaves of a plant helps keep the tissues in the leaves from becoming too warm in the sunlight

Van der Waals interactions

Even a molecule with non polar covalent bonds may have positively and negatively charged regions. Electrons are not always evenly distributed; at any instant, they may accumulate by chance in one part of a molecule or another. The results are ever-changing regions of positive and negative charge that enable all atoms and molecules to stick to one another. These van der Waals interactions are individually weak and occur only when atoms and molecules are very close together. When many such interactions occur simultaneously, however, they can be powerful.

Why do fats separate from water?

Fats separate from water because the water molecules hydrogen-bond to one another and exclude the fats. This is why vegetable oil (a liquid fat) separates from the aqueous vinegar solution in a bottle of salad dressing.

Give an example of how radioactive isotopes are used.

For example, certain kidney disorders are diagnosed by injecting small doses of radioactively labeled substances into the blood and then analyzing the tracer molecules excreted in the urine. Radioactive tracers are also used in combination with sophisticated imaging instruments, such as PET scanners that can monitor growth and metabolism of cancers in the body

Hormonal proteins

Function: Coordination of an organism's activities. Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration.

Contractile and motor proteins

Function: Movement Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles.

defensive proteins

Function: Protection against disease Example: Antibodies inactivate and help destroy viruses and bacteria.

Receptor proteins

Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells.

enzymatic proteins

Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecule.

Effect of global warming on life

Global warming, which is caused by carbon dioxide and other "greenhouse" gases in the atmosphere, is having a profound effect on icy environments around the globe.

how much cellulose do plants produce every year?

Globally, plants produce almost 1014 kg (100 billion tons) of cellulose per year; it is the most abundant organic compound on Earth.

how do glucose and galactose differ?

Glucose and galactose, for example, differ only in the placement of parts around one asymmetric carbon (see the purple boxes in Figure 5.3). What seems like a small difference is significant enough to give the two sugars distinctive shapes and binding activities, thus different behaviours. Although it is convenient to draw glucose with a linear carbon skeleton, this representation is not completely accurate.

Glycerol

Glycerol is an alcohol; each of its three carbons bears a hydroxyl group.

structural formula of hydrogen What does the single line represent ?

H ---- H The single line represents a single bond.

What does the hydrogen ion (H+) represent?

H+ (the hydrogen ion) is used to represent H3O+ (the hydronium ion), and we follow that practice in this book

Molecular formula of Hydrogen

H2 - Indicates that there are 2 hydrogen atoms

Hemoglobin

Hemoglobin, the oxygen-binding protein of red blood cells, is another example of a globular protein with quaternary structure. It consists of four polypeptide subunits, two of one kind (α) and two of another kind (β).

How are amino groups and carboxyl groups found in a cell?

Here the amino groups and carboxyl groups are all depicted in ionized form, the way they usually exist at the pH found in a cell.

What happens if 0.01 mol of strong acid

If 0.01 mol of a strong acid is added to a liter of pure water, the pH drops from 7.0 to 2.0. If the same amount of acid is added to a liter of blood, however, the pH decrease is only from 7.4 to 7.3.

What will happen if there are no double bonds between carbon atoms composing a chain?

If there are no double bonds between carbon atoms composing a chain, then as many hydrogen atoms as possible are bonded to the carbon skeleton.

How does environment affect the strength of ionic bonds?

In a dry salt crystal, the bonds are so strong that it takes a hammer and chisel to break enough of them to crack the crystal in two. If the same salt crystal is dissolved in water, however, the ionic bonds are much weaker because each ion is partially shielded by its interactions with water molecules.

What has the FDA ordered?

In addition, the FDA has ordered trans fats to be removed from the U.S. food supply by 2018. Some countries, such as Denmark and Switzerland, have already banned trans fats in foods

(c) Cellulose: 1-4 linkage of β glucose monomers

In cellulose, every β glucose monomer is upside down with respect to its neighbors. (See the highlighted OH groups.)

triaglycerol (Triglyceride)

In making a fat, three fatty acid molecules are each joined to glycerol by an ester linkage, a bond formed by a dehydration reaction between a hydroxyl group and a carboxyl group. The resulting fat, also called a triacylglycerol, thus consists of three fatty acids linked to one glycerol molecule.

What bonds does carbon form in organic molecules?

In organic molecules, carbon usually forms single or double covalent bonds. Each carbon atom acts as an intersection point from which a molecule can branch off in as many as four directions. This enables carbon to form large, complex molecules.

How is carbon atom joined in Carbon dioxide?

In the carbon dioxide molecule (CO2), a single carbon atom is joined to two atoms of oxygen by double covalent bonds. The structural formula for CO2 is shown here :O= C=O. Each line in a structural formula represents a pair of shared electrons. Thus, the two double bonds in CO2 have the same number of shared electrons as four single bonds. The arrangement completes the valence shells of all atoms in the molecule:

Cellular respiration

In the process known as cellular respiration, cells extract energy from glucose molecules by breaking them down in a series of reactions.

In the structure of glucose

In the structure of glucose, we can see the trademarks of a sugar: The molecule has a carbonyl group, and multiple hydroxyl groups. Glucose, for example, is an aldose; fructose, an isomer of glucose, is a ketose.

atherosclerosis

In this condition, deposits called plaques develop within the walls of blood vessels, causing inward bulges that impede blood flow and reduce the resilience of the vessels.

surface tension

It is related to cohesion. a measure of how difficult it is to stretch or break the surface of a liquid

mole

Just as a dozen always means 12 objects, a mole (mol) represents an exact number of objects: 6.02 * 1023, which is called Avogadro's number. Because of the way in which Avogadro's number and the unit dalton were originally defined, there are 6.02 * 1023 daltons in 1 g. Because of the way in which Avogadro's number and the unit dalton were originally defined, there are 6.02 * 1023 daltons in 1 g. Once we determine the molecular mass of a molecule such as sucrose, we can use the same number (342), but with the unit gram, to represent the mass of 6.02 * 1023 molecules of sucrose, or 1 mol of sucrose (this is sometimes called the molar mass). To obtain 1 mol of sucrose in the lab, therefore, we weigh out 342 g.

composition of lactose

Lactose, the sugar present in milk, is another disaccharide, in this case a glucose molecule joined to a galactose molecule.

catalyst

Life would not be possible without enzymes, most of which are proteins. Enzymatic proteins regulate metabolism by acting as catalysts, chemical agents that selectively speed up chemical reactions without being consumed in the reaction.Because an enzyme can perform its function over and over again, these molecules can be thought of as workhorses that keep cells running by carrying out the processes of life

globular proteins

Many proteins are roughly spherical

_________________________ are major nutrients for cells.

Monosaccharides, particularly glucose, are major nutrients for cells.

cis double bond

Nearly every double bond in naturally occurring fatty acids is a cis double bond, which creates a kink in the hydrocarbon chain wherever it occurs. . (See Figure 4.7b to remind yourself about cis and trans double bonds.)

Why don't petroleum or fat dissolve in water?

Neither petroleum nor fat dissolves in water; both are hydrophobic compounds because the great majority of their bonds are relatively nonpolar carbon-to-hydrogen linkages

What is an additional role of simple sugar molecules for cellular work?

Not only are simple-sugar molecules a major fuel for cellular work, but their carbon skeletons also serve as raw material for the synthesis of other types of small organic molecules, such as amino acids and fatty acids.

Strong base & strong acid

Notice that single arrows were used in the reactions for HCl and NaOH. These compounds dissociate completely when mixed with water, so hydrochloric acid is called a strong acid and sodium hydroxide a strong base.

Complementary approaches to understanding protein structure & function.

Nuclear magnetic resonance (NMR) spectroscopy and bioinformatics are complementary approaches to understanding protein structure and function.

essential elements

Of the 92 natural elements, about 20-25% are essential elements that an organism needs to live a healthy life and reproduce. The essential elements are similar among organisms, but there is some variation—for example, humans need 25 elements, but plants need only 17.

joule

One joule equals 0.239 cal; one calorie equals 4.184 J.

Structural Polysaccharides

Organisms build strong materials from structural polysaccharides.

Denaturation agents

Other denaturation agents include chemicals that disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain a protein's shape

What are the four elements that make up approximately 96. 3% of the living matter?

Oxygen (65%), Carbon (18.5%), Nitrogen (3.3%), Hydrogen (9.5%)

Which is more electronegative, hydrogen or oxygen?

Oxygen is one of the most electronegative elements, attracting shared electrons much more strongly than hydrogen does.

What causes hydrogen bonding in water?

Polar covalent bonds in water

Ineffective Enantiomer

R ibuprofen

Effective Enantiomer -

R-Albuterol

How are radioactive isotopes used in medicine?

Radioactive isotopes are often used as diagnostic tools in medicine. Cells can use radioactive atoms just as they would use nonradioactive isotopes of the same element. The radioactive isotopes are incorporated into biologically active molecules, which are then used as tracers to track atoms during metabolism, the chemical processes of an organism.

Ibuprofen

Reduces inflammation and pain

Albuterol

Relaxes bronchial (airway) muscles, improving airflow in asthma patients

What happens to the released monomers, after hydrolysis (digestion)?

Released monomers are then absorbed into the bloodstream for distribution to all body cells. Those cells can then use dehydration reactions to assemble the monomers into new, different polymers that can perform specific functions required by the cell.

Ongoing research about serpentine plants:

Researchers are studying whether serpentine-adapted plants could be used to take up toxic heavy metals in contaminated areas, concentrating them for safer disposal.

Effective Enantiomer

S ibuprofen

Ineffective Enantiomer

S-Albuterol

Polar side chains; hydrophilic

Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) - Since cysteine is only weakly polar, it is sometimes classified as a nonpolar amino acid Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q)

Branching

Skeletons may be unbranched or branched. Butane & 2-Methylpropane (commonly called isobutane)

atom

Smallest particle of an element

What compound is table salt?

Sodium Chloride (NaCl)

basic solution

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

How do some bases reduce the H+ concentration?

Some bases reduce the H+ concentration directly by accepting hydrogen ions. Ammonia (NH3), for instance, acts as a base when the unshared electron pair in nitrogen's valence shell attracts a hydrogen ion from the solution, resulting in an ammonium ion NH4+. Other bases reduce the H+ concentration indirectly by dissociating to form hydroxide ions, which combine with hydrogen ions and form water. One such base is sodium hydroxide (NaOH), which in water dissociates into its ions:

Give some examples of how some evaporation occurs at any time.

Some evaporation occurs at any temperature; a glass of water at room temperature, for example, will eventually evaporate completely.

How can some microorganisms digest cellulose?

Some microorganisms can digest cellulose, breaking it down into glucose monomers.

Some uses of polysaccharides

Some polysaccharides serve as storage material, hydrolyzed as needed to provide sugar for cells. Other polysaccharides serve as building material for structures that protect the cell or the whole organism.

Can structural isomers may also differ in location of double bonds?

Structural isomers may also differ in the location of double bonds.

saturated and unsaturated

Such a structure is said to be saturated with hydrogen, and the resulting fatty acid is therefore called a saturated fatty acid. An unsaturated fatty acid has one or more double bonds, with one fewer hydrogen atom on each double-bonded carbon.

Dehydration reaction in the synthesis of sucrose.

Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose forms a five-sided ring, though it is a hexose like glucose

When an electron loses energy, it "falls back" to a shell closer to the nucleus, and the lost energy is usually released to the environment as heat. Give an example for this.

Sunlight excites electrons in the surface of a car to higher energy levels. When the electrons fall back to their original levels, the car's surface heats up. This thermal energy can be transferred to the air or to your hand if you touch the car.

Temperature

Temperature represents the average kinetic energy of the molecules in a body of matter, regardless of volume, whereas the thermal energy of a body of matter reflects the total kinetic energy, and thus depends on the matter's volume.

The 20 amino acids of proteins

The amino acids are grouped here according to the properties of their side chains (R groups) and shown in their prevailing ionic forms at pH 7.2, the pH within a cell. The three-letter and one-letter abbreviations for the amino acids are in parentheses. All of the amino acids used in proteins are L enantiomers

What determines the architecture and function of a polysaccharide?

The architecture and function of a polysaccharide are determined by its sugar monomers and by the positions of its glycosidic linkages.

Dehydration reaction in the synthesis of maltose

The bonding of two glucose units forms maltose. The 1-4 glycosidic linkage joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide

Structures of endorphin and morphine

The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule (right) is a close match.

What does the cumulative effect of weak interactions reinforce?

The cumulative effect of weak interactions is to reinforce the three-dimensional shape of the molecule.

What do differing effects of enantiomers demonstrate?

The differing effects of enantiomers in the body demonstrate that organisms are sensitive to even the subtlest variations in molecular architecture.

What does the differing in glycosidic linkages give?

The differing glycosidic linkages in starch and cellulose give the two molecules distinct three-dimensional shapes.

fatty acids

The fatty acids in a fat can all be the same, or they can be of two or three different kinds,. The terms saturated fats and unsaturated fats are commonly used in the context of nutrition. These terms refer to the structure of the hydrocarbon chains of the fatty acids

Which electron shell has the lowest energy level?

The first shell is closest to the nucleus and has the lowest energy level.

What does the formula of an ionic bond mean?

The formula for an ionic compound, such as NaCl, indicates only the ratio of elements in a crystal of the salt. "NaCl" by itself is not a molecule.

Tiburon Mariposa Lily

The insets show a close-up of serpentine rock and one of the plants, a Tiburon Mariposa lily (Calochortus tiburonensis). This specially-adapted species is found only on this one hill in Tiburon, a peninsula that juts into San Francisco Bay.

The major function of fats?

The major function of fats is energy storage. The hydrocarbon chains of fats are similar to gasoline molecules and just as rich in energy.

chemical reactions

The making and breaking of chemical bonds, leading to changes in the composition of matter

Why does the methane molecule have the shape of a completed tetrahedron?

The methane molecule (CH4) has the shape of a completed tetrahedron because all four hybrid orbitals of the carbon atom are shared with hydrogen atoms. The carbon nucleus is at the center, with its four covalent bonds radiating to hydrogen nuclei at the corners of the tetrahedron. Larger molecules containing multiple carbon atoms, including many of the molecules that make up living matter, have more complex overall shapes. However, the tetrahedral shape of a carbon atom bonded to four other atoms is often a repeating motif within such molecules.

X-ray crystallography

The method most commonly used to determine the 3-D structure of a protein is X-ray crystallography, which depends on the diffraction of an X-ray beam by the atoms of a crystallized molecule

Which is the most prevalent disaccharide?

The most prevalent disaccharide is sucrose, or table sugar. Its two monomers are glucose and fructose

Unless otherwise mentioned an atom is neutral in charge. What does this mean?

The number of Protons must be equal to the number of electrons

Other main type of secondary structure

The other main type of secondary structure is the β pleated sheet. As shown above, in this structure two or more segments of the polypeptide chain lying side by side (called β strands) are connected by hydrogen bonds between parts of the two parallel segments of polypeptide backbone.

What is the pH of a neutral aqueous solution at 25 degrees celsius?

The pH of a neutral aqueous solution at 25°C is 7, the midpoint of the pH scale. A pH value less than 7 denotes an acidic solution; the lower the number, the more acidic the solution. The pH for basic solutions is above 7.

pH of blood

The pH of human blood is very close to 7.4, which is slightly basic. A person cannot survive for more than a few minutes if the blood pH drops to 7 or rises to 7.8 and a chemical system exists in the blood that maintains a stable pH

What determines the shape of molecules?

The positions of the atom's orbitals

What is the advantage of measuring in moles?

The practical advantage of measuring a quantity of chemicals in moles is that a mole of one substance has exactly the same number of molecules as a mole of any other substance. If the molecular mass of substance A is 342 daltons and that of substance B is 10 daltons, then 342 g of A will have the same number of molecules as 10 g of B. Measuring in moles makes it convenient for scientists working in the laboratory to combine substances in fixed ratios of molecules.

Why does the addition of acid have so much less of an effect on the pH of blood than it does on the pH of water?

The presence of substances called buffers allows biological fluids to maintain a relatively constant pH despite the addition of acids or bases

What does the process of hydrogenating vegetable oils produce?

The process of hydrogenating vegetable oils produces not only saturated fats but also unsaturated fats with trans double bonds.

dehydration reaction

The reaction connecting monomers is a good example of a dehydration reaction, a reaction in which two molecules are covalently bonded to each other with the loss of a water molecule When a bond forms between two monomers, each monomer contributes part of the water molecule that is released during the reaction: One monomer provides a hydroxyl group ( ¬OH), while the other provides a hydrogen ( ¬H). This reaction is repeated as monomers are added to the chain one by one, making a polymer (also called polymerization).

Why do you burn your fingers by touching the side of an iron pot on the stove when water is still lukewarm?

The reason you can burn your fingers by touching the side of an iron pot on the stove when the water in the pot is still lukewarm is that the specific heat of water is ten times greater than that of iron. In other words, the same amount of heat will raise the temperature of 1 g of the iron much faster than it will raise the temperature of 1 g of the water. Specific heat can be thought of as a measure of how well a substance resists changing its temperature when it absorbs or releases heat.

specific heat

The specific heat of a substance is defined as the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1°C

Specific heat of water

The specific heat of a substance is defined as the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1°C.

hydration shell

The sphere of water molecules around each dissolved ion

Carbohydrate bank

The sugar can later be withdrawn by the plant from this carbohydrate "bank" by hydrolysis, which breaks the bonds between the glucose monomers.

What happens in lactose intolerance?

The sugar is instead broken down by intestinal bacteria, causing formation of gas and subsequent cramping. The problem may be avoided by taking the enzyme lactase when eating or drinking dairy products or consuming dairy products that have already been treated with lactase to break down the lactose

heat

Thermal energy in transfer from one body of matter to another is defined as heat.

Microfibils

These cable-like microfibrils are a strong building material for plants and an important substance for humans because cellulose is the major constituent of paper and the only component of cotton.

What is the basis for such diversity in life's polymers?

These molecules are constructed from only 40 to 50 common monomers and some others that occur rarely. Building a huge variety of polymers from such a limited number of monomers is analogous to constructing hundreds of thousands of words from only 26 letters of the alphabet. The key is arrangement—the particular linear sequence that the units follow. However, this analogy falls far short of describing the great diversity of macromolecules because most biological polymers have many more monomers than the number of letters in even the longest word

What are the rings formed for glucose

These two ring forms for glucose are called alpha (α) and beta (β), respectively

Serpentine plant community

They grow on serpentine soil, which contains toxic elements for plants.

Stanley miller & Harold Urey - The University of Chicago

They helped bring the abiotic (nonliving) synthesis of organic compounds into the context of evolution.

What happens to the orbitals on the valence shell during covalent bonding?

They undergo rearrangement

The white of an egg becomes opaque during cooking because the denatured proteins are insoluble and solidify.

This also explains why excessively high fevers can be fatal: Proteins in the blood tend to denature at very high body temperatures.

What does the asymmetry of the arrangement of water molecules at the interface between water and air cause?

This asymmetry gives water an unusually high surface tension, making it behave as though it were coated with an invisible film. You can observe the surface tension of water by slightly overfilling a drinking glass; the water will stand above the rim.

What does this constant relationship express of the behaviour of acids and bases in an aqueous solution?

This constant relationship expresses the behavior of acids and bases in an aqueous solution. An acid not only adds hydrogen ions to a solution, but also removes hydroxide ions because of the tendency for H+ to combine with OH- , forming water. A base has the opposite effect, increasing OH- concentration but also reducing H+ concentration by the formation of water.

Geckskin

This discovery has inspired development of an artificial adhesive called Geckskin: A patch the size of an index card can hold a 700-pound weight to a wall!

dynamic equilibrium

This is a dynamic equilibrium; reactions are still going on in both directions, but with no net effect on the concentrations of reactants and products. Equilibrium does not mean that the reactants and products are equal in concentration, but only that their concentrations have stabilized at a particular ratio.

What does the source of H+ result?

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

heat of vaporization of water

To evaporate 1 g of water at 25°C, about 580 cal of heat is needed—nearly double the amount needed to vaporize a gram of alcohol or ammonia.

Quaternary Structure - Association of two or more polypeptides (some proteins only)

Transthyretin protein (four identical polypeptides). Single polypeptide subunit. Some proteins consist of two or more polypeptide chains aggregated into one functional macromolecule. Quaternary structure is the overall protein structure that results from the aggregation of these polypeptide subunits.

What makes DNA molecule unique?

Unique among molecules, DNA provides directions for its own replication. DNA also directs RNA synthesis and, through RNA, controls protein synthesis; this entire process is called gene expression. DNA is the genetic material that organisms inherit from their parents

How can changes in potential energy of electrons occur?

Unlike the continuous flow of water downhill, changes in the potential energy of electrons can occur only in steps of fixed amounts

What can scientists do using the x- ray crystallography technique?

Using this technique, scientists can build a 3-D model that shows the exact position of every atom in a protein molecule.

Why is only one isomer biologically active?

Usually, only one isomer is biologically active because only that form can bind to specific molecules in an organism.

Valences of the major elements of organic molecules.

Valence, the number of covalent bonds an atom can form, is generally equal to the number of electrons required to complete the valence shell. All electrons are shown in the electron distribution diagrams (top), but only valence shell electrons are shown in the Lewis dot structures (bottom). Note that carbon can form four bonds. Hydrogen - 1, Oxygen - 2, Nitrogen - 3, Carbon - 4.

Effects of climate change on the Arctic.

Warmer temperatures in the Arctic cause more sea ice to melt in the summer, benefiting some organisms and harming others.

What happens when two atoms approach each other?

When two atoms approach each other during a chemical reaction, their nuclei do not come close enough to interact.

What can we think an electron orbital as?

You can think of an orbital as a component of an electron shell.

For a neutral aqueous solution

[H+] is 10-7 = -(-7) = 7

Friedrich Wohler

a German chemist, tried to make an "inorganic" salt, ammonium cyanate, by mixing solutions of ammonium ions (NH4 + ) and cyanate ions (CNO- ). Wöhler was astonished to find that instead he had made urea, an organic compound present in the urine of animals.

nonpolar covalent bond

a covalent bond in which the electrons are shared equally by the two atoms

What do the double arrows represent?

a reversible reaction that reaches a state of dynamic equilibrium when water molecules dissociate at the same rate that they are being reformed from H+ and OH- .

hydrogen ion (H+)

a single proton with a charge of 1+.

Amylopectin

a soluble polysaccharide and somewhat-branched polymer of glucose found in plants as one of the two components of starch (the other being amylose).

aqueous solution

a solution in which water is the solvent

Each pH unit represents

a tenfold change in the concentration of H+ and OH- in concentrations

Linear and ring forms of glucose

a) linear and ring forms of glucose- Chemical equilibrium between the linear and ring structures greatly favours the formation of rings. The carbons of the sugar are numbered 1 to 6, as shown. To form the glucose ring, carbon 1 (magenta) bonds to the oxygen (blue) attached to carbon 5. b) Each un labeled corner represents a carbon. The ring's thicker edge indicates that you are looking at the ring edge-on; the components attached to the ring lie above or below the plane of the ring.

Starch and cellulose structures.

a) α and β glucose ring structure-These two interconvertible forms of glucose differ in the placement of the hydroxyl group (highlighted in blue) attached to the number 1 carbon. α Glucose

What does the pH scale imply to and what is it based on?

although the pH scale is based on H+ concentration, it also implies OH- concentration. A solution of pH 10 has a hydrogen ion concentration of 10-10 M and a hydroxide ion concentration of 10-4 M.

Why is ammonia a weak base?

ammonia is a weak base. The double arrows in the reaction for ammonia indicate that the binding and release of hydrogen ions are reversible reactions, although at equilibrium there will be a fixed ratio of NH4 + to NH3.

chloride ion (Cl-)

anion

Lipids

are a diverse group of hydrophobic molecules. Lipids are the one class of large biological molecules that does not include true polymers, and they are generally not big enough to be considered macromolecules. The compounds called lipids are grouped with each other because they share one important trait: They mix poorly, if at all, with water.

a) One of three dehydration reactions in the synthesis of a fat

b) Fat molecule. triacylglycerol

Valence

bonding capacity of an atom. It is equal to the number of electrons required to complete the valence shell.

How can carbon atoms form diverse molecules ?

by bonding to four other atoms

How is a cellulose molecule?

cellulose molecule is straight. Cellulose is never branched, and some hydroxyl groups on its glucose monomers are free to hydrogen-bond with the hydroxyls of other cellulose molecules lying parallel to it.

inert

chemically inactive due completed valence shells. Helium, neon and argon

By the 1800s....

chemists had learned to make simple compounds in the laboratory by combining elements under the right conditions.

ionic compounds (salts)

compounds formed by ionic bonds

The strongest bonds are ..

covalent bonds & ionic bonds in dry ionic compounds

Lewis Dot Structure

diagram of a molecule using dots to represent valence electrons (H : H)

Structural isomers

differ in the covalent arrangements of their atoms.

Which subatomic particle is directly involved in chemical reaction?

electron

Trace elements

elements required by an organism in only minute quantities

anax imperator

emperor dragonfly. arthropods, shedding its old exoskeleton and emerging upside down in adult form.

The two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA):

enable living organisms to reproduce their complex components from one generation to the next.

Tranthyretin

four identical polypeptide chains, each composed of 127 amino acids. Shown here is one of these chains unraveled for a closer look at its primary structure. Each of the 127 positions along the chain is occupied by one of the 20 amino acids, indicated here by its three letter abbreviation.

Carbohydrates serve as

fuel and building material

The simplest organic compound is

hydrocarbon; It is the underlying framework for more complex organic molecules.

Valence of various elements:

hydrogen - 1 Oxygen - 2 Nitrogen - 3 Carbon - 4 Depending on the combination of single & double bonds made, phosphorous can have 3 or 5.

Which is the simplest atom?

hydrogen: No neutrons, 1 proton & 1 electron

How do plants generally transport carbohydrates leaves to roots and other nonphotosynthetic organs of the plant?

in the form of sucrose.

pH decreases as hydrogen ion concentration __________

increases

Why is CO2 considered inorganic?

is a very simple molecule and lacks hydrogen, it is often considered inorganic, even though it contains carbon. Whether we call CO2 organic or inorganic, however, it is clearly important to the living world as the source of carbon, via photosynthetic organisms, for all organic molecules in organisms

serpentine

jad like mineral that contains elevated concentrations of elements such as chromium, nickel, and cobalt.

Give an example of when an electron loses energy

light energy can excite an electron to a higher energy level. (Indeed, this is the first step taken when plants harness the energy of sunlight for photosynthesis, the process that produces food from carbon dioxide and water.

Steroids

lipids characterized by a carbon skeleton consisting of four fused rings. Different steroids are distinguished by the particular chemical groups attached to this ensemble of rings. Cholesterol, a type of steroid, is a crucial molecule in animals

What do chemical reactions do?

make and break chemical bonds

Why would brain cells carry receptors for opiates, compounds that are not made by the body?

ndorphins are signaling molecules made by the pituitary gland that bind to the receptors, relieving pain and producing euphoria during times of stress, such as intense exercise. Opiates have shapes similar to endorphins and mimic them by binding to endorphin receptors in the brain. That is why opiates and endorphins have similar effects

Macromolecules

polymers built from monomers

Protons give the nucleus.....

positive charge

PET

positron emission tomography

Four Levels of Protein Structure

primary, secondary, tertiary, quaternary - . A fourth level, quaternary structure, arises when a protein consists of two or more polypeptide chains.

What does the molecular hardware of the cell—the tools that carry out biological functions consist mostly of?

proteins

which are the electronically charged particles of an atom?

proton & electron.

subatomic particles

protons, neutrons, electrons

radioactive decay

scientists measure the ratio of different isotopes and calculate how many half-lives (in years) have passed since an organism was fossilized or a rock was formed

fibrous proteins

shaped like long fibers

electron distribution diagram

shows how each atom completes outer shell by sharing electrons

Monosaccharides

simple sugars; generally have molecular formulas that are some multiple of the unit CH2O. Glucose (C6H12O6), the most common monosaccharide, is of central importance in the chemistry of life

Synthesizing starch enables the plant to _______

stockpile surplus glucose

Carbohydrates include

sugars and polymers of sugars

Does hydrogen ion (H+) exist alone in aqeous solution?

t H+ does not exist on its own in an aqueous solution. It is always associated with a water molecule in the form of H3O+ .

trans isomer

the Xs on opposite sides is called a trans isomer. The two Xs are on opposite sides. Cis-trans isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon

Energy

the ability to do work

What are the amino acids grouped according to?

the amino acids are grouped according to the properties of their side chains. One group consists of amino acids with nonpolar side chains, which are hydrophobic. Another group consists of amino acids with polar side chains, which are hydrophilic.

What keeps the electrons in the vicinity of the nucleus?

the attraction between opposite charges that keeps the electrons in the vicinity of the nucleus.

If a liquid is heated......

the average kinetic energy of molecules increases and the liquid evaporates more rapidly.

The subtle difference in shape between such isomers can have a dramatic effect on the biological activities of organic molecules. Give example

the biochemistry of vision involves a light-induced change of retinal, a chemical compound in the eye, from the cis isomer to the trans isomer

chitin

the carbohydrate used by arthropods to build their exoskeletons. Chitin is similar to cellulose, with β linkages, except that the glucose monomer of chitin has a nitrogen-containing attachment

What is the trace element in vertebrates that if not consumed could cause goiter?

the element iodine (I) is an essential ingredient of a hormone produced by the thyroid gland. A daily intake of only 0.15 milligram (mg) of iodine is adequate for normal activity of the human thyroid. An iodine deficiency in the diet causes the thyroid gland to grow to abnormal size, a condition called goiter. Consuming seafood or iodized salt reduces the incidence of goiter

Mass of electron

the mass of an electron is only about 1/2,000 that of a neutron or proton, we can ignore electrons when computing the total mass of an atom.

The greater the electronegativity is...

the more strongly it pulls shared electrons toward itself.

Valence

the number of covalent bonds an atom can form

Urea CO(NH2)2

the organic compound found in urine that Wöhler synthesized in the early 1800. Urea and carbon dioxide are molecules with only one carbon atom.

What are also considered genes?

the stretches of DNA that direct synthesis of these RNAs are also considered genes

What do an element's properties depend on?

the structure of its atoms

Organic chemistry

the study of carbon compounds

Another characteristic of hydrocarbons

they can undergo reactions that release a relatively large amount of energy.

The hormone which requires iodine for proper functioning of the human thyroid is produced by which gland?

thyroid gland

Amylose

unbranched starch

outermost electrons

valence electrons

outermost electron shell

valence shell

Hydrophilic

water loving

One such secondary structure is the

α helix, a delicate coil held together by hydrogen bonding between every fourth amino acid, as shown above. Although each transthyretin polypeptide has only one α helix region other globular proteins have multiple stretches of α helix separated by non helical regions (see haemoglobin in the Quaternary Structure section). Some fibrous proteins, such as α-keratin, the structural protein of hair, have the α helix formation over most of their length.

Figure 5.18

▶ Spiders secrete silk fibers made of a structural protein containing β pleated sheets, which allow the spider web to stretch and recoil

solvent

A liquid substance capable of dissolving other substances

Polysaccharides of plants and animals.

(a) Starch stored in plant cells, (b) glycogen stored in muscle cells, and (c) structural cellulose fibers in plant cell walls are all polysaccharides composed entirely of glucose monomers (green hexagons). In starch and glycogen, the polymer chains tend to form helices in unbranched regions because of the angle of the linkages between glucose molecules. There are two kinds of starch: amylose and amylopectin. Cellulose, with a different kind of glucose linkage, is always unbranched.

Hydrogen bonds between water molecules.

* Because of its electron arrangement, oxygen has two regions with partial negative charge *The charged regions in a water molecule are due to its polar covalent bonds. *Regions of neighbouring water molecules with opposite partial charges are attracted to each other, forming hydrogen bonds. *Each water molecule can hydrogen-bond to several others; these associations are constantly changing.

Ice: crystalline structure and floating barrier.

* In ice, each molecule is hydrogen-bonded to four neighbors in a three-dimensional crystal. * Because the crystal is spacious, ice has fewer molecules than an equal volume of liquid water. In other words, ice is less dense than liquid water. *Floating ice becomes a barrier that insulates the liquid water below from the colder air *The marine organism shown here is a type of shrimp called krill; it was photographed beneath floating ice in the Southern Ocean near Antarctica.

Carbonyl group (C=O)

* Sugars with ketone groups are called ketoses; those with aldehydes are called aldoses. * Compound name: Ketone (carbonyl group is within a carbon skeleton) or aldehyde (carbonyl group is at the end of a carbon skeleton) *Acetone, the simplest ketone *Propanal, an aldehyde

Where does the reactivity of an atom arises from? What do the formation and function of molecules depend on?

* The reactivity of an atom arises from the presence of unpaired electrons in one or more orbitals of the atom's valence shell * chemical bonding between atoms

Estradiol vs. Testosterone

* These compounds are female and male sex hormones, respectively, in humans and other vertebrates. * Both are steroids, organic molecules with a common carbon skeleton in the form of four fused rings. * They differ only in the chemical groups attached to the rings *The different actions of these two molecules on many targets throughout the body are the basis of gender, producing the contrasting features of male and female vertebrates.

Carboxyl group

*Acts as an acid (can donate H+) because the covalent bond between oxygen and hydrogen is so polar. *Compound name: Carboxylic acid, or organic acid *Acetic acid, which gives vinegar its sour taste *Ionized form of COOH (carboxylate ion), found in cells

Variation in the architecture of organic molecules can be seen in isomers. What are isomers?

, compounds that have the same numbers of atoms of the same elements but different structures and hence different properties.

What happens if the H+ concentration in blood increases? That is when pH starts to decrease.

, the reaction proceeds to the left, with HCO3 - (the base) removing the hydrogen ions from the solution and forming H2CO3.

What happens in atoms with valence electrons in both p and s orbitals?

. For atoms with valence electrons in both s and p orbitals the single s and three p orbitals form four new hybrid orbitals shaped like identical teardrops extending from the region of the atomic nucleus, as shown in. If we connect the larger ends of the teardrops with lines, we have the outline of a geometric shape called a tetrahedron, a pyramid with a triangular base.

Perhaps the most significant impact of genomics and proteomics on the field of biology as a whole has been their contributions to our understanding of evolution

. In addition to confirming evidence for evolution from the study of fossils and characteristics of currently existing species, genomics has helped us tease out relationships among different groups of organisms that had not been resolved by previous types of evidence, and thus infer evolutionary history

How do we represent the mass of molecules?

. Once we determine the molecular mass of a molecule such as sucrose, we can use the same number (342), but with the unit gram, to represent the mass of 6.02 * 1023 molecules of sucrose, C12H22O11, by multiplying the number of atoms by the atomic mass of each element.

making a polypeptide chain

. Peptide bonds are formed by dehydration reactions, which link the carboxyl group of one amino acid to the amino group of the next. The peptide bonds are formed one at a time, starting with the amino acid at the amino end (N-terminus). The polypeptide has a repetitive backbone (purple) to which the amino acid side chains (yellow and green) are attached.

Proteins are built from

. Proteins, for example, are built from 20 kinds of amino acids arranged in chains that are typically hundreds of amino acids long. The molecular logic of life is simple but elegant: Small molecules common to all organisms act as building blocks that are ordered into unique macromolecules

Note that in RNA, adenine (A) pairs with uracil (U); thymine (T) is not present in RNA. Another difference between RNA and DNA is that DNA almost always exists as a double helix, whereas RNA molecules are more variable in shape

. RNAs are versatile molecules, and many biologists believe RNA may have preceded DNA as the carrier of genetic information in early forms of life

An example of a trace element is

. Some trace elements, such as iron (Fe), are needed by all forms of life; others are required only by certain species

nucleoside

. The beginning monomer used to build a polynucleotide has three phosphate groups, but two are lost during the polymerization process. The portion of a nucleotide without any phosphate groups is called a nucleoside.

Hydrogen bonds

. This attraction between a hydrogen and an electronegative atom is called a hydrogen bond. In living cells, the electronegative partners are usually oxygen or nitrogen atoms.

An unplanned but profound side benefit of this project— the Human Genome Project—was the rapid development of faster and less expensive methods of sequencing

. This trend has continued: The cost for sequencing 1 million bases in 2001, well over $5,000, has decreased to less than $0.02 in 2016. And a human genome, the first of which took over 10 years to sequence, could be completed at today's pace in just. a few days.

Ethene (ethylene) (C2H4)

. When two carbon atoms are joined by a double bond, all atoms attached to those carbons are in the same plane, and the molecule is flat.

polymer

A long molecule consisting of many similar or identical monomers linked together.

Disaccharide

A double sugar, consisting of two monosaccharides joined by a glycosidic linkage, a covalent bond formed between two monosaccharides by a dehydration reaction

Saturated fatty acids

A fat made from saturated fatty acids is called a saturated fat. Most animal fats are saturated: The hydrocarbon chains of their fatty acids—the "tails" of the fat molecules—lack double bonds, and their flexibility allows the fat molecules to pack together tightly. Saturated animal fats—such as lard and butter—are solid at room temperature

What is a functional protein?

A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape, which can be shown in several different types of models. And it is the amino acid sequence of each polypeptide that determines what three-dimensional structure the protein will have under normal cellular conditions.

What does a gram of fat store?

A gram of fat stores more than twice as much energy as a gram of a polysaccharide, such as starch. Because plants are relatively immobile, they can function with bulky energy storage in the form of starch.

The structure of some proteins is difficult to determine for a simple reason:

A growing body of biochemical research has revealed that a significant number of proteins, or regions of proteins, do not have a distinct 3-D structure until they interact with a target protein or other molecule.

solution

A homogeneous mixture of two or more substances

Proteins (general)

A human has tens of thousands of different proteins, each with a specific structure and function; proteins, in fact, are the most structurally sophisticated molecules known. Consistent with their diverse functions, they vary extensively in structure, each type of protein having a unique three dimensional shape.

kilocalorie

A kilocalorie (kcal), 1,000 cal, is the quantity of heat required to raise the temperature of 1 kilogram (kg) of water by 1°C. (The "Calories" on food packages are actually kilocalories.)

What is the relevance of water's high specific heat to life on Earth?

A large body of water can absorb and store a huge amount of heat from the sun in the daytime and during summer while warming up only a few degrees. At night and during winter, the gradually cooling water can warm the air. This capability of water serves to moderate air temperatures in coastal areas

Ethane(C2H6) - simple organic molecule

A molecule may have more than one tetrahedral group of single-bonded atoms. (Ethane consists of two such groups.)

Components of nucleic acids.

A polynucleotide has a sugar-phosphate backbone with variable appendages, the nitrogenous bases. (b) In a polynucleotide, each nucleotide monomer includes a nitrogenous base, a sugar, and a phosphate group. Note that carbon numbers in the sugar include primes (′). (c) A nucleoside includes a nitrogenous base (purine or pyrimidine) and a five-carbon sugar (deoxyribose or ribose).

What does a protein's specific structure determine?

A protein's specific structure determines how it works. In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecule. In an especially striking example of the marriage of form and function Figure 5.17 shows the exact match of shape between an antibody (a protein in the body) and the particular foreign substance on a flu virus that the antibody binds to and marks for destruction.

Complementarity of shape between two protein surfaces

A technique called X-ray crystallography was used to generate a computer model of an antibody protein (blue and orange, left) bound to a flu virus protein (yellow and green, right). This is a wireframe model modified by adding an "electron density map" in the region where the two proteins meet. Computer software was then used to back the images away from each other slightly

The reverberations of these developments have transformed the study of biology and related fields. Biologists often look at problems by analyzing large sets of genes or even comparing whole genomes of different species, an approach called genomics.

A similar analysis of large sets of proteins, including their sequences, is called proteomics. (Protein sequences can be determined either by using biochemical techniques or by translating the DNA sequences that code for them.)These approaches permeate all fields of biology, some examples of which are shown in

An example of ionic bonding

A sodium atom has a total of 11 electrons, with its single valence electron in the third electron shell. A chlorine atom has a total of 17 electrons, with 7 electrons in its valence shell. When these two atoms meet, the lone valence electron of sodium is transferred to the chlorine atom, and both atoms end up with their valence shells complete.

neutral solution

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

Consider, for example, the type of RNA called transfer RNA (tRNA), which brings amino acids to the ribosome during the synthesis of a polypeptide.

A tRNA molecule is about 80 nucleotides in length. Its functional shape results from base pairing between nucleotides where complementary stretches of the molecule can run antiparallel to each other

Adhesion

An attraction between molecules of different substances. Adhesion of water by hydrogen bonds to the molecules of cell walls helps counter the downward pull of gravity

What is the electron's energy level correlated with.

An electron's energy level is correlated with its average distance from the nucleus.

Given our evolutionary view of life, we can extend this concept of "molecular genealogy" to relationships between species: We would expect two species that appear to be closely related based on anatomical evidence (and possibly fossil evidence) to also share a greater proportion of their DNA and protein sequences than do less closely related species. In fact, that is the case

An example is the comparison of the β polypeptide chain of human hemoglobin with the corresponding hemoglobin polypeptide in other vertebrates. In this chain of 146 amino acids, humans and gorillas differ in just 1 amino acid, while humans and frogs, more distantly related, differ in 67 amino acids.

example of hydrolysis

An example of hydrolysis within our bodies is the process of digestion. The bulk of the organic material in our food is in the form of polymers that are much too large to enter our cells. Within the digestive tract, various enzymes attack the polymers, speeding up hydrolysis

exoskeleton

An exoskeleton is a hard case that surrounds the soft parts of an animal. Made up of chitin embedded in a layer of proteins, the case is leathery and flexible at first, but becomes hardened when the proteins are chemically linked to each other (as in insects) or encrusted with calcium carbonate (as in crabs)

Why does an ice cube cool a drink?

An ice cube cools a drink not by adding coldness to the liquid, but by absorbing thermal energy from the liquid as the ice itself melts

Primary Structure - linear chain of amino acids: The primary structure of a protein is its sequence of amino acids.

As an example, let's consider transthyretin, a globular blood protein that transports vitamin A and one of the thyroid hormones throughout the body

Give an example of a natural element that that occurs as a mixture of its isotopes

As an example, the element carbon, which has the atomic number 6, has three naturally occurring isotopes. The most common isotope is carbon-12, 12 6C, which accounts for about 99% of the carbon in nature. The isotope 12 6C has 6 neutrons. Most of the remaining 1% of carbon consists of atoms of the isotope 13 6C, with 7 neutrons. A third, even rarer isotope, 14 6C, has 8 neutrons. Notice that all three isotopes of carbon have 6 protons; otherwise, they would not be carbon.

Product of H+ and OH- in neutral solutions

As previously mentioned, in a neutral solution at 25°C, [H+ ] = 10-7 and [OH- ] = 10-7, Therefore, the product of [H+ ] and [OH- ] in a neutral solution at 25°C is 10-14

What happens as seawater acidifies?

As seawater acidifies, the extra hydrogen ions combine with carbonate ions (CO3 2- ) to form bicarbonate ions (HCO3 - ), thereby reducing the carbonate ion concentration

(b) Unsaturated fat

At room temperature, the molecules of an unsaturated fat such as olive oil cannot pack together closely enough to solidify because of the kinks in some of their fatty acid hydrocarbon chains. Structural formula of an unsaturated fat molecule. Space-filling model of oleic acid, an unsaturated fatty acid

What is the ordered arrangement of water molecules at the interface between water and air?

At the interface between water and air is an ordered arrangement of water molecules, hydrogen-bonded to one another and to the water below, but not to the air above

How are phospholipids arranged in the cell surface?

At the surface of a cell, phospholipids are arranged in a similar bilayer. The hydrophilic heads of the molecules are on the outside of the bilayer, in contact with the aqueous solutions inside and outside of the cell.

What will happen if a spoon of ionic compound sodium chloride/ table salt is placed in water?

At the surface of each crystal of salt, the sodium and chloride ions are exposed to the solvent. .These ions and regions of the water molecules are attracted to each other due to their opposite charges. The oxygens of the water molecules have regions of partial negative charge that are attracted to sodium cations. The hydrogen regions are partially positively charged and are attracted to chloride anions. As a result, water molecules surround the individual sodium and chloride ions, separating and shielding them from one another.

Where do hydrogen atoms attach to the carbon skeleton?

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

5.28

Automatic DNA sequencing machines and abundant computing power enable rapid sequencing of genes and genomes.

How does carbon account for the great diversity of species?

Because of carbon's ability to form four bonds, however, this limited assortment of atomic building blocks can be used to build an inexhaustible variety of organic molecules. Different species of organisms, and different individuals within a species, are distinguished by variations in the types of organic molecules they make. In a sense, the great diversity of living organisms we see on the planet (and in fossil remains) is made possible by the unique chemical versatility of the element carbon.

Water transport in plants

Because of the properties of cohesion and adhesion, the tallest trees can transport water more than 100 m upward—approximately one-quarter the height of the Empire State Building in New York City

Why do electrons have potential energy?

Because of their distance from the nucleus. The negatively charged electrons are attracted to the positively charged nucleus. It takes work to move a given electron farther away from the nucleus, so the more distant an electron is from the nucleus, the greater its potential energy

Why have scientists developed the PH?

Because the H+ and OH- concentrations of solutions can vary by a factor of 100 trillion or more, scientists have developed a way to express this variation more conveniently than in moles per liter. The pH scale compresses the range of H+ and OH- concentrations by employing logarithms.

Why do molecules of a liquid stay close together?

Because they are attracted to each other. Molecules moving fast enough to overcome these attractions can depart the liquid and enter the air as a gas. This transformation from a liquid to a gas is called vaporization, or evaporation. Even at low temperatures, the speediest molecules can escape into the air.

What does ice provide?

Besides insulating the water below, ice also provides a solid habitat for some animals, such as polar bears and seals.

pH scale

Biologists use something called the pH scale to describe how acidic or basic (the opposite of acidic) a solution is.

What are stable isotopes?

Both 12C and 13C are stable isotopes, meaning that their nuclei do not have a tendency to lose subatomic particles, a process called decay.

What is a radioactive isotope?

Both 12C and 13C are stable isotopes, meaning that their nuclei do not have a tendency to lose subatomic particles, a process called decay. The isotope 14C, however, is unstable, or radioactive. A radioactive isotope is one in which the nucleus decays spontaneously, giving off particles and energy. When the radioactive decay leads to a change in the number of protons, it transforms the atom to an atom of a different element

storage polysaccharides

Both plants and animals store sugars for later use in the form of storage polysaccharides.

hemoglobin

Both α and β subunits consist primarily of α-helical secondary structure. Each subunit has a nonpolypeptide component, called heme, with an iron atom that binds oxygen.

RNA molecules, by contrast, exist as single strands.

Complementary base pairing can occur, however, between regions of two RNA molecules or even between two stretches of nucleotides in the same RNA molecule. . In fact, base pairing within an RNA molecule allows it to take on the particular three-dimensional shape necessary for its function.

Structure of DNA

DNA molecules have two polynucleotides, or "strands," that wind around an imaginary axis, forming a double helix. The two sugar-phosphate backbones run in opposite 5′ S 3′ directions from each other; this arrangement is referred to as antiparallel, somewhat like a divided highway.The sugar-phosphate backbones are on the outside of the helix, and the nitrogenous bases are paired in the interior of the helix. The two strands are held together by hydrogen bonds between the paired bases. Most DNA molecules are very long, with thousands or even millions of base pairs. The one long DNA double helix in a eukaryotic chromosome includes many genes, each one a particular segment of the molecule

What determines if a sugar is an aldose or a ketose?

Depending on the location of the carbonyl group, a sugar is either an aldose (aldehyde sugar) or a ketose (ketone sugar)

What happens when a deep body of water cools?

During summer, only the upper few inches of the ocean would thaw. Instead, when a deep body of water cools, the floating ice insulates the liquid water below, preventing it from freezing and allowing life to exist under the frozen surface

Salt crystal

Each salt crystal is an aggregate of vast numbers of cations and anions bonded by their electrical attraction and arranged in a three-dimensional lattice

Which state do electrons tend to exist?

Electrons, like all matter, tend to exist in the lowest available state of potential energy. In an atom, this state is in the first shell.

Enantiomers

Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers here are designated the L and D isomers from the Latin for "left" and "right" (levo and dextro). Enantiomers cannot be superimposed on each other. Enantiomers are, in a way, left-handed and right-handed versions of the molecule.

Sickle-Cell Disease: A Change in Primary Structure:

Even a slight change in primary structure can affect a protein's shape and ability to function. For instance sickle cell disease, inherited blood disorder is caused by the substitution of one amino acid (valine) for the normal one (glutamic acid) at the position of the sixth amino acid in the primary structure of hemoglobin, the protein that carries oxygen in red blood cells. Normal red blood cells are disk-shaped, but in sickle-cell disease, the abnormal hemoglobin molecules tend to aggregate into chains, deforming some of the cells into a sickle shape

hydrogen bonds are constantly breaking and reforming.

Even in liquid water, many of the molecules are connected by hydrogen bonds, though only transiently: The hydrogen bonds are constantly breaking and re-forming.

Even when scientists

Even when scientists have a correctly folded protein in hand, determining its exact three-dimensional structure is not simple, for a single protein has thousands of atoms

chemical equilibrium

Eventually, the forward and reverse reactions occur at the same rate, and the relative concentrations of products and reactants stop changing. The point at which the reactions offset one another exactly is called chemical equilibrium.

Case Study: Evolution of Tolerance to Toxic Elements

Ex: Serpentine plant community. Although most plants cannot survive in soil that forms from serpentine rock, a small number of plant species have adaptations that allow them to do so..

Can organic molecules form under conditions estimated to simulate those on the early Earth?

Experiment: In 1953, Stanley Miller set up a closed system to mimic conditions thought at that time to have existed on the early Earth. A flask of water simulated the primeval sea. The water was heated so that some vaporized and moved into a second, higher flask containing the "atmosphere"—a mixture of gases. Sparks were discharged in the synthetic atmosphere to mimic lightning.

Atoms with the same number of valence electrons exhibit similar chemical behavior. Give an example for this.

For example, fluorine (F) and chlorine (Cl) both have 7 valence electrons, and both form compounds when combined with the element sodium (Na): Sodium fluoride (NaF) is commonly added to toothpaste to prevent tooth decay, and, as described earlier, NaCl is table salt

All chemical reactions are theoretically reversible, with the products of the forward reaction becoming the reactants for the reverse reaction. Provide an example

For example, hydrogen and nitrogen molecules can combine to form ammonia, but ammonia can also decompose to regenerate hydrogen and nitrogen:

What happens when two hydrogen atoms approach each other?

For example, let's consider what happens when two hydrogen atoms approach each other. Recall that hydrogen has 1 valence electron in the first shell, but the shell's capacity is 2 electrons. When the two hydrogen atoms come close enough for their 1s orbitals to overlap, they can share their electrons (Figure 2.9). Each hydrogen atom is now associated with 2 electrons in what amounts to a completed valence shell. Two or more atoms held together by covalent bonds constitute a molecule, in this case a hydrogen molecule.

Example of disaccharide

For example, maltose is a disaccharide formed by the linking of two molecules of glucose (Figure 5.5a). Also known as malt sugar, maltose is an ingredient used in brewing beer

Give one example when a substance can be hydrophilic and not dissolve in water. Explain.

For example, some molecules in cells are so large that they do not dissolve. Another example of a hydrophilic substance that does not dissolve is cotton, a plant product.

Not all salts have equal numbers of cations and anions. Give an example proving this.

For example, the ionic compound magnesium chloride (MgCl2) has two chloride ions for each magnesium ion. Magnesium (12Mg) must lose 2 outer electrons if the atom is to have a complete valence shell, so it has a tendency to become a cation with a net charge of 2+ (Mg2+ ). One magnesium cation can therefore form ionic bonds with two chloride anions (Cl- )

Although hydrocarbons are not prevalent in most living organisms, many of a cell's organic molecules have regions consisting of only carbon and hydrogen. Give an example of a cell's organic molecules that have regions consisting of only carbon and hydrogen.

For example, the molecules known as fats have long hydrocarbon tails attached to a nonhydrocarbon component

Oxygen carrier in red blood cells

For example, the oxygen carrier in red blood cells is the protein hemoglobin that you saw earlier (see Figure 5.18), not the DNA that specifies its structure.

Cellulose

For example, the polysaccharide called cellulose is a major component of the tough walls that enclose plant cells.

The sequence of bases along a DNA (or mRNA) polymer is unique for each gene and provides very specific information to the cell. Because genes are hundreds to thousands of nucleotides long, the number of possible base sequences is effectively limitless. The information carried by the gene is encoded in its specific sequence of the four DNA bases.

For example, the sequence 5′-AGGTAACTT-3′ means one thing, whereas the sequence 5′-CGCTTTAAC-3′ has a different meaning. (Entire genes, of course, are much longer.)

Example of radioactive isotope

For example, when an atom of carbon-14 (14C) decays, it loses a proton, becoming an atom of nitrogen (14N).

Acid example

For example, when hydrochloric acid (HCl) is added to water, hydrogen ions dissociate from chloride ions:

Water molecule - hybrid orbitals

For water molecules (H2O), two of the hybrid orbitals in the oxygen's valence shell are shared with hydrogens

storage proteins

Function: Storage of amino acids Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

Structural proteins

Function: Support Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues.

transport proteins

Function: Transport of substances Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across membranes, as shown here.

Nonpolar side chains; hydrophobic

Glycine (Gly or G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu or L), Isoleucine (Ile or I), Methionine (Met or M), Phenylalanine (Phe or F) , Tryptophan (Trp or W) , Proline(Pro or P)

glycogen

Glycogen granules stored in muscle tissue. Glycogen (extensively branched)

What does the configuration determine?

The kinds and the number of bonds an atom will form with other atoms

hydrochloric acid

HCl ---> H+ + Cl-

Why does the equilibrium favor the reaction when carbonic acid is added to pure water?

Here the equilibrium so favors the reaction in the left direction that when carbonic acid is added to pure water, only 1% of the molecules are dissociated at any particular time. Still, that is enough to shift the balance of H+ and OH- from neutrality.

Why does high humidity on a hot day increase discomfort?

High humidity on a hot day increases discomfort because the high concentration of water vapor in the air inhibits the evaporation of sweat from the body

continuation

However, biochemists have developed methods for tracking a protein through such stages and learning more about this important process.

Protein structure also depends on

However, protein structure also depends on the physical and chemical conditions of the protein's environment. If the pH, salt concentration, temperature, or other aspects of its environment are altered, the weak chemical bonds and interactions within a protein may be destroyed, causing the protein to unravel and lose its native shape, a change called denaturation.

Human lysozyme

Human lysozyme is a protein found in tears and saliva that has antibacterial action (see Figure 5.16). This model shows the lysozyme molecule (purple) in an aqueous environment. Ionic and polar regions on the protein's surface attract the partially charged regions on water molecules.

What does petroleum contain of and why is it a fossil fuel?

Hydrocarbons are the major components of petroleum, which is called a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago.

What are the common ingredients for these compounds?

Hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P) are other common ingredients of these compounds, but it is the element carbon (C) that accounts for the enormous variety of biological molecules.

tertiary structure

Hydrophobic interactions and van der Waals interactions - Ionic bond - Disulfide bridge - Hydrogen bond - Polypeptide backbone of small part of a protein

The pharmacological importance of enantiomers.

Ibuprofen and albuterol are drugs whose enantiomers have different effects. (S and R are used here to distinguish between enantiomers.) Ibuprofen is commonly sold as a mixture of the two enantiomers; the S enantiomer is 100 times more effective than the R form. Albuterol is synthesized and sold only as the R form of that particular drug; the S form counteracts the active R form.

Medical Science

Identifying the genetic basis for human diseases like cancer helps researchers focus their search for potential future treatments. Currently, sequencing the sets of genes expressed in an individual's tumor can allow a more targeted approach to treating the cancer, a type of "personalized medicine." (See Figures 12.20 and 18.27.)

Example of base pairing

If a stretch of one strand has the base sequence 5′-AGGTCCG-3′, then the base-pairing rules tell us that the same stretch of the other strand must have the sequence 3′-TCCAGGC-5′ The two strands of the double helix are complementary, each the predictable counterpart of the other. It is this feature of DNA that makes it possible to generate two identical copies of each DNA molecule in a cell that is preparing to divide

What happens if enough acid is added to a solution to increase to increase H+ to 10^-5?

If enough acid is added to a solution to increase [H+ ] to 10^-5 M, then [OH- ] will decline by an equivalent factor to 10^-9 M

What will happen if enough of a base is added to raise the OH - concentration to 10^-4 M?

If enough of a base is added to raise the OH- concentration to 10^-4 M, it will cause the H+ concentration to drop to 10-10 M. Whenever we know the concentration of either H+ or OH- in an aqueous solution, we can deduce the concentration of the other ion.

The ability of ice to float due to its lower density is an important factor in the suitability of the environment for life. Give an example:

If ice sank, then eventually all ponds, lakes, and even oceans would freeze solid, making life as we know it impossible on Earth.

adipose tissue

In addition to storing energy, adipose tissue also cushions such vital organs as the kidneys, and a layer of fat beneath the skin insulates the body. This subcutaneous layer is especially thick in whales, seals, and most other marine mammals, insulating their bodies in cold ocean water.

Product of H+ and OH- concentrations

In any aqueous solution at 25°C, the product of the H+ and OH- concentrations is constant at 10-14.

In aqueous solutions, why do glucose molecules as well as most other five and six carbon sugars form rings?

In aqueous solutions, glucose molecules, as well as most other five- and six-carbon sugars, form rings, because they are the most stable form of these sugars under physiological conditions

Base pairing

In base pairing, only certain bases in the double helix are compatible with each other. Adenine (A) in one strand always pairs with thymine (T) in the other, and guanine (G) always pairs with cytosine (C). Reading the sequence of bases along one strand of the double helix would tell us the sequence of bases along the other strand.

unsaturated fats

In contrast, the fats of plants and fishes are generally unsaturated, meaning that they are built of one or more types of unsaturated fatty acids. Usually liquid at room temperature, plant and fish fats are referred to as oils—olive oil and cod liver oil are examples.

The individual bonds of methane are much less polar, Why?

In contrast, the individual bonds of methane (CH4) are much less polar because the electronegativities of carbon and hydrogen are similar

Few organisms possess enzymes that can digest ____

In fact, few organisms possess enzymes that can digest cellulose.Almost all animals, including humans, do not

What could result in fatigue?

In humans, for example, glycogen stores are depleted in about a day unless they are replenished by eating. This is an issue of concern in lowcarbohydrate diets, which can result in weakness and fatigue.

How are parallel cellulose molecules held together in plant cell walls?

In plant cell walls, parallel cellulose molecules held together in this way are grouped into units called microfibrils

What is the concentration of H+ and OH- in water?

In pure water, only one water molecule in every 554 million is dissociated; the concentration of H+ and of OH- in pure water is therefore 10-7 M (at 25°C). This means there is only one ten-millionth of a mole of hydrogen ions per liter of pure water and an equal number of hydroxide ions. (Even so, this is a huge number—over 60,000 trillion—of each ion in a liter of pure water.)

As an example, let's calculate the molecular mass of table sugar (sucrose), C12H22O11, by multiplying the number of atoms by the atomic mass of each element

In round numbers of daltons, the mass of a carbon atom is 12, the mass of a hydrogen atom is 1, and the mass of an oxygen atom is 16. Thus, sucrose has a molecular mass of (12 * 12) + (22 * 1) + (11 * 16) = 342 daltons

ion

In some cases, two atoms are so unequal in their attraction for valence electrons that the more electronegative atom strips an electron completely away from its partner. The two resulting oppositely charged atoms (or molecules) are called ions.

Where are the glucose monomers in starch?

In starch, all the glucose monomers are in the α configuration. The arrangement we saw in Figures 5.4 and 5.5. In contrast, the glucose monomers of cellulose are all in the β configuration, making every glucose monomer "upside down" with respect to its neighbors

Effect of global warming in the Arctic

In the Arctic, the average air temperature has risen 2.2°C just since 1961. This temperature increase has affected the seasonal balance between Arctic sea ice and liquid water, causing ice to form later in the year, to melt earlier, and to cover a smaller area. The rate at which glaciers and Arctic sea ice are disappearing is posing an extreme challenge to animals that depend on ice for their survival .

Cholesterol in vertebrates

In vertebrates, cholesterol is synthesized in the liver and is also obtained from the diet. A high level of cholesterol in the blood may contribute to atherosclerosis, although some researchers are questioning the roles of cholesterol and saturated fats in the development of this condition

hydroxyl group (-OH); may be writtern (HO-)

Is polar due to electronegative oxygen. Forms hydrogen bonds with water, helping dissolve compounds such as sugars. * Compound name: Alcohol (specific name usually ends in -ol ) * Ethanol, the alcohol present in alcoholic beverages

trans fats contribute to:

It appears that trans fats can contribute to coronary heart disease. Because trans fats are especially common in baked goods and processed foods, the U.S. Food and Drug Administration (FDA) requires nutritional labels to include information on trans fat content

Why is molecular shape important?

It determines how biological molecules recognize and respond to one another with specificity. Biological molecules often bind temporarily to each other by forming weak interactions, but only if their shapes are complementary.

How does a buffer minimize changes in the concentrations 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. M

Cholesterol is a common component in

It is a common component of animal cell membranes and is also the precursor from which other steroids, such as the vertebrate sex hormones, are synthesized.

Linkages of starch and glycogen.

Like starch, cellulose is a polymer of glucose with 1-4 glycosidic linkages, but the linkages in these two polymers differ. The difference is based on the fact that there are actually two slightly different ring structures for glucose

Lipids are

Lipids are varied in form and function. They include waxes and certain pigments, but we will focus on the types of lipids that are most important biologically: fats, phospholipids, and steroids.

Misfolding of polypeptides in cells is a serious problem that has come under increasing scrutiny by medical researchers. Give examples

Many diseases—such as cystic fibrosis, Alzheimer's, Parkinson's, and mad cow disease—are associated with an accumulation of misfolded proteins. In fact, misfolded versions of the transthyretin protein featured in Figure 5.18 have been implicated in several diseases, including one form of senile dementia.

Mass vs. Weight

Mass is a measurement of the amount of matter something contains, while Weight is the measurement of the pull of gravity on an object.

What help stabilize the tertiary structure?

Meanwhile, hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged side chains also help stabilize tertiary structure. These are all weak interactions in the aqueous cellular environment, but their cumulative effect helps give the protein a unique shape.

What does messenger RNA do?

Messenger RNA conveys genetic instructions for building proteins from the nucleus to the cytoplasm. Prokaryotic cells lack nuclei but still use mRNA to convey a message from the DNA to ribosomes and other cellular equipment that translate the coded information into amino acid sequences.

Methane

Methane, the main component of natural gas, is a compound with the molecular formula CH4. It takes four hydrogen atoms, each with a valence of 1, to complement one atom of carbon, with its valence of 4

What were the results of Miller's experiment?

Miller concluded that complex organic molecules could arise spontaneously under conditions thought at that time to have existed on the early Earth. Miller identified a variety of organic molecules that are common in organisms. These included simple compounds, such as formaldehyde (CH2O) and hydrogen cyanide (HCN), and more complex molecules, such as amino acids and long chains of carbon and hydrogen known as hydrocarbons.

Evolution

More than 800 planets have been found outside our solar system, and there is evidence for the presence of water vapor on a few of them. In our own solar system, Mars has been a focus of study. Like Earth, Mars has an ice cap at both poles. Images from spacecraft sent to Mars showed that ice is present just under the surface of Mars and enough water vapor exists in its atmosphere for frost to form. In 2015, scientists found evidence of water flowing on Mars (Figure 3.10), and other studies suggested conditions existed that could have supported microorganismal life. Drilling below the surface may be the next step in the search for signs of life on Mars. If any life-forms or fossils are found, their study will shed light on the process of evolution from an entirely new perspective.

Sources of starch

Most animals, including humans, also have enzymes that can hydrolyze plant starch, making glucose available as a nutrient for cells. Potato tubers and grains—the fruits of wheat, maize (corn), rice, and other grasses—are the major sources of starch in the human diet.

pH of biological fluids

Most biological fluids, such as blood and saliva, are within the range of pH 6-8. There are a few exceptions, however, including the strongly acidic digestive juice of the human stomach (gastric juice), which has a pH of about 2.

Do most buffer solutions contain weak acid or strong acid?

Most buffer solutions contain a weak acid and its corresponding base, which combine reversibly with hydrogen ions.

How are most of the glucose monomers in starch joined?

Most of the glucose monomers in starch are joined by 1-4 linkages (number 1 carbon to number 4 carbon), like the glucose units in maltose

Species Interactions

Most plant species exist in a mutually beneficial partnership with fungi (right) and bacteria associated with the plants' roots; these interactions improve plant growth. Genome sequencing and analysis of gene expression have allowed characterization of plant-associated communities. Such studies will help advance our understanding of such interactions and may improve agricultural practices. (See the Chapter 31 Scientific Skills Exercise and Figure 37.11.)

dependance of proteins

Nearly every dynamic function of a living being depends on proteins. In fact, the importance of proteins is underscored by their name, which comes from the Greek word proteios, meaning "first," or "primary." Proteins account for more than 50% of the dry mass of most cells, and they are instrumental in almost everything organisms do. Some proteins speed up chemical reactions, while others play a role in defense, storage, transport, cellular communication, movement, or structural support

Mass of neutron & proton

Neutrons and protons each have a mass very close to 1 dalton

Paleontology

New DNA sequencing techniques have allowed decoding of minute quantities of DNA found in ancient tissues from our extinct relatives, the Neanderthals (Homo neanderthalensis). Sequencing the Neanderthal genome has informed our understanding of their physical appearance (as in this reconstruction), as well as their relationship with modern humans. (See Figures 34.51 and 34.52.)

What determines the chemical nature of a protein ?

Note that one end of the polypeptide chain has a free amino group (the N-terminus of the polypeptide), while the opposite end has a free carboxyl group (the C-terminus). The chemical nature of the molecule as a whole is determined by the kind and sequence of the side chains, which determine how a polypeptide folds and thus its final shape and chemical characteristics. The immense variety of polypeptides in nature illustrates an important concept introduced earlier—that cells can make many different polymers by linking a limited set of monomers into diverse sequences.

sugar in nucleic acids

Now let's add the sugar to which the nitrogenous base is attached. In DNA the sugar is deoxyribose; in RNA it is ribose. The only difference between these two sugars is that deoxyribose lacks an oxygen atom on the second carbon in the ring, hence the name deoxyribose. So far, we have built a nucleoside (base plus sugar). To complete the construction of a nucleotide, we attach one to three phosphate groups to the 5′ carbon of the sugar(the carbon numbers in the sugar include ′, the prime symbol; see Figure 5.23b). With one phosphate, this is a nucleoside monophosphate, more often called a nucleotide.

polynucleotide

Nucleic acids are macromolecules that exist as polymers called polynucleotides. As indicated by the name, each polynucleotide consists of monomers called nucleotides. A nucleotide, in general, is composed of three parts: a five-carbon sugar (a pentose), a nitrogen-containing (nitrogenous) base, and one to three phosphate groups.

Contributions of Genomics and Proteomics to Biology

Nucleotide sequencing and the analysis of large sets of genes and proteins can be done rapidly and inexpensively due to advances in technology and information processing. Taken together, genomics and proteomics have advanced our understanding of biology across many different fields.

The high amount of energy required to vaporize water has a wide range of effects.

On a global scale, for example, it helps moderate Earth's climate. A considerable amount of solar heat absorbed by tropical seas is consumed during the evaporation of surface water. Then, as moist tropical air circulates poleward, it releases heat as it condenses and forms rain

severity of steam burns

On an organismal level, water's high heat of vaporization accounts for the severity of steam burns. These burns are caused by the heat energy released when steam condenses into liquid on the skin

What happened once the structure of DNA molecule was described?

Once the structure of the DNA molecule was described in 1953, and the linear sequence of nucleotide bases was understood to specify the amino acid sequence of proteins, biologists sought to "decode" genes by learning their nucleotide sequences (often called "base sequences")

Methamphetamine also occurs in two enantiomers that have very different effects :

One enantiomer is the highly addictive stimulant drug known as "crank," sold illegally in the street drug trade. The other has a much weaker effect and is the active ingredient in an over-the-counter vapor inhaler for treatment of nasal congestion.

A serious environment threat

One of the most serious environmental threats is radioactive fallout from nuclear accidents. The doses of most isotopes used in medical diagnosis, however, are relatively safe.

Several buffers contribute to pH stability in human blood and many other biological solutions. Give an example

One of these is carbonic acid (H2CO3), which is formed when CO2 reacts with water in blood plasma. As mentioned earlier, carbonic acid dissociates to yield a bicarbonate ion (HCO3 - ) and a hydrogen ion (H+ ).

How many & what orbital does the first shell have? How many & what orbitals does the second shell have?

One spherical s orbital Four orbitals: one large spherical s orbital (called 2s) and three dumbbell-shaped p orbitals (called 2p orbitals) (The third shell and other higher electron shells also have s and p orbitals, as well as orbitals of more complex shapes.)

Effects of opiates, drugs such as morphine and heroin derived from opium.

Opiates relieve pain and alter mood by weakly binding to specific receptor molecules on the surfaces of brain cells

What was the conclusion of this experiment?

Organic molecules, a first step in the origin of life, may have been synthesized abiotically on the early Earth. Although new evidence indicates that the early Earth's atmosphere was different from the "atmosphere" used by Miller in this experiment, recent experiments using the revised list of chemicals also produced organic molecules. (We will explore this hypothesis in more detail in Concept 25.1.)These experiments support the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been an early stage in the origin of life

Where do plants store starch?

Plants store starch, a polymer of glucose monomers, as granules within cellular structures known as plastids. (Plastids include chloroplasts.)

A single amino acid substitution in a protein causes sickle-cell disease.

Primary Structure : Normal hemoglobin vs sickle cell hemoglobin Secondary and Tertiary Structures: Normal β subunit vs Sickle-cell β subunit Quaternary Structure - Normal hemoglobin vs Sickle-cell hemoglobin Function : Normal hemoglobin proteins do not associate with one another; each carries oxygen. vs Hydrophobic interactions between sickle-cell hemoglobin proteins lead to their aggregation into a fiber; capacity to carry oxygen is greatly reduced. Red Blood Cell Shape : Normal red blood cells are full of individual hemoglobin proteins. vs Fibers of abnormal hemoglobin deform red blood cell into sickle shape.

Polypeptide

Proteins are all constructed from the same set of 20 amino acids, linked in unbranched polymers. The bond between amino acids is called a peptide bond, so a polymer of amino acids is called a polypeptide. A protein is a biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific three-dimensional structure.

How does a termite digest cellulose?

Similarly, a termite, which is unable to digest cellulose by itself, has prokaryotes or protists living in its gut that can make a meal of wood. Some fungi can also digest cellulose in soil and elsewhere, thereby helping recycle chemical elements within Earth's ecosystems.

Why are most drugs manufactured as salts?

Since salts are quite stable when dry and dissociate when dissolved in water.

What do single bonds allow the atoms to do?

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

Atmospheric CO2 from human activities and its fate in the ocean.

Some carbon dioxide (CO2) in the atmosphere dissolves in the ocean, where it reacts with water to form carbonic acid (H2CO3). Carbonic acid dissociates into hydrogen ions (H+) and bicarbonate ions (HCO3 -). The added H+ combines with carbonate ions (CO3 2-), forming more HCO3 -. Less CO3 2- is available for calcification —the formation of calcium carbonate (CaCO3)—by marine organisms such as corals.

How are carbon skeleton variations an important source of molecular complexity?

Some carbon skeletons have double bonds, which vary in number and location. Such variation in carbon skeletons is one important source of the molecular complexity and diversity that characterize living matter. In addition, atoms of other elements can be bonded to the skeletons at available sites.

Tertiary Structure - Three-dimensional shape stabilized by interactions between side chains

Superimposed on the patterns of secondary structure is a protein's tertiary structure, shown here in a ribbon model of the transthyretin polypeptide. While secondary structure involves interactions between backbone constituents, tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids

ATP

The "Phosphate group" row in Figure 4.9 shows a simple example of an organic phosphate molecule. A more complicated organic phosphate, adenosine triphosphate, or ATP, is worth mentioning here because its function in the cell is so important. 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,

The structures of DNA and tRNA molecules

The DNA molecule is usually a double helix, with the sugar-phosphate backbones of the antiparallel polynucleotide strands (symbolized here by blue ribbons) on the outside of the helix. Hydrogen bonds between pairs of nitrogenous bases hold the two strands together. As illustrated here with symbolic shapes for the bases, adenine (A) can pair only with thymine (T), and guanine (G) can pair only with cytosine (C). Each DNA strand in this figure is the structural equivalent of the polynucleotide diagrammed in Figure 5.23a. (b) A tRNA molecule has a roughly L-shaped structure due to complementary base pairing of antiparallel stretches of RNA. In RNA, A pairs with U

From where does the ability of water to stabilise temperature stems from?

The ability of water to stabilize temperature stems from its relatively high specific heat

If the primary structure of polypeptides determines a protein's shape, what determines primary structure?

The amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a gene. Genes consist of DNA, which belongs to the class of compounds called nucleic acids. Nucleic acids are polymers made of monomers called nucleotides.

example of van der Waals interactions

The anatomy of the gecko's foot— including many minuscule hairlike projections from the toes and strong tendons underlying the skin—strikes a balance between maximum surface contact with the wall and necessary stiffness of the foot. The van der Waals interactions between the foot molecules and the molecules of the wall's surface are so numerous that despite their individual weakness, together they can support the gecko's body weight.

chemical bond

The atoms either share or transfer valence electrons. These interactions usually result in atoms staying close together, held by attractions called chemical bonds.

Electron transfer and ionic bonding.

The attraction between oppositely charged atoms, or ions, is an ionic bond. An ionic bond can form between any two oppositely charged ions, even if they have not been formed by transfer of an electron from one to the other

Electronegativity

The attraction of a particular atom for the electrons of a covalent bond is called its electronegativity

What does the bright yellow spot mark ?

The bright yellow spot marks an area with an elevated level of radioactively labeled glucose, which in turn indicates high metabolic activity, a hallmark of cancerous tissue.

What determines the chemical behaviour of an atom?

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

What does the chemical equilibrium between carbonic acid and bicarbonate act as?

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

What does the gasoline that fuels a car?

The gasoline that fuels a car consists of hydrocarbons, and the hydrocarbon tails of fats serve as stored fuel for plant embryos (seeds) and animals.

Why does the high specific heat also tend to stabilize ocean temperatures?

The high specific heat of water also tends to stabilize ocean temperatures, creating a favorable environment for marine life.

And this conclusion holds true as well when comparing whole genomes

The human genome is 95-98% identical to that of the chimpanzee, but only roughly 85% identical to that of the mouse, a more distant evolutionary relative. Molecular biology has added a new tape measure to the toolkit biologists use to assess evolutionary kinship.

What do hydrogen bonds do?

The hydrogen bonds keep the molecules at "arm's length," far enough apart to make ice about 10% less dense (10% fewer molecules in the same volume) than liquid water at 4°C. When ice absorbs enough heat for its temperature to rise above 0°C, hydrogen bonds between molecules are disrupted.

What is the hydrophobic behavior of lipids based on their molecular structure?

The hydrophobic behavior of lipids is based on their molecular structure.Although they may have some polar bonds associated with oxygen, lipids consist mostly of hydrocarbon regions

hydrophobic tale of the bilayer

The hydrophobic tails point toward the interior of the bilayer, away from the water. The phospholipid bilayer forms a boundary between the cell and its external environment and establishes separate compartments within eukaryotic cells; in fact, the existence of cells depends on the properties of phospholipids.

why can even a slight change in living cells pH be harmful?

The internal pH of most living cells is close to 7. Even a slight change in pH can be harmful because the chemical processes of the cell are very sensitive to the concentrations of hydrogen and hydroxide ions.

thermal energy

The kinetic energy associated with the random movement of atoms or molecules is called thermal energy. Thermal energy is related to temperature, but they are not the same thing.

What do the kinks where the cis double bonds prevent?

The kinks where the cis double bonds are located prevent the molecules from packing together closely enough to solidify at room temperature.

What specifies the amino acid sequence/ primary structure?

The linear order of bases in a gene specifies the amino acid sequence—the primary structure—of a protein, which in turn specifies that protein's 3-D structure, thus enabling its function in the cell.

sugar-phosphate backbone

The linkage of nucleotides into a polynucleotide involves a dehydration reaction. ( You will learn the details in Concept 16.2.) In the polynucleotide, adjacent nucleotides are joined by a phosphodiester linkage, which consists of a phosphate group that links the sugars of two nucleotides. This bonding results in a repeating pattern of sugar-phosphate units called the sugar-phosphate backbone

1)

The lone valence electron of a sodium 2 atom is transferred to join the 7 valence electrons of a chlorine atom.

The synthesis and structure of a fat, or triacylglycerol.

The molecular building blocks of a fat are one molecule of glycerol and three molecules of fatty acids. (a) One water molecule is removed for each fatty acid joined to the glycerol. (b) A fat molecule with three fatty acid units, two of them identical. The carbons of the fatty acids are arranged zigzag to suggest the actual orientations of the four single bonds extending from each carbon (see Figures 4.3a and 4.6b).

Bioinformatics

The number of genomes that have been fully sequenced has burgeoned, generating reams of data and prompting development of bioinformatics, the use of computer software and other computational tools that can handle and analyze these large data sets

Hydrogenated vegetable oils

The phrase "hydrogenated vegetable oils" on food labels means that unsaturated fats have been synthetically converted to saturated fats by adding hydrogen, allowing them to solidify. Peanut butter, margarine, and many other products are hydrogenated to prevent lipids from separating out in liquid (oil) form.

What affect the side chain and determine the unique characteristics of amino acid?

The physical and chemical properties of the side chain determine the unique characteristics of a particular amino acid, thus affecting its functional role in a polypeptide.

From where do the properties of water arise from?

The properties of water arise from attractions between oppositely charged atoms of different water molecules: The partially positive hydrogen of one molecule is attracted to the partially negative oxygen of a nearby molecule. The two molecules are thus held together by a hydrogen bond

The molecule in which the proton binds to?

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

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. For the same reason that water has a high specific heat, it also has a high heat of vaporization relative to most other liquids

What does the repeating sequence of atoms highlight?

The repeating sequence of atoms highlighted in purple in Figure 5.15 is called the polypeptide backbone.Extending from this backbone are the different side chains (R groups) of the amino acids. Polypeptides range in length from a few amino acids to 1,000 or more. Each specific polypeptide has a unique linear sequence of amino acids.

monomers

The repeating units that serve as the building blocks of a polymer are smaller molecules called monomers. In addition to forming polymers, some monomers have functions of their own.

What happens when two of the hybrid orbitals in the oxygen's valence shell are shared with hydrogens in the water molecule?

The result is a molecule shaped roughly like a V, with its two covalent bonds at an angle of 104.5°

How is the reversibility of weak interactions an advantage?

The reversibility of weak interactions can be an advantage: Two molecules can come together, affect one another in some way, and then separate.

What happens as products accumulate?

The same holds true for products. As products accumulate, collisions resulting in the reverse reaction become more frequent.

Most important chemical groups

The seven chemical groups most important in biological processes are the hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups. The first six groups can be chemically reactive; of these six, all except the sulfhydryl group are also hydrophilic and thus increase the solubility of organic compounds in water. The methyl group is not reactive, but instead often serves as a recognizable tag on biological molecules.

Which electron shell has the highest energy level?

The shell farthest to the nucleus

Amino acid glycine and glutamine

The side chain (R group) may be as simple as a hydrogen atom, as in the amino acid glycine, or it may be a carbon skeleton with various functional groups attached, as in glutamine.

amylose and amylopectin

The simplest form of starch, amylose, is unbranched. Amylopectin, a more complex starch, is a branched polymer with 1-6 linkages at the branch points.

Molecular shapes due to hybrid orbitals: Hybridization of orbitals:

The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron

What are the sites of protein synthesis?

The sites of protein synthesis are cellular structures called ribosomes. In a eukaryotic cell, ribosomes are in the cytoplasm— the region between the nucleus and the plasma membrane, the cell's outer boundary—but DNA resides in the nucleus

The carbon skeletons can vary in......

The skeletons vary in length and may be straight, branched, or arranged in closed ring

β pleated sheets make up the core of many globular proteins, as is the case for transthyretin (see Tertiary Structure), and dominate some fibrous proteins, including the silk protein of a spider's web.

The teamwork of so many hydrogen bonds makes each spider silk fiber stronger than a steel strand of the same weight.

The term ion also applies to

The term ion also applies to entire molecules that are electrically charged. In the salt ammonium chloride (NH4Cl), for instance, the anion is a single chloride ion (Cl- ), but the cation is ammonium (NH4 + ), a nitrogen atom covalently bonded to four hydrogen atoms. The whole ammonium ion has an electrical charge of 1+ because it has given up 1 electron and thus is 1 electron short.

What can the amino acid sequence of a polypeptide tell us about the three-dimensional structure (commonly referred to simply as the "structure") of the protein and its function?

The term polypeptide is not synonymous with the term protein. Even for a protein consisting of a single polypeptide, the relationship is somewhat analogous to that between a long strand of yarn and a sweater of particular size and shape that can be knitted from the yarn.

Accordingly, the concentric-circle diagrams do not give a real picture of an atom. In reality, we can never know the exact location of an electron. What we can do instead is describe the space in which an electron spends most of its time.

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

Conservation Biology

The tools of molecular genetics and genomics are increasingly used by forensic ecologists to identify which species of animals and plants are killed illegally. In one case, genomic sequences of DNA from illegal shipments of elephant tusks were used to track down poachers and pinpoint the territory where they were operating. (See Figure 56.9.)

What does cohesion due to hydrogen bonding contribute to?

The transport of water and dissolved nutrients against gravity in plants. Water from the roots reaches the leaves through a network of water-conducting cells

What do the two ends of phospholipids show?

The two ends of phospholipids show different behaviors with respect to water. The hydrocarbon tails are hydrophobic and are excluded from water. However, the phosphate group and its attachments form a hydrophilic head that has an affinity for water. When phospholipids are added to water, they self-assemble into a double-layered sheet called a "bilayer" that shields their hydrophobic fatty acid tails from water

polynucleotides

The two free ends of the polymer are distinctly different from each other. One end has a phosphate attached to a 5′ carbon, and the other end has a hydroxyl group on a 3′ carbon; we refer to these as the 5′ end and the 3′ end, respectively. We can say that a polynucleotide has a built-in directionality along its sugar-phosphate backbone, from 5′ to 3′, somewhat like a one-way street. The bases are attached all along the sugar-phosphate backbone.

Unbranched structure of cellulose

The unbranched structure of cellulose thus fits its function: imparting strength to parts of the plant

What is the water molecule that has lost a proton?

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

Protein's flexibility and indefinite structure are important .....

Their flexibility and indefinite structure are important for their function, which may require binding with different targets at different times. These proteins, which may account for 20-30% of mammalian proteins, are called intrinsically disordered proteins and are the focus of current research.

phospholipid structure

Their structure provides a classic example of how form fits function at the molecular level. a phospholipid is similar to a fat molecule but has only two fatty acids attached to glycerol rather than three. The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell.

John Dalton

discovered the atomic theory

Water resists changing its temperature because

Water resists changing its temperature; when it does change its temperature, it absorbs or loses a relatively large quantity of heat for each degree of change.

hydrogen bond between Water and ammonia

This hydrogen bond (dotted line) results from the attraction between the partial positive charge on a hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.

Choline

Typically, an additional small charged or polar molecule is also linked to the phosphate group. Choline is one such molecule, but there are many others as well, allowing formation of a variety of phospholipids that differ from each other.

Scientists predict that ocean acidification will cause the carbonate ion concentration to decrease by 40% by the year 2100. Why is this a great concern?

This is of great concern because carbonate ions are required for calcification, the production of calcium carbonate (CaCO3) by many marine organisms, including reef-building corals and animals that build shells.

Collagen

This suits collagen fibers to their function as the girders of connective tissue in skin, bone, tendons, ligaments, and other body parts. (Collagen accounts for 40% of the protein in a human body.)

What makes water polar?

This unequal sharing of electrons and water's V-like shape make it a polar molecule, meaning that its overall charge is unevenly distributed

Molecular-shape models

Three models representing molecular shape are shown for water and methane. The positions of the hybrid orbitals determine the shapes of the molecules.

Why is cellulose important?

Thus, although cellulose is not a nutrient for humans, it is an important part of a healthful diet. Most fruits, vegetables, and whole grains are rich in cellulose. On food packages, "insoluble fiber" refers mainly to cellulose.

Give an example of how most buffers are acid- base pairs.

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

Sulfhydryl group ( - SH)

Two —SH groups can react, forming a "cross-link" that helps stabilize protein structure. Hair protein cross-links maintain the straightness or curliness of hair; in hair salons, permanent treatments break cross-links, then re-form them while the hair is in the desired shape. * Compound name: Thiol *Cysteine, a sulfurcontaining amino acid

The first chemical techniques for DNA sequencing, or determining the sequence of nucleotides along a DNA strand, one by one, were developed in the 1970s. Researchers began to study gene sequences, gene by gene, and the more they learned, the more questions they had: How was expression of genes regulated?Genes and their protein products clearly interacted with each other, but how?Genes and their protein products clearly interacted with each other, but how?

To fully understand the genetic functioning of a living organism, the entire sequence of the full complement of DNA, the organism's genome, would be most enlightening. . In spite of the apparent impracticality of this idea, in the late 1980s several prominent biologists put forth an audacious proposal to launch a project that would sequence the entire human genome—all 3 billion bases of it! This endeavor began in 1990 and was effectively completed in the early 2000s.

How do you understand reactions that include solutes dissolved in a water?

To understand such reactions, we must know how many atoms and molecules are involved and calculate the concentration of solutes in an aqueous solution

Many different kinds of polar compounds are dissolved (along with ions) in the water of such biological fluids as blood, the sap of plants, and the liquid within all cells. True or false?

True

. Although the isotopes of an element have slightly different masses, they behave identically in chemical reactions. True or false?

True. (For an element with more than one naturally occurring isotope, the atomic mass is an average of those isotopes, weighted by their abundance. Thus carbon has an atomic mass of 12.01 daltons.)

How do two oxygen atoms form a molecule?

Two oxygen atoms form a molecule by sharing two pairs of valence electrons. The atoms are thus joined by what is called a double bond (O==O). Each atom that can share valence electron

Where do vertebrates store glycogen?

Vertebrates store glycogen mainly in liver and muscle cells. Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases.

Evidence for liquid water on Mars

Water appears to have helped form these dark streaks that run downhill on Mars during the summer. NASA scientists also found evidence of hydrated salts, indicating water is present.

Why is water effective as a heat bank?

Water is effective as a heat bank because it can absorb or release a relatively large amount of heat with only a slight change in its own temperature

How does water moderate air temperature?

Water moderates air temperature by absorbing heat from air that is warmer and releasing the stored heat to air that is cooler

Conclusion

We can conclude that the information for building specific shape is intrinsic to the protein's primary structure; this is often the case for small proteins.

How can we summarize the flow of genetic information?

We can summarize the flow of genetic information as DNA ----> RNA -----> protein

How do we trace water's specific heat?

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. A calorie of heat causes a relatively small change in the temperature of water because much of the heat is used to disrupt hydrogen bonds before the water molecules can begin moving faster. And when the temperature of water drops slightly, many additional hydrogen bonds form, releasing a considerable amount of energy in the form of heat.

How would we make a liter (L) of solution consisting of 1 mol of sucrose dissolved in water?

We would measure out 342 g of sucrose and then gradually add water, while stirring, until the sugar was completely dissolved. We would then add enough water to bring the total volume of the solution up to 1 L. At that point, we would have a 1-molar (1 M) solution of sucrose. Molarity—the number of moles of solute per liter of solution—is the unit of concentration most often used by biologists for aqueous solutions.

Example of weak acid

Weak acids are acids that reversibly release and accept back hydrogen ions. An example is carbonic acid: view page 51 for equation.

ocean acidification

When CO2 dissolves in seawater, it reacts with water to form carbonic acid, which lowers ocean pH. Alters the delicate balance of conditions for life in the oceans

What happens when a carbon atom forms four single covalent bonds?

When a carbon atom forms four single covalent bonds, the arrangement of its four hybrid orbitals causes the bonds to angle toward the corners of an imaginary tetrahedron

Methane (CH4) - simple organic molecule

When a carbon atom has four single bonds to other atoms, the molecule is tetrahedral.

What happens when cells synthesize a polypeptide?

When a cell synthesizes a polypeptide, the chain may fold spontaneously, assuming the functional structure for that protein. This folding is driven and reinforced by the formation of various bonds between parts of the chain, which in turn depends on the sequence of amino acids

When a protein in a test tube solution....

When a protein in a test-tube solution has been denatured by heat or chemicals, it can sometimes return to its functional shape when the denaturing agent is removed. ( Sometimes this is not possible: For example, a fried egg will not become liquefied when placed back into the refrigerator!)

What would cause an aqueous solution to have an imbalance in H+ and OH- concentrations?

When acids dissolve in water, they donate additional H+ to the solution. An acid is a substance that increases the hydrogen ion concentration of a solution

What happens when glucose forms a ring?

When glucose forms a ring, the hydroxyl group attached to the number 1 carbon is positioned either below or above the plane of the ring.

What happens when the cell divides?

When the cell divides, the copies are distributed to the daughter cells, making them genetically identical to the parent cell. Thus, the structure of DNA accounts for its function of transmitting genetic information whenever a cell reproduces.

Occasionally, a hydrogen atom participating in a hydrogen bond between two water molecules shifts from one molecule to the other. What happens then?

When this happens, the hydrogen atom leaves its electron behind, and what is actually transferred is a hydrogen ion H+

What are the structures and mechanisms that defend wood ants from attack?

When threatened from above, the ants shoot volleys of formic acid into the air from their abdomens, and the acid bombards the potential predator, such as a hungry bird (Figure 2.1). Formic acid is produced by many species of ants and in fact got its name from the Latin word for ant, formica. For quite a few ant species, the formic acid isn't shot out, but probably serves as a disinfectant that protects the ants against microbial parasites.

Now that we have examined amino acids, let's see how they are linked to form polymers:

When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration reaction, with the removal of a water molecule. The resulting covalent bond is called a peptide bond. Repeated over and over, this process yields a polypeptide, a polymer of many amino acids linked by peptide bonds.

What happens when water is heated in a coffeemaker?

When water is heated in a coffeemaker, the average speed of the molecules increases, and the thermometer records this as a rise in temperature of the liquid. The total amount of thermal energy also increases in this case. Note, however, that although the pot of coffee has a much higher temperature than, say, the water in a swimming pool, the swimming pool contains more thermal energy because of its much greater volume.

Why are most of the water molecules most of the time hydrogen bonded to their neighbours?

When water is in its liquid form, its hydrogen bonds are very fragile, each only about 1/20 as strong as a covalent bond. The hydrogen bonds form, break, and re-form with great frequency

ATP ---> ADP

Where three phosphates are present in series, as in ATP, one phosphate may be split off as a result of a reaction with water. This inorganic phosphate ion, HOPO3 2- , is often abbreviated P i in this book, and a phosphate group in an organic molecule is often written as P .. Having lost one phosphate, ATP becomes adenosine diphosphate, or ADP.

How does water dissolve the ions Nacl.

Working inward from the surface of each salt crystal, water eventually dissolves all the ions. The result is a solution of two solutes, sodium cations and chloride anions, homogeneously mixed with water, the solvent. Other ionic compounds also dissolve in water. Seawater, for instance, contains a great variety of dissolved ions, as do living cells.

Can a carbon atom use one or more valence electrons?

a carbon atom can also use one or more valence electrons to form covalent bonds to other carbon atoms, each of which can also form four bonds. Thus, the atoms can be linked into chains of seemingly infinite variety.

WHat determines an electrons potential energy?

an electron's potential energy is determined by its energy level. An electron can exist only at certain energy levels, not between them.

Electrically charged side chains; hydrophilic

aspartic acid (Asp or D), glutamic acid(Glu or E) , lysine(Lys or K) , arginine (Arg or R) , histidine(His or H)

Why is the concept of enantiomers important in the pharmaceutical industry?

because the two enantiomers of a drug may not be equally effective, as is the case for both ibuprofen and the asthma medication albuterol

Why is carbon so special compared to other elements?

carbon is unparalleled in its ability to form molecules that are large, complex, and varied, making possible the diversity of organisms that have evolved on Earth. Proteins, DNA, carbohydrates, and other molecules that distinguish living matter from inanimate material are all composed of carbon atoms bonded to one another and to atoms of other elements.

Four main atoms in organic molecules

carbon, hydrogen, oxygen, nitrogen

cis-trans isomers

carbons 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 the bond axis without changing the compound

What is one factor affecting the rate of a reaction?

concentration of the reactants. The greater the concentration of reactant molecules, the more frequently they collide with one another and have an opportunity to react and form products.

What represent electron shells in diagrams?

concentric circles

What happens when two carbon atoms are connected by double bonds?

double bonds do not permit such rotation. If a double bond joins two carbon atoms, and each C also has two different atoms (or groups of atoms) attached to it, then two distinct cis-trans isomers are possible

What measurement unit do we use for subatomic particles?

dalton

Example of Structural isomer

differ in the covalent arrangements of their atoms. Compare, for example, the two five-carbon compounds Pentane & 2-methylbutane. Structural isomers differ in covalent partners, as shown in this example of two isomers of C5H12. Both have the molecular formula C5H12, but they differ in the covalent arrangement of their carbon skeletons. The skeleton is straight in one compound but branched in the other. The number of possible isomers increases tremendously as carbon skeletons increase in size. There are only three forms of C5H12

A compound has characters same or different than its elements?

different

What must we remember about the concentric circles?

each concentric circle represents only the average distance between an electron in that shell and the nucleus

Atoms with incomplete valence shells can interact with certain other atoms in such a way that.......

each partner atom completes its valence shell: The atoms either share or transfer valence electrons.

The __________________ of carbon gives it covalent compatibility with many different elements

electron configuration

What is the key to an atom's characteristics?

electron configuration

examples of the marriage of form and function

endorphin molecules (produced by the body) and morphine molecules (a manufactured drug), both of which fit into receptor proteins on the surface of brain cells in humans, producing euphoria and relieving pain. . Morphine, heroin, and other opiate drugs are able to mimic endorphins because they all have a shape similar to that of endorphins and can thus fit into and bind to endorphin receptors in the brain. This fit is very specific, something like a lock and key. The endorphin receptor, like other receptor molecules, is a protein. The function of a protein—for instance, the ability of a receptor protein to bind to a particular pain-relieving signaling molecule—is an emergent property resulting from exquisite molecular order.

How is ethane shaped?

ethane (C2H6) is shaped like two overlapping tetrahedrons

fatty acid

has a long carbon skeleton, usually 16 or 18 carbon atoms in length. The carbon at one end of the skeleton is part of a carboxyl group, the functional group that gives these molecules the name fatty acid. . The rest of the skeleton consists of a hydrocarbon chain.

How are polymers broken down?

hydrolysis: a process that is essentially the reverse of the dehydration reaction. Hydrolysis means water breakage (from the Greek hydro, water, and lysis, break). The bond between monomers is broken by the addition of a water molecule, with a hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other.

One type of interaction that contributes to tertiary structure is called—somewhat misleadingly—a

hydrophobic interaction; . As a polypeptide folds into its functional shape, amino acids with hydrophobic (non polar) side chains usually end up in clusters at the core of the protein, out of contact with water. Thus, a "hydrophobic interaction" is actually caused by the exclusion of non polar substances by water molecules. . Once non polar amino acid side chains are close together, van der Waals interactions help hold them together

Proteins

include a diversity of structures, resulting in a wide range of functions

arthropods

insects, spiders, crustaceans and related animals

The specific activities of proteins result from their.......

intricate three dimensional architecture, the simplest level of which is the sequence of their amino acids.

The primary structure is like the

order of letters in a very long word. If left to chance, there would be 20127 different ways of making a polypeptide chain 127 amino acids long. However, the precise primary structure of a protein is determined not by the random linking of amino acids, but by inherited genetic information. The primary structure in turn dictates secondary and tertiary structure, due to the chemical nature of the backbone and the side chains (R groups) of the amino acids along the polypeptide.

Hydrocarbons

organic molecules consisting of only carbon and hydrogen

What happens to materials other than water when they solidify?

other materials contract and become denser when they solidify, water expands

The chemical behavior of an atom depends on the number of electrons in its ___________shell.

outermost ;

There are two families of nitrogenous bases: pyrimidines and purines

pyrimidine: A pyrimidine has one six-membered ring of carbon and nitrogen atoms. The members of the pyrimidine family are cytosine (C), thymine (T), and uracil (U). purine: Purines are larger, with a six-membered ring fused to a five-membered ring. The purines are adenine (A) and guanine (G). The specific pyrimidines and purines differ in the chemical groups attached to the rings. Adenine, guanine, and cytosine are found in both DNA and RNA; thymine is found only in DNA and uracil only in RNA.

What happens as water evaporates from a leaf ?

s water evaporates from a leaf, hydrogen bonds cause water molecules leaving the veins to tug on molecules farther down, and the upward pull is transmitted through the water-conducting cells all the way to the roots.

Most proteins have segments of their polypeptide chains repeatedly coiled or folded in patterns that contribute to the protein's overall shape. These coils and folds, collectively referred to as_______________

secondary structure; These are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone (not the amino acid side chains)

What is pure sodium & pure chlorine?

sodium - metal., chlorine - poisoning gas

Nucleic acids

store, transmit, and help express hereditary information.

potential energy

stored energy

Name the three types of isomers

structural isomers, cis-trans isomers, enantiomers

mass number

the total number of protons and neutrons in the nucleus of an atom

Another source of diversity for simple sugars

the way their parts are arranged spatially around asymmetric carbons. (Recall that an asymmetric carbon is a carbon attached to four different atoms or groups of atoms.)

What happens when two objects of different temperatures are brought together?

thermal energy passes from the warmer to the cooler object until the two are the same temperature. Molecules in the cooler object speed up at the expense of the thermal energy of the warmer object

Genomics and proteomics have

transformed biological inquiry and applications

A fat is constructed from

two kinds of smaller molecules: glycerol and fatty acids

calorie

unit of heat ; A calorie is the amount of heat it takes to raise the temperature of 1 g of water by 1°C. Conversely, a calorie is also the amount of heat that 1 g of water releases when it cools by 1°C

Example of potential energy

water in a reservoir on a hill has potential energy because of its altitude. When the gates of the reservoir's dam are opened and the water runs downhill, the energy can be used to do work, such as moving the blades of turbines to generate electricity. Because energy has been expended, the water has less energy at the bottom of the hill than it did in the reservoir. Matter has a natural tendency to move toward the lowest possible state of potential energy; in our example, the water runs downhill. To restore the potential energy of a reservoir, work must be done to elevate the water against gravity

What do we use to calculate the number of molecules?

we use mass to calculate the number of molecules. We must first calculate the molecular mass, which is the sum of the masses of all the atoms in a molecule

When does the reaction involving ammonia, reach equillibrium?

when ammonia decomposes as rapidly as it forms. s. In some chemical reactions, the equilibrium point may lie so far to the right that these reactions go essentially to completion; that is, virtually all the reactants are converted to products.

When did Chemists begin to chip out the notion that artificial synthesis of the complex molecules extracted from living matter seemed impossible?

when they learned to synthesize organic compounds in the laboratory.

How can an electron in an atom lose energy to go from a higher energy level to a lower energy level?

y. An electron can move from one shell to another, but only by absorbing or losing an amount of energy equal to the difference in potential energy between its position in the old shell and that in the new shell. When an electron absorbs energy, it moves to a shell farther out from the nucleus.