unit 1.2 ap bio

amino acids,

All proteins are made up of monomers called amino acids, which bond together to form polymers called polypeptides.

Peptide bonds are

Amino acid monomers are linked together through dehydration reactions, forming covalent bonds called peptide bonds.

Starch vs. Cellulose

-Both are polysaccharides composed of glucose monomers, however ​the glycosidic linkages formed between the monomers differ. -This is due to the fact that there are two ring structures for glucose, called alpha (α) and beta (β). - In starch, all the glucose monomers are in the α configuration, while in cellulose they are all in the b configuration

Two types of nucleic acids

-DNA (deoxyribonucleic acid): Genetic material that stores information for its own replication and for the sequence of amino acids in proteins - RNA (ribonucleic acid): Perform a wide range of functions within cells which include protein synthesis and regulation of gene expression

There are two families of nitrogenous bases:

-Pyrimidines are bases with one ring and include cytosine (C), thymine (T), and uracil (U). - Purines are bases with two rings and include adenine (A), and guanine (G).

R groups fall into three main groups:

-Some are hydrophobic: do not like to interact with (touch) water. -Some are hydrophilic: like to interact with water and other polar/charged molecules. -Some are ionic: are positively or negatively charged.

denaturation.

A denatured protein is biologically inactive and does not work. ● Denature proteins can usually return to their functional structure once conditions return to normal (renaturation

Each nucleotide is composed of three parts

A phosphate group, a pentose (5-carbon) sugar, and a nitrogen-containing (nitrogenous) base.

If you located a single-stranded piece of nucleic acid in a cell, what would it be made of? A. nucleotides B. amino acids C. fatty acids D. sugars E. glycerol

A. nucleotides

Where in the structure of a protein would you most likely expect to find glutamic acid, a hydrophilic amino acid. A. on the exterior surface of the protein B. in the interior of the protein, away from water C. at the active site, binding oxygen D. at the heme-binding site E. at a site where hemoglobin binds to a negatively charged protein

A. on the exterior surface of the protein

How does RNA differ from DNA? A. DNA encodes hereditary information; RNA does not. B. DNA is made of nucleotides, RNA is not C. DNA contains thymine; RNA contains uracil. D. DNA contains five bases; RNA contains four. E. all of the above

C. DNA contains thymine; RNA contains uracil.

Which type of macromolecule serves NO structural function in organisms? A. Carbohydrates B. Lipids C. Nucleic Acids D. Proteins E. All of the above serve a structural role in organisms

C. Nucleic Acids

Enzyme Specificity

Enzymes have a specific shape and active site that only binds to a specific substrate. Thus, enzymes control very specific reactions. ● The name of an enzyme always end with the suffix "-ase" and typically refer to the substrate they bind to or the type of reaction they catalyze. ○ EX: Lactase catalyzes the hydrolysis of lactose into glucose and galactose. ○ EX: ATP Synthase catalyzes the reaction that synthesizes ATP in the cell. ● Enzymes can catalyze both the forward and reverse reactions.

Cofactors

Many enzymes require nonprotein helpers called cofactors to help them catalyze reactions. There are inorganic and organic cofactors ○ Inorganic cofactors include things such as metal ions (zinc, iron, and copper). ○ Organic cofactors, called coenzymes, include things such as vitamins. ● Enzymes only become active when all the appropriate cofactors and coenzymes are present and bind to the appropriate sites on the enzyme.

Hormonal Proteins

Many hormones are proteins that are released into the blood and regulate the activities of an organism.

Contractile and Motor Proteins:

Motor proteins help cells move and help move substances inside cells. Contractile proteins are found in muscles and are responsible for muscle contraction.

pH

The optimal pH values for most enzymes fall in the range of pH 6-8, but there are some exceptions. ● EX: Pepsin, a digestive enzyme in the stomach works best at a pH of 2. ● EX: Trypsin, a digestive enzyme in the intestines works best at a pH of 8.

Increasing Enzyme Activity

The rate of enzyme activity can be sped up by increasing the substrate concentration in a solution. ● When all enzyme molecules in a solution are bonded with substrate, the enzyme is saturated. ● At enzyme saturation, reaction speed can only be increased by adding more enzyme.

substrate.

The reactant an enzyme binds to is known as the enzyme's substrate.

active site.

The region on the enzyme where the substrate binds to is called the active site.

Amino Acids

There are 20 different amino acids. - Each has an amino group (-NH2) and an acidic carboxyl group (-COOH) connected to a central carbon atom - Amino acids differ in their properties due to different side chains, called R (or variable) groups.

Structure of Proteins

There are four levels of protein structure, which result in the final shape of a protein. ○ Primary ○ Secondary ○ Tertiary ○ Quaternary

Phospholipids

consists of one glycerol molecule linked to two fatty acids and a modified phosphate group. - The fatty acids (tails) are nonpolar and hydrophobic. - The modified phosphate group (head) is polar and hydrophilic. - Phospholipids have a structural function, being the main component of all cell membranes.

functional protein

consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape

Disaccharide

contains two monosaccharides bonded together by dehydration synthesis. -The covalent bond formed between monosaccharides is called a glycosidic linkage

Polysaccharides

is a polymer of monosaccharides (sugars). -Two main types: storage and structural -Plants and animals store sugars for later use in the form of storage polysaccharides.

Chitin

is another important structural polysaccharide use by insects and crustaceans to build their exoskeletons. It is also the building material for the cell walls found in fungi.

activation energy (EA)

is the initial amount of energy needed to start a chemical reaction. ● This energy is typically supplied in the form of heat from the surroundings.

RNA

is usually a single-stranded molecule, whereas DNA is a double-stranded molecule.

Saturated

no double bonds between carbons - Saturated fats are usually solid at room temperature. - EX: Animal fat (like butter)

backbone

of the nucleic acid strand is composed of alternating sugar-phosphate molecules. ● RNA is usually a single-stranded molecule, whereas DNA is a double-stranded molecule. ● DNA is composed of two strands held together by hydrogen bonds between the nitrogen-containing bases. The two strands twist around each other, forming to a double helix.

Unsaturated

one or more double bonds between carbons. ○ Unsaturated fats are usually called oils, and tend to be liquid at room temperature. ex: oils

enzymatic proteins

proteins that act as catalysts to accelerate chemical reactions within cells.

Receptor Proteins

proteins that bind to chemical signals and initiate a cell response.

Defense Proteins

proteins, such as antibodies, assist the immune system in destroying viruses and bacteria.

Competitive inhibitors:

reduce the productivity of enzymes by attaching to the enzyme's active site and thus blocking substrates from attaching. ○ Competitive inhibitors have similar chemical properties as the enzyme's substrate, allowing it to bind to the active site.

ATP (adenosine triphosphate)

s a nucleotide composed of adenine, ribose, and three phosphates. ● ATP is a high-energy molecule due to the presence of the last unstable phosphate bonds, which is easily broken.

Fatty acids can be either

saturated or unsaturated.

feedback inhibition

the end product of a metabolic pathway shuts down the pathway by binding to and inhibiting an enzyme that is used earlier in the pathway. ● Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

polypeptides.

Long chains of amino acids joined together (polymers) are called

In which type of macromolecule would you find glycosidic linkages? A. Carbohydrates B. Lipids C. Nucleic Acids D. Proteins E. None of the above

A. Carbohydrates

If you were asked to chose a lipid subunit/monomer, which would it be? A. fatty acid B. steroid C. cholesterol D. amino acid E. none of the above

A. fatty acid

The magnesium chelatase protein has quaternary structure. This means that magnesium chelatase A. is composed of multiple subunits. B. binds to the surface of membranes. C. forms part of a quadruple complex. D. changes over time. E. has four-fold symmetry.

A. is composed of multiple subunits.

Vioxx and other prescription nonsteroidal anti-inflammatory drugs (NSAIDs) are potent inhibitors of the cyclooxygenase-2 (COX-2) enzyme. High substrate concentrations reduce the efficacy of inhibition by these drugs. These drugs are A. competitive inhibitors. B. noncompetitive inhibitors. C. allosteric regulators. D. prosthetic groups. E. feedback inhibitors.

A. competitive inhibitors

If you took a bacterium living in a stream with 20°C water and placed it in a hot spring with 50°C water, what might happen? A. It would thrive, with more thermal energy to speed reactions. B. It would die because its enzymes would malfunction at high temperature. C. It would grow as usual, since temperature has little effect on bacteria. D. It would die because faster reactions would deplete cellular ATP. E. B and D

B. It would die because its enzymes would malfunction at high temperature.

Leucine and valine have side chains consisting entirely of C and H; therefore, the side chains A. are hydrophilic. B. are nonpolar. C. contain sulfur atoms. D. are electrically charged.

B. are nonpolar.

Which is not a function of proteins? A. help make up membranes B. carry the genetic code for translation from the nucleus to the ribosome C. bind to hormones (hormone receptor) D. can be hormones E. speed chemical reactions

B. carry the genetic code for translation from the nucleus to the ribosome

Which sugar is most important for making RNA? A. glucose B. ribose C. fructose D. glyceraldehyde E. sucrose

B. ribose

If you were going to be shown the structure of the amino acid glycine, what functional group(s) would you definitely see? A. hydroxyl and amino B. amino and carbonyl C. carboxyl and amino D. carbonyl and hydroxyl E. carbonyl and sulfhydryl

C. carboxyl and amino

Which is not a lipid? A. estrogen B. cholesterol C. glucose D. triglyceride E. saturated fat

C. glucose

Energy is stored in the chemical bonds that hold molecules together. In organic chemistry, energy is typically stored in C-H bonds. Which type of macromolecule would you expect to have the most compact energy storage? A. proteins B. carbohydrates C. lipids D. nucleic acids E. All provide about the same amount of energy stored per unit volume.

C. lipids

Enzyme Localization in a Cell

Cells control where certain reactions take place within the cell. ○ Many enzymes are incorporated into specific membranes within the cell. ○ Some are contained in solutions enclosed within a specific membrane-bound organelle. ○ EX: the enzyme ATP synthase is embedded in the inner membrane of the mitochondria, the organelle where ATP synthesis occurs

Between strands there is complimentary base pairing

Cytosine (pyrimidine) makes three hydrogen bonds with guanine (purine). ○ Adenine (purine) makes two hydrogen bonds with thymine (pyrimidine) in DNA, or uracil in RNA.

Between strands there is complimentary base pairing

Cytosine (pyrimidine) makes three hydrogen bonds with guanine (purine). ○ Adenine (purine) makes two hydrogen bonds with thymine (pyrimidine) in DNA, or uracil in RNA.

Imagine that you have discovered a new enzyme, but when you isolate it for further study, it does not work properly. What might have been lost? A. a cofactor B. a coenzyme C. bound reactant D. A and B E. A, B, and C

D. A and B

If you were designing an organism, and a critical chemical reaction occurred too slowly at the organism's body temperature, what would you need to add to the design? A. an enzyme B. a catalyst C. a molecule that lowers the activation energy of the reaction D. A, B, and C E. A and C

D. A, B, and C

The enzyme glucose oxidase binds the 6-carbon sugar glucose and catalyzes its conversion to glucono-1,5-lactone. Mannose is also a 6-carbon sugar, but glucose oxidase cannot bind mannose. The specificity of glucose oxidase is based on the A. free energy of the transition state. B. activation energy of the reaction. C. change in free energy of the reaction. D. three-dimensional shape and structure of the active site. E. rate constant of the reaction.

D. three-dimensional shape and structure of the active site.

The primary structure of proteins is the _______. The primary structure contains the information necessary for the formation of secondary structure, including the _______ and the _______. Secondary structure of proteins is stabilized by the formation of _______ bonds. A. amino acid sequence; β pleated sheet; ⍺ helix; disulfide B. ⍺ helix; amino acid sequence; β pleated sheet; hydrophobic C. amino acid sequence; ⍺ helix; β pleated sheet; peptide D. amino acid sequence; ⍺ helix; β pleated sheet; hydrogen E. β pleated sheet; ⍺ helix; amino acid sequence; hydrogen

D. amino acid sequence; ⍺ helix; β pleated sheet; hydrogen

The arrangement of glycosidic linkages in _______ makes it a much more structurally stable molecule than _______. A. guanine; cytosine B. RNA; DNA C. sucrose; lactose D. cellulose; starch E. testosterone; cortisone

D. cellulose; starch

If a mechanic tries to change as many tires as possible in a short time by bringing car after car into the garage before previously repaired cars can be removed, eventually no more work can be done until the fixed cars are removed. What enzyme function is this like? A. cooperativity B. denaturation C. optimal temperature D. feedback inhibition E. noncompetitive inhibition

D. feedback inhibition

double helix

DNA is composed of two strands held together by hydrogen bonds between the nitrogen-containing bases. The two strands twist around each other, forming to a double helix.

Which interactions are not directly involved in the formation of a protein's tertiary structure? A. Hydrogen bonds B. Hydrophobic interactions C. Disulfide bonds D. Ionic bonds E. Peptide bonds

E. Peptide bonds

Which statement about purines and pyrimidines is true? A. Purines include the bases of cytosine and thymine; pyrimidines include the bases of adenine and guanine. B. Pyrimidines are found in RNA, whereas purines are found in DNA. C. Purines consist of hydrogen, carbon, oxygen, and nitrogen, whereas pyrimidines have phosphorus, hydrogen, carbon, oxygen, and nitrogen. D. Purines have only single bonds in their structure, whereas pyrimidines have both single and double bonds. E. Purines are double-ring structures, whereas pyrimidines are single-ring structures.

E. Purines are double-ring structures, whereas pyrimidines are single-ring structures.

Which of the following is true of all lipids? A. are made from glycerol and fatty acids. B. contain nitrogen. C. have low energy content. D. are acidic when mixed with water. E. are not very water soluble

E. are not very water soluble.

Nucleotides

Each nucleotide is composed of three parts: -A phosphate group, a pentose (5-carbon) sugar, and a nitrogen-containing (nitrogenous) base. ● The pentose sugar found in RNA nucleotides in ribose, and in DNA nucleotides it is deoxyribose.

types of proteins

Enzymatic Proteins Transport Proteins Hormonal Proteins Receptor Proteins Defense Proteins Contractile and Motor Proteins Structural Proteins Storage Proteins

Inhibitors

Enzyme inhibitors are chemicals that selectively attach to an enzyme and inhibit it from binding to its substrate. Two types: ● Competitive inhibitors: reduce the productivity of enzymes by attaching to the enzyme's active site and thus blocking substrates from attaching. ○ Competitive inhibitors have similar chemical properties as the enzyme's substrate, allowing it to bind to the active site. -Competitive inhibitors can be overcome by increasing the concentration of substrate, but noncompetitive inhibitors cannot be overcome by increasing the substrate concentration.

Structural Proteins

Fibrous proteins form many structures. For example, keratin proteins form hair, nails, and horns, and collagen proteins form connective tissue that holds organs together

Secondary Level

Hydrogen bonding between amino acids causes the polypeptide to form alpha helices (coils) and beta pleated sheets (folds).

Temperature:

Increasing temperature generally increases the rate of a reaction, until the temperature affects the stability of the enzyme (denaturing). ● EX: Most human enzymes have optimal temperatures of about 35-40 °C (close to human body temperature)

Polynucleotides

Nucleotides are joined together by a series of dehydration reactions to form a strand (polymer) called a polynucleotide

polynucleotide.

Nucleotides are joined together by a series of dehydration reactions to form a strand

cellulose

Plant cells are enclosed by cell walls made primarily with cellulose, a polysaccharide made of glucose monomers (just like starch).

lipid bilayer

Polar phosphate heads are oriented toward the outsides of the bilayer, interacting with the water inside and outside a cell. - Nonpolar fatty acid tails are oriented toward the inside of the bilayer, away from water

Primary Level

Primary level is the linear sequence of amino acids (coded by genes in DNA) ○ Hundreds of thousands of different polypeptides can be built from just 20 amino acids. ○ Changing the sequence of amino acids can produce different proteins.

There are two families of nitrogenous bases:

Pyrimidines are bases with one ring and include cytosine (C), thymine (T), and uracil (U). ○ Purines are bases with two rings and include adenine (A), and guanine (G). ● Thymine is found only in DNA, and uracil only in RNA; the rest are found in both DNA and RNA.

Quaternary Level

Quaternary level consists of two or more folded polypeptides interacting to perform a biological function All proteins have the first three levels of structure, but only some proteins have a quaternary structure.

Allosteric Regulation of Enzymes

Reactions taking place in a cell need to be carefully regulated (controlled). ● For this reason, enzymes have active and inactive forms (shapes), meaning they can be turned "on" and "off." ● Allosteric regulation is the term used to describe any case in which a protein's function at one site is affected by binding of a regulatory molecule at another site. ○ Enzymes change shape when regulatory molecules bind to specific sites, affecting the enzyme's function. ● Allosteric regulation can either activate or inhibit an enzyme's activity.

Storage Proteins:

Some proteins are used to store amino acids for organisms to use when needed. Such as ovalbumin, the protein in egg whites, that is used as an amino acid source for developing embryos.

Factors Affecting Enzyme Activity

Temperature: pH Cofactors Inhibitors

Tertiary Level

Tertiary level is the overall three-dimensional (globular) shape of a polypeptide. ○ Determined by interactions between side chains (R-Groups), such as: ■ hydrophobic interactions ■ hydrogen bonding ■ ionic and covalent bonding -In a globular protein, the hydrophobic amino acids usually fold into the inside of the protein while the hydrophilic amino acids are usually found on the outside of the protein (the part that interacts with water).

induced fit,

The binding of a substrate(s) to the active site creates an induced fit, in which the enzyme changes shape to embrace the substrate(s) to insure it does not detach.

enzyme-substrate complex

The binding of the enzyme and substrate forms an enzyme-substrate complex

Cholesterol

an important steroid, is a component in animal cell membranes

Proteins

are a class of macromolecules that include a huge diversity of structures, resulting in a wide range of functions. ○ Functions include defense, storage, transport, cellular communication, movement, and structural support. ● Composed of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur.

Carbohydrates

are a class of macromolecules whose functions include energy storage and providing building material to cells and organisms. -Composed of carbon, hydrogen, and oxygen. -The monomers of carbohydrates are called monosaccharides

Lipids

are a diverse group of macromolecules with the unifying feature of being mostly hydrophobic. ○ Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds. ● Composed of carbon, hydrogen, oxygen, and sometimes phosphorus. ● Lipids are the only class of macromolecules that do not form true polymers. ● The most biologically important lipids are fats, phospholipids, and steroids.

phosphodiester linkages

are formed between the phosphate group of one nucleotide, and the pentose sugar of the next nucleotide.

Triglycerides

are formed from the bonding together of four monomers: three fatty acid monomers bonded to one glycerol monomer. ○ Fatty acids are bonded to glycerol via dehydration reactions, forming three covalent bonds called ester linkages. ● The main function of fat is energy storage. Fat is also used to insulate body heat in mammals.

Steroids

are lipids characterized by a carbon skeleton of four fused carbon rings. --Some hormones, such as the sex hormones testosterone and estrogen, are steroids that regulate and control the body

Fats

are made up of large nonpolar molecules called triglycerides

Nucleic acids

are polymers of monomers called nucleotides. ● Composed of carbon, hydrogen, oxygen, phosphorus, and nitrogen.

Enzymes

are proteins that act as biological catalysts.

Noncompetitive inhibitors

bind to another part of the enzyme, causing it to change shape and thus preventing the enzyme's active site from attaching to the substrate.

A change in just one amino acid in a polypeptide (a protein's primary structure)...

can change the structure of the protein and its ability to function

If you were given a sample of a polysaccharide and told that the only subunit was glucose, what would you have? A. glycogen B. starch C. cellulose D. You cannot know from the information given

d. You cannot know from the information given.

Transport Proteins

embedded in the cell membrane that control the movement of substances in and out of a cell.

Chaperone proteins

help proteins fold into their normal shapes and may also correct misfolding of new proteins. ○ Defects in chaperone proteins may play a role in several human diseases such as Alzheimer's disease and cystic fibrosis.

catalyst

is a chemical that speeds up a reaction without being consumed by the reaction ● Enzymes speed up metabolic reactions by lowering the activation energy.

Allosteric Inhibition

is a form of allosteric regulation that inhibits enzyme activity. This is the same thing as noncompetitive inhibition. - Occurs when the binding of a regulatory molecule, called an inhibitor, stabilizes the inactive form of the enzyme, in which substrates cannot bind to the active site of the enzyme.

Allosteric Activation

is a form of allosteric regulation that stimulates enzyme activity. - Occurs when the binding of a regulatory molecule, called an activator, stabilizes the active conformation (shape) of the enzyme.