CH.2 : THE CHEMICAL LEVEL OF ORGANIZATION Flashcards
What is chemistry?
the science of the structure and interactions of matter.
All living and nonliving things consist of ___, which is anything that occupies space and has ____.
matter, mass
Explain mass.
the amount of matter in any object, which does not change.
Explain weight.
the force of gravity acting on matter, does change.
Matter exists in three states, what are they?
solid, liquid, and gas.
Explain solids and give an example in the body
Solids, such as bones and teeth, are compact and have a definite shape and volume.
Explain liquids and give an example in the body
such as blood plasma, have a definite volume and assume the shape of their container.
Explain gases and give an example in the body
like oxygen and carbon dioxide, have neither a definite shape nor volume.
All forms of matter—both living and nonliving—are made up of a limited number of building blocks called ___ ____
chemical elements.
Just four elements, called the major elements, constitute about 96% of the body’s mass. What are they?
oxygen, carbon, hydrogen, and nitrogen.
Eight others, the lesser elements, contribute about 3.6% to the body’s mass. What are they?
calcium, phosphorus (P), potassium (K), sulfur (S), sodium, chlorine (Cl), magnesium (Mg), and iron (Fe).
An additional 14 elements—the ____ _____ —are present in tiny amounts.
trace elements
Each element is made up of?
atoms
What are the three types of subatomic particles important for understanding the chemical reactions in the human body?
protons, neutrons, and electrons
The dense central core of an atom is its ___
nucleus
Where are the protons, neuron and electrons located?
- Within the nucleus are positively charged protons and uncharged (neutral) neutrons
- The tiny, negatively charged electrons move about in a large space surrounding the nucleus. They do not follow a fixed path or orbit but instead form a negatively charged “cloud” that envelops the nucleus
Explain the ordering of electron shells.
The first electron shell (nearest the nucleus) never holds more than 2 electrons. The second shell holds a maximum of 8 electrons, and the third can hold up to 18 electrons.
The number of electrons in an atom of an element always equals the number of ___
protons
What is an atomic number?
The number of protons in the nucleus of an atom is an atom’s atomic number
What is the mass number of an atom?
the sum of its protons and neutrons.
What are isotopes?
- atoms of an element that have different numbers of neutrons and therefore different mass numbers.
- stable
Explain radioactive isotopes.
they are unstable; their nuclei decay (spontaneously change) into a stable configuration.
What is the half-life of an isotope?
-the time required for half of the radioactive atoms in a sample of that isotope to decay into a more stable form
Some radioisotopes can be used as _____ to follow the movement of certain substances through the body
tracers
What is the standard unit for measuring the mass of atoms and their subatomic particles?
- a dalton, also known as an atomic mass unit (amu)
What is the atomic mass/ atomic weight of an element?
- the average mass of all its naturally occurring isotopes
What is an ion?
-an atom that has a positive or negative charge
Explain ionization.
process of giving up or gaining electrons.
When two or more atoms share electrons, the resulting combination is called a _____
molecule
What is a molecular formula?
indicates the elements and the number of atoms of each element that make up a molecule.
What is a compound? Give an example in the body.
- a substance that contains atoms of two or more different elements.
- Water (H2O)
A molecule of oxygen (O2) is not a compound. True or False
True, because it consists of atoms of only one element.
What is a free radical? Give an example
- an atom or group of atoms with an unpaired electron in the outermost shell
- superoxide, which is formed by the addition of an electron to an oxygen molecule
What do antioxidants do?
-substances that inactivate oxygen-derived free radicals
What are chemical bonds?
The forces that hold together the atoms of a molecule or a compound
The likelihood that an atom will form a chemical bond with another atom depends on the number of electrons in its outermost shell, also called the ____ ____
valence shell
Explain the octet rule.
- The atoms of most biologically important elements do not have 8 electrons in their valence shells.
- two or more atoms can interact in ways that produce a chemically stable arrangement of 8 valence electrons for each atom.
- atom either empties its partially filled valence shell, fills it with donated electrons, or shares electrons with other atoms.
What are the three types of chemical bonds?
ionic bonds, covalent bonds, and hydrogen bonds
What is an ionic bond?
The force of attraction that holds together ions with opposite charges
What are cations and anions?
positively and negatively charged ions
What is an electrolyte?
An ionic compound that breaks apart into positive and negative ions in solution
Explain covalent bonds.
When a covalent bond forms, two or more atoms share electrons rather than gaining or losing them
Explain a single covalent bond. Give an example
- results when two atoms share one electron pair.
- For example, a molecule of hydrogen forms when two hydrogen atoms share their single valence electrons which allows both atoms to have a full valence shell at least part of the time
Explain a double covalent bond. Give an example
- results when two atoms share two pairs of electrons, as happens in an oxygen molecule
Explain a triple covalent bond. Give an example
-occurs when two atoms share three pairs of electrons, as in a molecule of nitrogen
What is a nonpolar covalent bond?
- two atoms share the electrons equally—one atom does not attract the shared electrons more strongly than the other atom.
The bonds between two identical atoms are always what type of chemical bonds?
nonpolar covalent bonds
Explain a polar covalent bond.
-the sharing of electrons between two atoms is unequal—the nucleus of one atom attracts the shared electrons more strongly than the nucleus of the other atom.
What is electronegativity?
the power to attract electrons
Explain hydrogen bonds.
- forms when a hydrogen atom with a partial positive charge attracts the partial negative charge of neighbouring electronegative atoms, most often larger oxygen or nitrogen atoms.
- result from attraction of oppositely charged parts of molecules
- these bonds are weak, cannot bind atoms into molecules but important in linking molecules
The hydrogen bonds that link neighbouring water molecules give water considerable ___ , the tendency of like particles to stay together.
cohesion
The cohesion of water molecules creates a very high _____ ____ , a measure of the difficulty of stretching or breaking the surface of a liquid.
surface tension
When does a chemical reaction occur?
-when new bonds form or old bonds break between atoms.
What are reactants and products?
-in chemical reactions, reactants are the starting substances and products are the ending substances
What is energy, what are the two different forms of it and explain them?
- capacity to do work
- potential : energy stored by matter due to its position
- kinetic: the energy associated with matter in motion.
What is chemical energy?
-a form of potential energy that is stored in the bonds of compounds and molecules.
Explain the law of conservation of energy.
-Although energy can be neither created nor destroyed, it may be converted from one form to another
What happens in an exergonic reaction?
- release more energy than they absorb.
What happens in an endergonic reaction?
-absorb more energy than they release
What is the activation energy of a reaction?
The collision energy needed to break the chemical bonds of the reactants
What influences the chance that a collision will occur and cause a chemical reaction?
- Concentration: The more particles of matter present in a confined space, the greater the chance that they will collide
- As temperature rises, particles of matter move about more rapidly.
What do catalysts do? Which ones are the most important in our bodies?
- chemical compounds that speed up chemical reactions by lowering the activation energy needed for a reaction to occur
- enzymes
Describe a synthesis reaction. All the synthesis reactions that occur in your body are collectively referred to as ____
When two or more atoms, ions, or molecules combine to form new and larger molecules
-anabolism
Explain decomposition reactions. The decomposition reactions that occur in your body are collectively referred to as ____
split up large molecules into smaller atoms, ions, or molecules
-catabolism
Describe exchange reactions.
they consist of both synthesis and decomposition reactions
Explain reversible reactions.
- the products can revert to the original reactants.
- some need catalysts (under certain conditions)
Explain oxidation.
refers to the loss of electrons, and in the process the oxidized substance releases energy.
Explain reduction.
refers to the gain of electrons, and in the process the reduced substance gains energy
What are inorganic compounds?
- usually lack carbon and are structurally simple.
- Their molecules also have only a few atoms and cannot be used by cells to perform complicated biological functions.
- include water and many salts, acids, and bases.
- may have either ionic or covalent bonds
What are organic compounds?
- always contain carbon, usually contain hydrogen, and always have covalent bonds.
- Most are large molecules and many are made up of long chains of carbon atoms.
- carbs, lipids
What is the most important and abundant inorganic compound in all living systems?
water
In a solution, a substance called the____ dissolves another substance called the ____
solvent, solute
What does it mean if solutes are hydrophilic? Give examples
Solutes that are charged or contain polar covalent bonds are hydrophilic
-sugar and salt
What does it mean if solutes are hydrophobic? Give examples
Molecules that contain mainly nonpolar covalent bonds
- animal fats and vegetable oils
What is a hydrolysis reaction?
-decomposition reactions break down large molecules into smaller molecules by the addition of water molecules.
What is a dehydration synthesis reaction?
-when two smaller molecules join to form a larger molecule and a water molecule is one of the products formed.
What is a colloid?
- differs from a solution mainly because of the size of its particles.
- The solute particles in a colloid are large enough to scatter light
- For this reason, colloids usually appear translucent or opaque.
What is a suspension? Give an example.
- the suspended material may mix with the liquid or suspending medium for some time, but eventually it will settle out.
- Blood is an example of a suspension.
Name the different ways to measure concentration and explain them.
- by a mass per volume percentage, which gives the relative mass of a solute found in a given volume of solution.
- moles per liter (mol/L), which relate to the total number of molecules in a given volume of solution.
- mole is the amount of any substance that has a mass in grams equal to the sum of the atomic masses of all its atoms.
What is Avogadro’s number?
- a mole of anything has the same number of particles: 6.023 x 10^23.
When inorganic acids, bases, or salts dissolve in water, they dissociate which means?
they separate into ions and become surrounded by water molecules.
What is an acid? (also know as proton donor)
-substance that dissociates into one or more hydrogen ions (H) and one or more anions.
What is a base? (also know as proton acceptor)
- removes H from a solution
- Many bases dissociate into one or more hydroxide ions (OH) and one or more cations.
What happens when a salt is dissolved water?
-when dissolved in water, dissociates into cations and anions, neither of which is H or OH
A solution’s acidity or alkalinity is expressed on the __ ____, which extends from 0 to 14
pH scale
The pH scale is based on what? A solution that has more H than OH is an ___ solution and has a pH below 7. A solution that has more OH than H is a ___ (____) solution and has a pH above 7.
- concentration of H in moles per liter.
- acidic
- basic (alkaline)
What do buffer systems do?
function to convert strong acids or bases into weak acids or bases. -They do so by removing or adding protons
Explain the carbonic acid–bicarbonate buffer system.
Carbonic acid (H2CO3) can act as a weak acid, and the bicarbonate ion (HCO3) can act as a weak base. Hence, this buffer system can compensate for either an excess or a shortage of protons.
The chain of carbon atoms in an organic molecule is called the ___ _____. Many of the carbons are bonded to hydrogen atoms, yielding a ________. Also attached to the carbon skeleton are distinctive ____ ______, other atoms or molecules bound to the hydrocarbon skeleton.
carbon skeleton, hydrocarbon, functional groups
What are macromolecules?
Small organic molecules can combine into very large molecules
What is a polymer?
-large molecule formed by the covalent bonding of many identical or similar small building-block molecules called monomers
What are isomers?
Molecules that have the same molecular formula but different structures
What are carbohydrates? What are the 3 main types?
- include sugars, glycogen, starches, and cellulose.
- In humans and animals, they function as a source of chemical energy for generating ATP needed to drive metabolic reactions.
- Only a few are used for building structural units.
- 3 types: monosaccharides, disaccharides, and polysaccharides
Monosaccharides and disaccharides are known as ___ ____
simple sugars
What are monosaccharides?
- The monomers of carbohydrates
- contain from three to seven carbon atoms.
- designated by names ending in “-ose” with a prefix that indicates the number of carbon atoms.
What is a disaccharide?
a molecule formed from the combination of two monosaccharides by dehydration synthesis
What are polysaccharides? Name three types and explain them.
- Each polysaccharide molecule contains tens or hundreds of monosaccharides joined through dehydration synthesis reactions
- glycogen, which is made entirely of glucose monomers linked to one another in branching chains
- Starches are formed from glucose by plants.
- Cellulose is formed from glucose by plants that cannot be digested by humans but does provide bulk to help eliminate feces
What are lipids?
- contain carbon, hydrogen, and oxygen.
- The proportion of electronegative oxygen atoms in lipids is usually smaller than in carbohydrates, so there are fewer polar covalent bonds.
- hydrophobic
How do lipid molecules become more soluble in blood plasma?
- join with hydrophilic protein molecules.
- The resulting lipid/protein complexes are termed lipoproteins.
- Lipoproteins are soluble because the proteins are on the outside and the lipids are on the inside.
The diverse lipid family includes:
-fatty acids, triglycerides, phospholipids, steroids, eicosanoids, and a variety of other lipids, including fat-soluble vitamins and lipoproteins.
Among the simplest lipids are the fatty acids, which are used to do what? Fatty acids can also be catabolized to generate ____ ____.
synthesize triglycerides and phospholipids.
-adenosine triphosphate (ATP)
A fatty acid consists of what?
-a carboxyl group and a hydrocarbon chain
Describe a saturated fatty acid.
- contains only single covalent bonds between the carbon atoms of the hydrocarbon chain.
- Because they lack double bonds, each carbon atom of the hydrocarbon chain is saturated with hydrogen atoms
Describe an unsaturated fatty acid.
- contains one or more double covalent bonds between the carbon atoms of the hydrocarbon chain
- has a kink (bend) at the site of the double bond
What is a monounsaturated fatty acid?
- If the fatty acid has just one double bond in the hydrocarbon chain, it is monounsaturated and it has just one kink.
What is a polyunsaturated fatty acid?
If a fatty acid has more than one double bond in the hydrocarbon chain, it is polyunsaturated and it contains more than one kink
What is a triglyceride?
- consists of a single glycerol molecule and three fatty acid molecules.
A 3-carbon glycerol molecule forms the backbone of a triglyceride. Three fatty acids are attached by dehydration synthesis reactions, one to each carbon of the glycerol backbone. The chemical bond formed where each water molecule is removed is called what?
ester linkage
What is a fat?
- a triglyceride that is a solid at room temperature
What is a saturated fat?
-A fat that mainly consists of saturated fatty acids
What is an oil?
- a triglyceride that is a liquid at room temperature
The kinks at the sites of the ___ ____ prevent the unsaturated fatty acids of an oil from closely packing together and solidifying.
double bonds
What are monounsaturated fats? Name a few.
- contain triglycerides that mostly consist of monounsaturated fatty acids.
- Olive oil, peanut oil, canola oil, most nuts, and avocados
What are polyunsaturated fats? Name a few.
- contain triglycerides that mostly consist of polyunsaturated fatty acids.
- Corn oil, safflower oil, sunflower oil, soybean oil, and fatty fish (salmon, tuna, and mackerel)
What are phospholipids?
- have a glycerol backbone and two fatty acid chains attached to the first two carbons.
- In the third position, however, a phosphate group (PO43) links a small charged group that usually contains nitrogen (N) to the backbone
Molecules that have both polar and nonpolar parts are said to be _____
amphipathic
- In phospholips, the “head” is ___ and can form ____ bonds with water molecules.
- The two fatty acids (the “tails”), by contrast, are ____ and can interact only with other lipids.
- polar, hydrogen
- nonpolar
Phospholipids are amhipathic molecules. True or False
true
Explain steroids.
- have four rings of carbon atoms
- Body cells synthesize other steroids from cholesterol
In the body, the commonly encountered steroids, such as ___, estrogens, testosterone, cortisol, bile salts, and vitamin D, are known as ___ because they also have at least one ____ (alcohol) group.
In the body, the commonly encountered steroids, such as cholesterol, estrogens, testosterone, cortisol, bile salts, and vitamin D, are known as sterols because they also have at least one hydroxyl (alcohol) group (OOH).
Another type of lipid are eicosanoids, describe them.
-lipids derived from a 20-carbon fatty acid called arachidonic acid.
The two principal subclasses of eicosanoids are what? What do they do?
- prostaglandins: modify responses to hormones, contribute to the inflammatory response, prevent stomach ulcers, dilate airways to the lungs, regulate body temp
- leukotrienes participate in allergic and inflammatory responses.
What are proteins? Name some along with their functions.
- large molecules that contain carbon, hydrogen, oxygen, and nitrogen.
- Enzymes are proteins that speed up most biochemical reactions.
- Antibodies are proteins that defend against invading microbes
What are the monomers of proteins? How many are there?
-20 amino acids
What is each amino acid made up of?
- a hydrogen (H) atom and three important functional groups attached to a central carbon atom: (1) an amino group (ONH2), (2) an acidic carboxyl group (OCOOH), and (3) a side chain (R group).
What is a peptide bond? Where does it form?
- The covalent bond joining each pair of amino acids
- It always forms between the carbon of the carboxyl group (OCOOH) of one amino acid and the nitrogen of the amino group (ONH2) of another.
- As the peptide bond is formed, a molecule of water is removed
What is a dipeptide bond? Tripeptide? chainlike peptide?Polypeptide?
- When two amino acids combine
- Adding another amino acid to a dipeptide produces a tripeptide.
- Further additions of amino acids result in the formation of a chainlike peptide (4–9 amino acids) or polypeptide (10–2000 or more amino acids).
Proteins exhibit four levels of structural organization. Name them and explain them.
1) The primary structure is the unique sequence of amino acids that are linked by covalent peptide bonds to form a polypeptide chain
2) secondary structure of a protein is the repeated twisting or folding of neighboring amino acids in the polypeptide chain
- stabilized by hydrogen bonds, which form at regular intervals along the polypeptide backbone.
3) The tertiary structure is the overall folding pattern that produces a distinctive, three-dimensional shape.
4) The quaternary structure in a protein is the arrangement of two or more polypeptide chains relative to one another
What is sickle-cell disease?
- a nonpolar amino acid (valine) replaces a polar amino acid (glutamate) through two mutations in the oxygen-carrying protein hemoglobin.
- This change diminishes hemoglobin’s water solubility.
- thus, the altered hemoglobin tends to form crystals inside RBCs, producing deformed, sickle- shaped cells that cannot properly squeeze through narrow blood vessels.
On the basis of overall shape, proteins are classified as what? (2)
- Fibrous proteins are insoluble in water and their polypeptide chains form long strands that are parallel to each other and have structural functions (for ex: collagen (strengthens bones, ligaments, and tendons))
- Globular proteins are more or less soluble in water and their polypeptide chains are spherical (globular) in shape and have metabolic functions. (ex: enzymes, which function as catalysts)
Explain denaturation.
- If a protein encounters an altered environment, it may unravel and lose its characteristic shape (secondary, tertiary, and quaternary structure). This process is called denaturation.
Some enzymes consist of two parts—a protein portion, called the ____, and a nonprotein portion, called a ___.
apoenzyme, cofactor
The cofactor of an enzyme may be a ___ ion (such as iron, magnesium, zinc, or calcium) or an organic molecule called a ____.
metal, coenzyme
Name the 3 important properties of enzymes and explain them.
1) Enzymes are highly specific. Each particular enzyme binds only to specific substrates—the reactant molecules on which the enzyme acts.
- sometimes, the part of the enzyme that catalyzes the reaction, called the active site, is thought to fit the substrate like a key fits in a lock.
- other times, the active site changes its shape which is known as induced fit
2) Enzymes are very efficient.
3) Enzymes are subject to a variety of cellular controls.
How does an enzyme work?
1) Enzyme and substrate come together at active site of enzyme, forming an enzyme–substrate complex
2) Enzyme catalyzes reaction and transforms substrate into products
3) When reaction is complete, enzyme is unchanged and free to catalyze same reaction again on a new substrate
What are nucleic acids? Name the two types and explain them.
- huge organic molecules that contain carbon, hydrogen, oxygen, nitrogen, and phosphorus.
1) deoxyribonucleic acid (DNA): forms the inherited genetic material inside each human cell.
2) Ribonucleic acid (RNA) relays instructions from the genes to guide each cell’s synthesis of proteins from amino acids.
A nucleic acid is a chain of repeating monomers called ____. Each one has 3 parts, what are they?
- nucleotides
1) Nitrogenous base. In DNA the four nitrogenous bases are adenine (A), thymine (T), cytosine (C), and guanine (G).
2) Pentose sugar. A five-carbon sugar called deoxyribose attaches to each base in DNA
3) Phosphate group. Phosphate groups (PO43) alternate with pentose sugars to form the “backbone” of a DNA strand
What are purines and pyrimidines?
- Adenine and guanine are larger, double-ring bases called purines
- thymine and cytosine are smaller, single-ring bases called pyrimidines
In the Watson–Crick double helix model, DNA resembles a spiral ladder. Explain it.
- Two strands of alternating phosphate groups and deoxyribose sugars form the uprights of the ladder.
- Paired bases, held together by hydrogen bonds, form the rungs.
- adenine always pairs with thymine, and cytosine always pairs with guanine
- Each time DNA is copied, the two strands unwind.
- Each strand serves as the template or mold on which to construct a new second strand.
What is the difference between DNA and RNA?
- RNA is single-stranded and DNA is double-stranded
- the RNA nucleotide is the pentose ribose (as oppose to deoxyribose sugar in DNA), and RNA contains the pyrimidine base uracil (U) instead of thymine.
Cells contain three different kinds of RNA, what are they?
messenger RNA, ribosomal RNA, and transfer RNA.
What is Adenosine triphosphate or ATP? What does it do and what does it consist of?
- the “energy currency” of living systems
- transfers the energy liberated in exergonic catabolic reactions to power cellular activities that require energy (endergonic reactions).
- consists of three phosphate groups attached to adenosine, a unit composed of adenine and the five-carbon sugar ribose
When a water molecule is added to ATP, the third phosphate group (PO43), is ___, and the overall reaction liberates ___.
The enzyme that catalyzes the hydrolysis of ATP is called _____. Removal of the third phosphate group produces a molecule called ____ ____ (___).
When a water molecule is added to ATP, the third phosphate group (PO43), is removed, and the overall reaction liberates energy.
The enzyme that catalyzes the hydrolysis of ATP is called ATPase. Removal of the third phosphate group produces a molecule called adenosine diphosphate (ADP)
As the supply of ATP at any given time is limited, a mechanism exists to replenish it: The enzyme ATP synthase catalyzes the addition of a ___ group to ADP
As the supply of ATP at any given time is limited, a mechanism exists to replenish it: The enzyme ATP synthase catalyzes the addition of a phosphate group to ADP
Where does the cell get the energy required to produce ATP?
The energy needed to attach a phosphate group to ADP is supplied mainly by the catabolism of glucose in a process called cellular respiration.
Cellular respiration has two phases, anaerobic and aerobic:
1) Anaerobic phase. In a series of reactions that do not require oxygen, glucose is partially broken down by a series of catabolic reactions into pyruvic acid. Each glucose molecule that is converted into a pyruvic acid molecule yields two molecules of ATP.
2. Aerobic phase. In the presence of oxygen, glucose is completely broken down into carbon dioxide and water. These reactions generate heat and 36 or 38 ATP molecules.
