BIO Chapter 2

One method to prepare a sample for viewing under the microscope is to make a wet mount. The advantages of a wet mount may include:

Fast preparation. Requires no special equipment other than a transfer pipette, slide, and cover slip. Organisms may be viewed in their living state. Movement of motile microorganisms can be observed

a hydrogen bond is a type of chemical bond. Extensive networks of hydrogen bonds largely define the physical properties of

water

step 1 of scientific process

observation

A polar covalent bond is due to:

unequal sharing of electrons in a covalent bond.

Ionic bonds, Covalent bonds(two types)

Polar covalent which is an unequal sharing of electrons and nonpolar covalent where there is equal sharing Each bond type occurs in life Each band tape has different properties and therefore lens itself to different uses in biology (Ionic=enzymes)

Four polymers

Protein nucleic acid carbohydrates fats Each of these make polymers in the same way But each has different functions based on additional Atoms and molecules that are added onto the back bone

The bonds between hydrogen atoms and an oxygen atom in a water molecule _____ hydrogen bonds because hydrogen bonds _____ based on slight charge differences, rather than sharing of electrons

are not, are

Are polar molecules hydrophilic or hydrophobic?

hydrophilic

pH is a measure of the concentration of _in solution.

protons

atoms sticking together comes down to

Gaining or losing electrons in the outer shell

core concepts

2.1 PROPERTIES OF ATOMS: The atom is the fundamental unit of matter. Atoms consist of positively charged protons and electrically neutral neutrons in the nucleus, as well as negatively charged electrons moving around the nucleus. page 29 The number of protons determines the identity of an atom. page 29 The number of protons and neutrons together determines the mass of an atom. page 29 The number of protons versus the number of electrons determines the charge of an atom. page 30 Negatively charged electrons travel around the nucleus in regions called orbitals. page 30 The periodic table of the elements reflects a regular and repeating pattern in the chemical behavior of elements. page 31 2.2 MOLECULES AND CHEMICAL BONDS: Atoms can combine to form molecules linked by chemical bonds. Valence electrons occupy the outermost energy level (shell) of an atom and determine the ability of an atom to combine with other atoms to form molecules. page 32 A covalent bond results from the sharing of electrons between atoms to form a molecular orbital. page 32 A polar covalent bond results when two atoms do not share electrons equally as a result of a difference in the ability of the atoms to attract electrons, a property called electronegativity. page 33 An ionic bond results from the attraction of oppositely charged ions. page 33 2.3 WATER: Water is abundant and essential for life. Water is a polar molecule because shared electrons are distributed asymmetrically between the oxygen and hydrogen atoms. page 35 Hydrophilic molecules dissolve readily in water, whereas hydrophobic molecules in water tend to associate with one another, minimizing their contact with water. page 35 A hydrogen bond results when a hydrogen atom covalently bonded to an electronegative atom interacts with an electronegative atom of another molecule. page 35 Water forms hydrogen bonds, which help explain its high cohesion, surface tension, and resistance to rapid temperature change. page 36 The pH of an aqueous solution is a measure of the acidity of the solution. page 36 2.4 CARBON: Carbon is the backbone of organic molecules. A carbon atom can form up to four covalent bonds with other atoms. page 37 The geometry of these covalent bonds helps explain the structural and functional diversity of organic molecules. page 38 2.5 ORGANIC MOLECULES: Organic molecules include proteins, nucleic acids, carbohydrates, and lipids, each of which is built from simpler units. Amino acids are linked by covalent bonds to form proteins. page 39 An amino acid consists of a carbon atom (the α carbon) attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain. page 39 The side chain determines the properties of an amino acid. page 40 Nucleotides assemble to form nucleic acids, which store and transmit genetic information. page 40 Nucleotides are composed of a 5-carbon sugar, a nitrogen-containing base, and a phosphate group. page 40 Nucleotides in DNA incorporate the sugar deoxyribose, and nucleotides in RNA incorporate the sugar ribose. page 40 The bases are pyrimidines (cytosine, thymine, and uracil) and purines (guanine and adenine). page 40 Sugars are carbohydrates, molecules composed of C, H, and O atoms, usually in the ratio 1:2:1, and are a source of energy. page 41 Monosaccharides assemble to form disaccharides or longer polymers called complex carbohydrates. page 42 Lipids are hydrophobic. page 43 Triacylglycerols store energy and are made up of glycerol and fatty acids. page 43 Fatty acids consist of a linear hydrocarbon chain of variable length with a carboxyl group at one end. page 43 Fatty acids are either saturated (no carbon-carbon double bonds) or unsaturated (one or more carbon-carbon double bonds). page 44 The tight packing of fatty acids in lipids is the result of van der Waals forces, a type of weak, noncovalent bond. page 44 2.6 LIFE'S ORIGINS: Life likely originated on Earth by a set of chemical reactions that gave rise to the molecules of life. In 1953, Stanley Miller and Harold Urey demonstrated that amino acids can be generated in the laboratory in conditions that mimic those found on the early Earth

The age of the Earth is 4.6 billion years. For what percentage of this time is Earth thought to have been anaerobic?

44%

No sugars exist as the cyclic compound and solution instead of a linear structure glucose

Cyclic glucose is how it's found and used in our body but can move back and forth as needed

Is oil nonpolar or polar?

nonpolar (and hydrophobic)

main points of each section

2.1 PROPERTIES OF ATOMS: The atom is the fundamental unit of matter. 2.2 MOLECULES AND CHEMICAL BONDS: Atoms can combine to form molecules linked by chemical bonds. 2.3 WATER: Water is essential for life. 2.4 CARBON: Carbon is the backbone of organic molecules. 2.5 ORGANIC MOLECULES: Organic molecules include proteins, nucleic acids, carbohydrates, and lipids, each of which is built from simpler units. 2.6 LIFE'S ORIGINS: Life likely originated on Earth by a set of chemical reactions that gave rise to the molecules of life.

Protein monomers- amino acids

20 different amino acid to use to make proteins All ionized amino acid proteins have the basic structure of a carboxyl group (where the oxygen is for reaction) an R group (which differentiates the different amino acid and thereby function) amino group (H3N+ that's where hydrogen is for reactions) and a carbon group (center alpha carbon) and hydrogen attached to alpha carbon When two amino acids bond by hydroxyl it's called a peptide bond

Nucleic acid monomers

8 different nucleotides used to make DNA and RNA 4 for each DNA (hydrogen) RNA (hydroxyl) Each have phosphate group and OH on third carbon

a chemical reaction involves breaking and forming chemical bonds. Describe a chemical reaction and example how does it apply to biology

A chemical reaction involves breaking and forming chemical bonds. The chemical bonds that link atoms in molecules can change in a chemical reaction, a process by which atoms or molecules, called reactants, are transformed into different molecules, called products. During a chemical reaction, atoms keep their identity but change which atoms they are bonded to. For example, two molecules of hydrogen gas (2H2) and one molecule of oxygen gas (O2) can react to form two molecules of water (2H2O), as shown in Fig. 2.9. In this reaction, the numbers of each type of atom are conserved, but their arrangement is different in the reactants and the products. Specifically, the H—H bond in hydrogen gas and the O═O bond in oxygen are broken. At the same time, each oxygen atom forms new covalent bonds with two hydrogen atoms, forming two molecules of water. In fact, this reaction is the origin of the word "hydrogen," which literally means "water former." The reaction releases a good deal of energy and is used in some rockets as a booster in satellite launches. In biological systems, chemical reactions provide a way to build and break down molecules for use by the cell, as well as to harness energy, which can be held in chemical bonds

nonpolar covalent bonds

A covalent bond between atoms that have the same, or nearly the same, electronegativity is described as a nonpolar covalent bond, which means that the atoms share the bonding electron pair almost equally. Nonpolar covalent bonds include those in gaseous hydrogen (H2) and oxygen (O2), as well as carbon-carbon (C—C) and carbon-hydrogen (C—H) bonds. Molecules held together by nonpolar covalent bonds are important in cells because they do not mix well with water.

What are the differences between covalent bonds and polar covalent, hydrogen, and ionic bonds?

A covalent bond is present when two atoms share their valence electrons (the electrons in the outermost orbital of an atom). Each shared pair of valence electrons makes a covalent bond depicted by a single line connecting the two chemical symbols for the atoms. A polar covalent bond is present when the valence electrons are not shared equally by the two atoms, thus giving areas of the molecule a positive or negative charge. A hydrogen bond forms when a hydrogen atom that is covalently bound to an electronegative atom (giving the hydrogen a partial positive charge) interacts with an electronegative atom of another molecule. A hydrogen bond is typically depicted by a dotted line connecting the two chemical symbols for the atoms. An ionic bond is formed by the attraction between a molecule that has a positive charge (due to the Joss of one electron) and a molecule that has a negative charge (due to the gain of one electron). The two molecules are not covalently bound, but they associate with each other due to their opposite charges

Polar covalent bonds

A covalent bond where electrons are not shared equally between the two atoms. This creates a condition where one atom is slightly positive and one is slightly negative. The resulting positive and negative charges can act like ionic bonds ands interact with oppositely charged Atoms. Classic example is H2O Oxygen slightly pulls more share of electron so it's slightly negative snd leaves hydrogens slightly positive

polar covalent bond example

A polar covalent bond is characterized by unequal sharing of electrons. In hydrogen gas (H2), the electrons are shared equally by the two hydrogen atoms. In many bonds, however, the electrons are not shared equally by the two atoms. A notable example is the bonds in a water molecule (H2O): it consists of two hydrogen atoms, each of which covalently bound to a single oxygen atom

describe the simplest chain of carbons (covalently bonded)

Among the simplest chains is ethane, shown in Fig. 2.14a. Ethane forms when two carbon atoms become connected by a covalent bond. In this case, the orbitals of unpaired electrons in two carbon atoms form the covalent bond. Each carbon atom is also bound to three hydrogen atoms.

ionic bond forms

An ionic bond forms between oppositely charged ions. an atom of very high electronegativity is paired with an atom of very low electronegativity, the difference in electronegativity is so great that the electronegative atom "steals" the electron from its less electronegative partner. In this case, the atom with the extra electron has a negative charge and is a negative ion. The atom that has lost an electron has a positive charge and is a positive ion. The two ions are not covalently bound, but because opposite charges attract, they associate with each other in an ionic bond. An example of a compound formed by the attraction of a positive ion and a negative ion is sodium chloride (NaCl), commonly known as table salt

hydrophillic compounds are

Attracted to water- polar, dissolve readily in water

Water

Because it is polar covalent and prove it went everywhere much of biological molecules interact with and in water. Positive charges and water interact with negative charges on proteins. Negative charges and water interactive positive charges on protein. This is the same for lipids, nucleic acids, and carbohydrates as well Hydrogen bonds are the ionic bonds between water molecules

observation in scientific process biological relevance chemical relevance real world relevance

Big Question: What do we mean by observation? Scientific Process: Observation is the foundation for all science disciplines. It is the connection of the world around us to ourselves. It requires the use of one of our senses. Biological Relevance: Microscopes and all other equipment are tools designed to allow us to observe things not easily observed directly by our five senses. Chemical Relevance: The chemistry of the components of what we want to observe determine the methods used for observation. Real-World Relevance: From day one you have been using your senses to observe and make decisions about the world around you. Learning how to manipulate things so that you can "see", what was formerly not seen, will profoundly change your life

Carbon

Biological molecules/ organic It is used almost solely as a structural component. A back bone of the molecule. Important functions are built upon the back bone. Carbon has four valence electrons which means it has four electrons in the outer shell. It wants a total of eight. Therefore it can make for total bonds to other atoms. Carbon is key in biology because it is the simplest Adam that exhibits three dimensional shape before carbon on the periodic table all the other elements are linear. The structure is called a tetrahedron in the carbon atom sits at the center of a three sided pyramid Is the simplest and easiest way to build a three dimensional biological world and also is the reason why we suspect to find that all life has a carbon basis

How to read a simplified structure to know how many carbon atoms and hydrogen atoms it has

By convention, we know that at each end and each junction of the simplified structure there is a carbon atom. We also know that each carbon will have 4 covalent bonds and that if those bonds are not shown they are occupied by a hydrogen atom. This allows us to count 5 carbons and 12 hydrogens in the simplified structure in the question

Lipid monomers- fatty acid

Carboxyl group Long chain hydrocarbon with carboxyl group at one end denotes it as a fatty acid

organic molecules and their functions

Chemical processes in the cell depend on just a few classes of carbon-based molecules. Proteins provide structural support and act as catalysts that facilitate chemical reactions. Nucleic acids encode and transmit genetic information. Carbohydrates provide a source of energy and make up the cell wall in bacteria, plants, and algae. Lipids make up cell membranes, store energy, and act as signaling molecules.

Lipids phospholipids

Choline and phosphate are hydrophilic Phospholipids are hydrophobic Helps separate membranes and keep liquids out

experiments have shown how polymers could have formed in the conditions of the early Earth.

Clay minerals that form from volcanic rocks can bind nucleotides on their surfaces (Fig. 2.29a). The clays provide a surface that places the nucleotides near one another, making it possible for them to join to form chains or simple strands of nucleic acid In a classic experiment, biochemist Leslie Orgel placed a short nucleic acid sequence into a reaction vessel and then added individual chemically modified nucleotides. The nucleotides spontaneously joined into a polymer, forming the sequence complementary to the nucleic acid already present (Fig. 2.29b). Such experiments show that nucleic acids can be synthesized experimentally from nucleotides, but until recently the synthesis of nucleotides themselves presented a formidable problem for researchers seeking to uncover the origins of life. Many researchers tried to generate nucleotides from their sugar, base, and phosphate components, but no one succeeded until 2009. That year, John Sutherland and his colleagues showed that nucleotides can be synthesized under conditions thought to resemble those on the young Earth. These chemists showed how simple organic molecules likely to have formed in abundance on the early Earth react in the presence of phosphate molecules, yielding the long-sought nucleotides.

correct order of steps to view a specimen at 40X (400 magnification)

Click power switch to turn on light Adjust light to appropriate brightness Focus at 4X using coarse focus knob Adjust ocular lenses to view one image Focus using fine focus knob Adjust the stage to move the star to the center of microscope view Put 10X objective in place Focus using fine focus knob Put 40X objective in place Adjust using fine focus knob

Carbohydrate monomer

Each carbon has a hydrogen and I hydroxyl ( H & an OH) One carbon has a double bond oxygen. Location of double bonds in orientation of hydroxyl creates different carbohydrates that have different properties Very diverse, (second to fat)

Molecules stability occurs when

Each orbital is filled One atom shares with another for instance to hydrogen gas may come together so that they have for outer most shell's. A carbon has only two atoms in its outer most shell and so it needs four more to be happy. It may fill this with for hydrogen since each hydrogen has one atom there by fulfilling the hydrogen's desire for one more Adam and also for filling carbons desire for four more atoms. That creates methane and it is a stable molecule

electronegativity on the periodic table

Electronegativity tends to increase across a row in the periodic table; as the number of positively charged protons across a row increases, negatively charged electrons are held more tightly to the nucleus. Therefore, oxygen is more electronegative than hydrogen and attracts electrons more readily than does hydrogen. In a molecule of water, oxygen has a slight negative charge, while the two hydrogen atoms have a slight positive charge

periodic table organization (general, horizontal, and vertical)

Elements are arranged by increasing number of protons, the atomic number. The elements in a column share similar chemical properties. In the periodic table, the elements are indicated by their chemical symbols and arranged in order of increasing atomic number. For the first three horizontal rows in the periodic table, elements in the same row have the same number of shells, so they also have the same number and types of orbitals available to be filled by electrons. Across a row, therefore, electrons fill the shell until a full complement of electrons is reached on the right-hand side of the table. The elements in a vertical column are called a group or family. Members of a group all have the same number of electrons in their outermost shell. For example, carbon (C) and lead (Pb) both have four electrons in their outermost shell. The number of electrons in the outermost shell determines in large part how elements interact with other elements to form a diversity of molecules, as we will see in the next section.

Hydrogen and helium are far and away the most abundant elements in the universe. In contrast, the solid Earth is dominated by ________________________________. In other words, Earth is not a typical sample of the universe

Hydrogen and helium are far and away the most abundant elements in the universe. In contrast, the solid Earth is dominated by silicon, oxygen, aluminum, iron, and calcium (Chapter 1). In other words, Earth is not a typical sample of the universe

Hydrogen bonds are much ______than covalent bonds

Hydrogen bonds are much weaker than covalent bonds, but it is hydrogen bonding that gives water many interesting properties, described next. In addition, the presence of many weak hydrogen bonds can help stabilize biological molecules, as in the case of nucleic acids and proteins

Difference between covalent bonds in water and hydrogen bond

Hydrogen bonds are the ionic bonds between water molecules (not sharing). Covalent bonds are the bonds in the molecule

immersion oil is used

Immersion oil can only be used with the 100X objective lens. The oil must be properly removed before using the 4X, 10X, or 40X objectives lenses. Your instructor may have a different specific protocol for cleaning the microscope objective lens and the slide than presented in this simulation.

In a sequence of two nucleotides, the number of possible combinations is _______________ For six nucleotides, _____________

In a sequence of two nucleotides, the number of possible combinations is 4 × 4 = 16 = 42. For six nucleotides, 46 = 4,096

In any solution of water, a small proportion of the water molecules exist as protons (H+) and hydroxide ions (OH−). The pH of a solution measures the __________concentration ([H+]), which is important because the pH influences many chemical reactions and biological processes. It is calculated by the following formula: pH=______________. describe pH scale and water's pH

In any solution of water, a small proportion of the water molecules exist as protons (H+) and hydroxide ions (OH−). The pH of a solution measures the proton concentration ([H+]), which is important because the pH influences many chemical reactions and biological processes. It is calculated by the following formula: pH=−log[H+] The pH of a solution can range from 0 to 14. Since the pH scale is logarithmic, a difference of one pH unit corresponds to a tenfold difference in hydrogen ion concentration. A solution is neutral (pH=7) when the concentrations of protons (H+) and hydroxide ions (OH−) are equal. When the concentration of protons is higher than that of hydroxide ions, the pH is lower than 7 and the solution is acidic. When the concentration of protons is lower than that of hydroxide ions, the pH is higher than 7 and the solution is basic. In turn, an acid can be described as a molecule that releases a proton (H+), and a base is a molecule that accepts a proton in aqueous solution. Pure water has a pH of 7—that is, it is neutral, with an equal concentration of protons and hydroxide ions. The pH of most cells is approximately 7 and is tightly regulated, as most chemical reactions can be carried out only in a narrow pH range. Certain cellular compartments, however, have a much lower pH. The pH of blood is slightly basic, with a pH around 7.4. This value is sometimes referred to in medicine as physiological pH. Freshwater lakes, ponds, and rivers tend to be slightly acidic because carbon dioxide from the air dissolves in the water and forms carbonic acid

where on the periodic table do you find an atom with high electronegativity

It will most likely be located near the right-most side of the periodic table of elements.

How do we know How many bonds an element can make with other elements?

Look at how many balance electrons are in the outer shell and what the potential filling is and subtract (8 total possible - 4 current = 4 possible bonds with others)

Non polar covalent bonds

Many nonpolar covalent bonds are used to create the back bone structure of molecules. Others are used to attach additional items that do the work of the molecule When hydrogen gases add to carbon it makes methane so that all the hydrogens have full shells and so does carbon Carbon is the essential core to molecules in organic molecules

Hydrophilic versus hydrophobic bi layer of phospholipids

Membrane protects inside and outside from liquid

The hydrogen bonds of water also influence how water responds to heating. describe

Molecules are in constant motion, and this motion increases as the temperature increases. When water is heated, some of the energy added by heating is used to break hydrogen bonds instead of causing more motion among the molecules. As a consequence, the temperature increases less in these situations than if there were no hydrogen bonding. The abundant hydrogen bonds make water more resistant to temperature changes than other substances, a property that is important for living organisms on a variety of scales. In the cell, water resists temperature variations that would otherwise result from numerous biochemical reactions. On a global scale, the oceans minimize temperature fluctuations, stabilizing the temperature on Earth in a range compatible with life

carbon atom structure and shells/orbitals

Most carbon atoms have six protons, six neutrons, and six electrons. The net charge of any atom is neutral because there are the same numbers of electrons and protons Of carbon's six electrons, two occupy the small spherical orbital representing the lowest energy level. The remaining four are distributed among four possible orbitals at the next highest energy level: one of these four orbitals is a sphere (larger in diameter than the orbital at the lowest energy level) and three are dumbbell-shaped. In carbon, the outermost spherical orbital has two electrons, two of the dumbbell-shaped orbitals have one electron each, and one of the dumbbell-shaped orbitals is empty. Because a full orbital contains two electrons, it would take a total of four additional electrons to completely fill all of the orbitals at this energy level. Therefore, after the first shell, the maximum number of electrons per energy level is eight

Moving one position from left to right in the periodic table of elements adds _______________, _______________, _______________.

Moving one position from left to right in the periodic table of elements adds one proton, one neutron, and one electron.

hydrophobic compounds are

Nonpolar compounds that do not dissolve well in water and are repelled from water.

atomic mass and isotopes

Number of protons and neutrons The number of neutrons in atoms of a particular element can differ, changing its mass. Isotopes are atoms of the same element that have different numbers of neutrons. For example, carbon has three isotopes: approximately 99% of carbon atoms have six neutrons and six protons, for an atomic mass of 12; approximately 1% have seven neutrons and six protons, for an atomic mass of 13; and only a very small fraction have eight neutrons and six protons, for an atomic mass of 14. The atomic mass is sometimes indicated as a superscript to the left of the chemical symbol. For instance, 12C is the isotope of carbon with six neutrons and six protons.

Generally Covalent bonds

Occur by sharing of electrons between two atoms. These items are physically attached. Very strong bonds. (Two hydrogen atoms share an electron to make both shells full)

Ionic bonds

Occurs when one atom gives up completely an electron and one gains in electron. Association after exchange is through the difference in charge not anything to do with the physical electron These bonds are found in all biological molecules and always have some role in function Enzyme (Sodium chloride sodium gets rid of extra electron to gain full orbital, and chlorine receives that electron to gain full orbital and together sodium ion and chloride ion interact with each other bc of the charges on the molecules not because of sharing an electron )

Carbon atoms form four covalent bonds. discuss the structural makeup/diversity of carbon-based molecules

One of the special properties of carbon is that, in forming molecular orbitals, a carbon atom behaves as if it had four unpaired electrons. This behavior occurs because one of the electrons in the outermost spherical orbital moves into the empty dumbbell-shaped orbital (see Fig. 2.2). In this process, the single large spherical orbital and three dumbbell-shaped orbitals change shape, becoming four equivalent hybrid orbitals, each with one electron. Fig. 2.13 shows the molecular orbitals that result when one atom of carbon combines with four atoms of hydrogen to form the gas methane (CH4). Each of the four valence electrons of carbon shares a new molecular orbital with the electron of one of the hydrogen atoms. These bonds can rotate freely about their axis. Furthermore, because of the shape of the orbitals, the carbon atom lies at the center of a three-dimensional structure called a tetrahedron, and the four molecular orbitals point toward the four corners of this structure. The ability of carbon to form four covalent bonds, the spatial orientation of these bonds in the form of a tetrahedron, and the ability of each bond to rotate freely all contribute in important ways to the structural diversity of carbon-based molecules

polar vs non polar hydrophillic/hydrophobic

Polar molecules tend to interact with other polar molecules, whereas nonpolar molecules tend not to interact with polar molecules. Therefore molecules, or even different regions of the same molecule, can be organized into two general classes, depending on how they interact with water: hydrophilic ("water loving") and hydrophobic ("water fearing"). Hydrophilic compounds are polar; they dissolve readily in water. That is, water is a good solvent, capable of dissolving many substances. Think of what happens when you stir a teaspoon of sugar into water: the sugar seems to disappear as it dissolves. The sugar molecules disperse through the water and separate from one another, forming a solution in the watery, or aqueous, environment. By contrast, hydrophobic compounds are nonpolar. Nonpolar compounds do not have regions of positive and negative charge, so they arrange themselves to minimize their contact with water. For example, oil molecules are hydrophobic. Thus, when oil and water are mixed, the oil molecules organize themselves into droplets that limit the oil-water interface. This hydrophobic effect, in which polar molecules like water exclude nonpolar ones, drives such biological processes as the folding of proteins (Chapter 4) and the formation of cell membranes (

If Water wasn't partially charged on the hydrogen and oxygen then what state will it remain in?

Steam. But because there is a slight charge on the oxygen and hydrogen's it can be liquid. The slower the molecules move the more they interact and more bonds made

field of view total magnification

The microscope you are using has four objective lenses to magnify the image: 4X, 10X, 40X, and 100X. When focusing on a slide, start on the scanning, or low power, objective lens. The lower the power objective, the greater the field of view. The field of view is the amount of the slide you are able to see through the eyepiece. Total magnification is the overall enlargement of the image of a specimen. To calculate total magnification, multiply the magnification of the ocular lens (10X) with the magnification of the objective lens. Often what you want to visualize is not in the middle of the field of view and you must move the slide around to find what you want to study. To move the slide, you move the stage. As you look at the microscope the stage knob on the top moves the stage forward and back. The stage knob on the bottom moves the stage side to side. Additional adjustments to the microscope can be made regarding lighting. These fine adjustments will not be addressed in this simulation.As magnification of the image increases, the light intensity decreases and will have to be adjusted.The condenser lens focuses the light on the slide The sliding bar on the condenser lens is the aperture. As you move the aperture to decrease the light to the slide, the contrast increases. As you move the aperture to increase the light to the slide, the contrast decreases

atomic number/ identifying an element

The number of protons, or the atomic number, specifies an atom as a particular element. An atom with one proton is hydrogen, for example, and an atom with six protons is carbon.

orbitals and shells

The orbital of an electron can be visualized as a cloud of points that is denser where the electron is more likely to be. The hydrogen atom contains a single orbital, in a single energy level (a and c). The carbon atom has five orbitals, one in the first energy level and four in the second energy level (b and c). In the second energy level, electrons in the spherical orbital have slightly less energy than those in the dumbbell-shaped orbitals.

functional groups

The simple repeating units of polymers are often based on a nonpolar core of carbon atoms. Attached to these carbon atoms are functional groups, groups of one or more atoms that have particular chemical properties on their own, regardless of what they are attached to. Among the functional groups frequently encountered in biological molecules are amine (═NH), amino (—NH2), carboxyl (—COOH), hydroxyl (—OH), ketone (═O), phosphate (—O—PO3H2), sulfhydryl (—SH), and methyl (—CH3). The nitrogen, oxygen, phosphorus, and sulfur atoms in these functional groups are more electronegative than the carbon atoms, and functional groups containing these atoms are polar. The methyl group (—CH3), in contrast, is nonpolar. Because many functional groups are polar, molecules that contain these groups—molecules that would otherwise be nonpolar—become polar. As a result, these molecules become soluble in the cell's aqueous environment. In other words, they disperse in solution throughout the cell. Moreover, because many functional groups are polar, they are reactive. Notice in the following sections that the reactions joining simpler molecules into polymers usually take place between functional groups.

composition of main five organic molecules

These molecules are all large, consisting of hundreds or thousands of atoms, and many are polymers, complex molecules made up of repeated simpler units connected by covalent bonds. Proteins are polymers of amino acids, nucleic acids are polymers of nucleotides, and carbohydrates such as starch are polymers of simple sugars. Lipids are a bit different, as we will see, in that they are defined by a property rather than by their chemical structure. The lipid membranes that define cell boundaries consist of fatty acids bonded to other organic molecules.

describe the difference found in double bonds

Two adjacent carbon atoms can also share two pairs of electrons, forming a double bond, as shown in Fig. 2.15. Note that each carbon atom has exactly four covalent bonds, but in this case two are shared between adjacent carbon atoms. The double bond is shorter than a single bond and is not free to rotate, so all of the covalent bonds formed by the carbon atoms connected by a double bond are in the same geometrical plane. As with single bonds, double bonds can be found in chains of atoms or ring structures.

ions

Typically, an atom has the same number of protons and electrons. Because a carbon atom has six protons and six electrons, the positive and negative charges cancel each other out and the carbon atom is electrically neutral. Some chemical processes cause an atom to either gain or lose electrons. An atom that has lost an electron is positively charged, and one that has gained an electron is negatively charged. Electrically charged atoms are called ions. The charge of an ion is specified as a superscript to the right of the chemical symbol. Thus, H+ indicates a hydrogen ion that has lost an electron and is positively charged

why are electrons more attracted to the oxygen atom in water than the hydrogen atoms the result is that the oxygen atom has a slight _______ charge and the hydrogen atoms have slight _______ charge the slight negative charge on one water molecule will attract what? This results in?

because oxygen is more electronegative than hydrogen negative, positive a slight positive charge on another. The slight negative charge of the oxygen on one water molecule bonds to the slight positive hydrogen atom on another water molecule, and results in a hydrogen bond

Chemistry is the foundation of

biology physics underlies chemistry, chemistry underlies biology

If present in a molecule, which atom is least likely to participate in hydrogen bonds with water? oxygen nitrogen carbon hydrogen sulfur

carbon (is positively charged, the rest are negative)

chemical analyses of Earth's oldest sedimentary rocks indicate that, for the first 2 billion years of our planet's history, Earth's surface contained little or no

chemical analyses of Earth's oldest sedimentary rocks indicate that, for the first 2 billion years of our planet's history, Earth's surface contained little or no oxygen.

on a microscope, ___________ can be altered by light intensity and staining.

contrast

in a water atom, one oxygen is __________ bonded to two hydrogen atoms

covalently

Molecules that have the same chemical formula but different structures are known as _____________ describe.

isomers While the types of atoms making up a molecule help characterize the molecule, the spatial arrangement of atoms is also important. For example, 6 carbon atoms, 13 hydrogen atoms, 2 oxygen atoms, and 1 nitrogen atom can join covalently in many different arrangements to produce molecules with different structures. Two of these many arrangements are shown in Fig. 2.16. Note that some of the connections between atoms are identical in the two molecules (black) and some are different (green), even though the chemical formulas are the same (C6H13O2N1).

What else is necessary in order for a hydrogen atom in a molecule to participate in a hydrogen bond?

it must be bonded to a more electronegative atom

just four elements—________________________________________________________—account for approximately 90% of the total dry mass on earth, and that the most abundant element is _____________.

just four elements—carbon (C), oxygen (O), hydrogen (H), and nitrogen (N)—account for approximately 90% of the total dry mass, and that the most abundant element is carbon.

What is a polymer?

long chain of monomers

Organic molecules

molecules that contain carbon Synthesis of polymers which is multiple monomers, occurs by dehydration or condensation reaction Condensation reaction- a monomer has to have a covalent lyk bonded hydrogen and hydroxyl (h and Ho +h and Ho add enzyme yields a waste product of water and yields a result of H and Ho) Hydration is the opposite order True for all major organic molecules

Hydrogen bonds also give water molecules the property of cohesion, meaning

that they tend to stick to one another. A consequence of cohesion is high surface tension, a measure of the difficulty of breaking the surface of a liquid. Cohesion between molecules contributes to water movement in plants. As water evaporates from leaves, water is pulled upward through the plant's vessels. Sometimes this water may rise as high as 100 meters above the ground in giant sequoia and coast redwood trees, which are among the tallest trees on Earth

in liquid water the hydrogen bonds constantly form and break as water molecules move around due to the result is a dense network of water molecules held together by the dynamic forming and breaking of ' as water freezes and becomes ice, thermal motion is reduced and more stable hydrogen bonds form. Each water molecule typically forms hydrogen bonds with _________other water molecules disable hydrogen bonds form a crystalline lattice like structure that is highly ordered but less ______than liquid water this is why ice floats on water and therefore why aquatic plants and animals are able to survive winter under a layer of ice

thermal energy in the environment hydrogen bonds four dense

True or false The maximum number of electrons in any orbital is two Several orbitals can exist at a given energy level, or shell.

true

The power of compound light microscopy results from its ability to: In addition to the compound light microscope, scientists use dissecting microscopes and electron microscopes. While electron microscopes are excellent for resolving very small structures like organelles, they have several disadvantages:

view small living and non-living objects use colored dyes to differentiate between different cell types, organelles or molecules that make up a cell or organelle use wavelengths of light that we can see with our eyes use visible light that can be transmitted through thin sections of aqueous material (all life is water based) expensive to maintain and purchase extensive experience is needed to prepare the tissue samples cannot detect colors cannot be used to observe live organisms (water needs to be removed before viewing in electron microscopy)