AP Bio Test #2

Properties of a phospholipid

-Two fatty acid "tails": nonpolar and hydrophobic -Phosphate "head"" polar and hydrophilic

List the functions of proteins:

1. Structural: support (like keratin in hair, collagen in connective tissue, etc) 2. Storage: storage of amino acids (like casein in milk, zein in corn seeds, and ovalbumin in egg whites) 3. Transport: transport of substances (like oxygen-carrying hemoglobin) 4. Defensive: protection against disease (like antibodies that fight against the invasion of harmful microbes) 5. Enzymes: selective acceleration of chemical processes (like digestive enzymes that help speed up food breakdown) 6. Hormonal: coordination of an organism's activities (like insulin) 7. Receptor: response of cell to chemical stimuli (like receptors on a cell detecting signaling molecules released by other cells) 8. Contractile and motor: movement (Like actin and myosin responsible for the contraction of muscles)

What are some instances in which denaturation can occur?

1. When proteins are relocated from aqueous solutions to a non polar solvent like ether or chloroform (refolding occurs so that hydrophobic regions face outward towards the solvent) 2. Chemicals that disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain a protein's shape 3. Excessive heat (agitates the polypeptide chain to overpower the weak interactions)

Gene

A discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA or RNA (in some viruses)

Monounsaturated fatty acid

A fatty acid with one double covalent bond and each of the two carbons in this bond has only one hydrogen atom bonded to it.

Polyunsaturated fatty acid

A fatty acid with two or more double covalent bonds between carbon atoms in the hydrocarbon chain.

What makes up a nucleotide?

A five carbon sugar (pentose), a nitrogen-containing (nitrogenous) base, and 1-3 phosphate groups (With one phosphate, this is a nucleoside monophosphate, more often called a nucleotide).

What programs the amino acid sequence of a polypeptide?

A gene which contains DNA.

Polymer

A long molecule consisting of many similar or identical building blocks (monomers) linked together by covalent bonds.

Polynucleotides

A polymer consisting of nucleotide monomers in a chain

Explain why the electronically charged side chain group is divided into acidic and basic.

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. Basic amino acids have amino groups in their side chains that are generally positive in charge.

Manufacturers make vegetable oils solid or semisolid at room temperature by __________.

Adding hydrogen atoms to the fatty acid hydrocarbon chains, thereby converting carbon-carbon double bonds to single bonds.

Which nitrogenous bases are compatible?

Adenine pairs with thymine; guanine pairs with cytosine (in RNA, adenine pairs with uracil instead).

In respect to these nitrogenous bases, what are the differences and similarities between DNA and RNA?

Adenine, guanine, and cytosine are found in both DNA and RNA; thymine is found only in DNA and uracil only in RNA.

How are nucleotides linked?

Adjacent nucleotides are joined by a phosphodiester linkage, which consists of a phosphate group that links the sugars of two nucleotides; this creates a repetition of units called a sugar-phosphate backbone.

What is true regarding complementary base pairing in DNA and RNA molecules?

Although the base pairing between two strands of DNA in a DNA molecule can be thousands to millions of base pairs long, base pairing in an RNA molecule is limited to short stretches of nucleotides in the same molecule or between two RNA molecules.

What diseases are associated with the misfolding of polypeptides in cells?

Alzheimer's, Parkinson's, and mad cow disease.

What is one example of the relationship between the form and function of a protein?

An antibody's (which is a protein) ability to bind to a particular foreign substance on a virus and destroy it.

What is trans fats and what does it contribute to?

An artificial unsaturated fat (made from hydrogenation of oils {the addition of hydrogen}) containing one or more trans double bonds. It can contribute to coronary heart disease and is most commonly found in processed foods/baked goods.

What is one known effect of a diet consisting of saturated fats?

Atherosclerosis; a cardiovascular disease in which plaques develop within the walls of blood vessels, causing inward bulges that impede blood flow and reduce the resilience of the vessels.

High cholesterol levels are considered a major risk factor for heart disease. If it is so bad for humans, why does the body make cholesterol in the first place?

Cholesterol is the precursor for many important molecules such as sex hormones.

What are examples of steroids?

Cholestrol, Estradiol (an estrogen), and testosterone.

Saturated Fatty acid

Contains only single covalent bonds between each pair of carbon atoms, and each carbon has two hydrogens bonded to it; allowing as many hydrogen atoms as possible bonded to the carbon skeleton and thus referred to as saturated.

Messenger RNA

Conveys genetic instructions for building proteins from the nucleus to the cytoplasm; where the ribosomes (site or protein synthesis) then translate the coded information into amino acid sequences.

The type of bond that forms to join monomers (such as sugars and amino acids) into polymers (such as starch and proteins) is a(n) __________ bond.

Covalent

How many polynucleotides are in a DNA molecule?

DNA molecules have two polynucleotides, or "strands," that wind around an imaginary axis, forming a double helix.

A shortage of phosphorus in the soil would make it especially difficult for a plant to manufacture __________.

DNA; The backbone of a nucleic acid consists of alternating sugar and phosphate groups.

What are the two types of nucleic acids?

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

How are steroids distinguished?

Different steroids are distinguished by the particular chemical groups attached to this ensemble of rings.

What is an example of hydrolysis within the body?

Digestion; within the digestive tract, various enzymes attack the polymers, speeding up hydrolysis. Released monomers are then absorbed into the bloodstream for distribution to all body cells.

What exactly happens during dehydration synthesis/reaction?

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).

Why are they called '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.)

What is the major function of fats?

Energy storage; the hydrocarbons in the skeleton are rich in energy. Mobile mammals and animals store their energy in adipose cells (which swell and shrink as fat is deposited and withdrawn from storage).

What are the three types of Lipids?

Fats (triacylglycerols), phospholipids, and Steroids.

What are the two forms of shape a protein can become?

Globular proteins and Fibrous proteins.

Phospholipid

Has only two fatty acids attached to glycerol rather than three, the third hydroxyl group is attached to a phosphate group (negative electrical charge in the cell). Often, an additional charge/polar molecule is linked to the phosphate group (represented by 'R').

Why are human sex hormones considered lipids?

Human sex hormones are steroids, a type of compound that is hydrophobic and thus classified as a lipid.

Where are the nitrogenous bases paired in DNA?

In the interior of the helix.

Can complementary base pairing occur in RNA molecules? How is it beneficial?

It can occur between regions of two RNA molecules or even between two stretches of nucleotides in the same RNA molecule; allowing the molecule to take on the particular three-dimensional shape necessary for its function.

What is another purpose to adipose tissue?

It cushions vital organs like the kidneys and beneath the skin is a layer of fat which insulates the body.

Why is cholesterol an important steroid?

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. However, high levels of cholesterol in the blood may contribute to atherosclerosis.

Steroids

Lipids characterized by a carbon skeleton consisting of four fused rings.

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

Macromolecules are constructed from 40-50 common monomers and some other rare ones.

How many molecules of water are needed to completely hydrolyze a polymer that is ten monomers long?

Nine, with one water molecule required to hydrolyze each connection between adjacent monomers.

What distinguishes the two free ends of the nucleotide polymer?

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 (thus, the polynucleotide has dircetionality from 5' to 3').

Unsaturated Fatty acid

One or more double bonds, with one fewer hydrogen atom on each double bonded carbon; allowing them to pack more loosely, have lower melting temperatures, and usually liquid at room temperature (i.e. oils).

Amino acid

Organic molecule with both an amino group and a carboxyl group, and at the center is an asymmetric carbon atom called an alpha carbon.

What is one comparison between phospholipids and triacylglycerols (fats and oils)?

Phospholipid molecules have a distinctly polar "head" and a distinctly nonpolar "tail," whereas triacylglycerols are predominantly nonpolar.

What are the two families of nitrogenous bases and how are they defined?

Pyrimidines: they have one six-membered ring of carbon and nitrogen atoms (cytosine, thymine, uracil) Purines: they are larger, with a six-membered ring fused to a five-membered ring. (adenine, guanine)

Polypeptide backbone

Repeating sequence of atoms along the core of the polypeptide chain.

What parts of a polypeptide participate in the bonds that hold together secondary structure? Tertiary structure?

Secondary structure involves hydrogen bonds between atoms of the polypeptide backbone. Tertiary structure involves interactions between atoms of the side chains of the amino acid subunits.

Enzyme

Specialized macromolecules that speed up chemical reactions.

Which prime carbon is the phosphate group attached to?

The 5' carbon.

What determines the function of a protein?

The amino acid sequence of each polypeptide determines the structure of the protein. In turn, the structure and shape determines the functionality of that protein. Protein structure also depends on the physical and chemical conditions of the protein's environment.

If you eat a piece of fish, what reactions must occur for the amino acid monomers in the protein of the fish to be converted to new proteins in your body?

The amino acids in the fish protein must be released in hydrolysis reactions and incorporated into other proteins in dehydration reactions.

Hydrolysis

The chemical process that breaks the bond between monomers through the addition of a water molecule, with a hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other.

Why are phospholipids essential to cells?

The existence of cells depends on the properties of phospholipids, which include hydrophilic heads of the molecules on the outside of the bilayer and hydrophobic tails that point toward the interior of the bilayer (away from the water). This forms a boundary between the cell and its external environment and establishes separate compartments within eukaryotic cells.

What are the four levels of Protein structure?

The four levels are- Primary: linear sequence of amino acids that use three-letter abbreviations to indicate one of 20 amino acids (i.e. transthyretin with 127 amino acids) Secondary: coils and folds that occur as a result of hydrogen bonding between the carboxyl group and the amino group of the polypeptide backbone (not the side chains); there are two kinds: the alpha helix (a spiral) and the B pleated sheet (the folded pleats on a skirt) Tertiary: three-dimensional shape stabilized by interactions between side chains including hydrophobic interactions (nonpolar amino acid side chains held by van der Waals interaction at the core of the protein, away from water), hydrogen and ionic bonds (electrically charged side chains), and disulfide bridges (when the sulfur atom in the amino acid cysteine bonds to the sulfur atom in another cysteine) Quaternary: a protein consisting of two of more peptide chains (polypeptides); including hemoglobin, collagen, and transthyretin.

What are the four main classes of large biological molecules? Which class does not consist of polymers?

The four main classes are proteins, carbohydrates, lipids, and nucleic acids. Lipids are not polymers.

Why is the sequence of the four DNA bases important?

The information carried by the gene is encoded in its specific sequence of the four DNA bases, which 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.

Suppose a membrane surrounded an oil droplet, as it does in the cells of plant seeds and in some animal cells. Describe and explain the form it might take.

The oil droplet membrane could consist of a single layer of phospholipids rather than a bilayer, because an arrangement in which the hydrophobic tails of the membrane phospholipids were in contact with the hydrocarbon regions of the oil molecules would be more stable.

What is the difference between the sugars that are attached to the nitrogenous base?

The only difference is that deoxyribose lacks an oxygen atom on the second carbon in the ring, hence the name deoxyribose.

Nucleoside

The portion of a nucleotide without any phosphate groups; The beginning monomer used to build a polynucleotide has three phosphate groups, but two are lost during the polymerization process. (base+sugar)

Gene Expression

The process by which information encoded in DNA directs the synthesis of proteins or RNA that isn't translated into proteins. It is the process that allows for the control of protein synthesis through DNA. *DNA->RNA-> Protein

What feature of DNA is crucial to the creation of two identical copies of each DNA molecule in a cell that is about to divide?

The two strands of the double helix are complementary, each the predictable counterpart of the other.

How many amino acids are there?

There are 20 amino acids that cells use to build their thousands of proteins.

How are the amino acids grouped? List the acids in each group:

There are 3 amino acid groups: ~Nonpolar side chains (hydrophobic): Glycine, Alanine, Valine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline ~Polar side chains (hydrophilic): Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine ~Electrically charged side chains (hydrophilic): Aspartic, glutamic, Lysine, Arginine, Histidine

What are the four bonds of the alpha carbon of an amino acid? How does each amino acid differ?

There's an amino group, a carboxyl group, a hydrogen atom, and a variable group symbolized by R (the side chain). 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.

Where would you expect a polypeptide region rich in the amino acids valine, leucine, and isoleucine to be located in a folded polypeptide? Explain.

These are all nonpolar, hydrophobic amino acids, so you would expect this region to be located in the interior of the folded polypeptide, where it would not contact the aqueous environment inside the cell.

What does a fat consist of?

Three fatty acids attached to a glycerol molecule

True of False: 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).

True

True of False: Proteins are all constructed from the same set of 20 amino acids, linked in unbranched polymers.

True

True of false: DNA is the genetic material that organisms inherit from their parents.

True

True of False: Because genes are hundreds to thousands of nucleotides long, the number of possible base sequences is effectively limitless.

True.

True of False: Saturated Fats pack together more tightly, have higher melting temperatures, and are usually solid at temperature.

True; the lack of double bonds allows for this statement to be true.

Dehydration Reaction

Two molecules are covalently bonded to each other with the loss of water molecule.

Why do fats separate from water?

Water molecules hydrogen bond to one another (cohesion) and exclude fats.

Denaturation

When a protein loses it shape due to the change in pH, salt concentrations, temperature, or other environmental aspects that cause the weak chemical bonds to be destroyed.

How are amino acids joined together?

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; this results in a peptide bond.

Trans double bond

When two groups attached to the carbons of the double bond are on the opposite sides of the double bond.

What is the method scientist rely on to determine the 3-D structure of a protein? How does it work?

X-ray crystallography; the diffraction (bend) of an X-ray beam by the atoms of a crystallized molecule.

Protein

a biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific three-dimensional structure.

Fatty Acid

a carboxylic acid that has a long carbon chain, usually 16-18 carbon atoms in length. The carbon at one end of the skeleton is part of a carboxyl group.

A glucose molecule is to starch as __________.

a nucleotide is to a nucleic acid

If a small droplet of triacylglycerol molecules is suspended in water, the fat molecules form a "ball of spaghetti" with no particular orientation. But if a droplet of phospholipid molecules is put in water, all the molecules point outward, toward the water. Phospholipids are forced into this orientation because phospholipids have __________. a. a charged or polar end and an uncharged or nonpolar end b. both a saturated fatty acid and an unsaturated fatty acid c. two charged or polar ends d. three fatty acid molecules, all pointing in different directions e. two fatty acid molecules pointing in different directions

a. a charged or polar end and an uncharged or nonpolar end

Nearly every double bond in naturally occurring fatty acids is a _______________, which creates a kink in the hydrocarbon chain wherever it occurs. a. cis double bond b. trans double bond c. neither

a. cis double bond

Lipid

any group of large biological molecules including fats, phospholipids, and steroids, that are insoluble in with water but highly soluble in nonpolar substances.

Lipids consist of mostly _____________: a. hydroxyl regions b. hydrocarbon regions c. all of the above

b. hydrocarbon regions; these nonpolar bonds attribute to the hydrophobic behavior of a lipid (hydrocarbons= chains of covalently bonded carbons and hydrogens with a carboxyl group {COOH} at the end of the chain)

Glycerol is an _________. a. acid b. base c. alcohol

c. alcohol; each of its three carbons bears a hydroxyl group.

Nutritionally, saturated triacylglycerols are considered to be less healthful than unsaturated triacylglycerols. What is the difference between them? a. Saturated triacylglycerols are fats; unsaturated triacylglycerols are carbohydrates. b. Saturated triacylglycerols have more double bonds than unsaturated triacylglycerols do. c. Saturated triacylglycerols have more double bonds than unsaturated triacylglycerols do. d. For carbon skeletons of equal length, saturated triacylglycerols have more hydrogen atoms than unsaturated triacylglycerols do. e. All of the listed responses are correct.

d. For carbon skeletons of equal length, saturated triacylglycerols have more hydrogen atoms than unsaturated triacylglycerols do; Remember that Saturated triacylglycerols are saturated with hydrogen atoms.

Which type of protein shields a newly forming protein from cytoplasmic influences while it is folding into its functional form? a. receptor proteins b. antibodies c. fibrous proteins d. chaperonins e. enzymes

d. chaperonins; Chaperonins shield proteins from "bad influences" (interactions with other molecules in the cytoplasm) while they are folding into their functional forms.

Enzyme molecules require a specific shape to perform their catalytic function. Which of the following might alter the shape of an enzymatic protein? a. a change in salt concentrations or pH b. heating the protein c. treating the protein with a chemical that breaks hydrogen bonds d. denaturing the protein e. All of the listed responses are correct.

e. All of the listed responses are correct; All of the listed responses would affect the shape and therefore the catalytic activity of the enzymatic protein.

Which of the following describes a difference between DNA and RNA? a. RNA molecules generally consist of a single polynucleotide chain, whereas DNA molecules generally consist of two polynucleotide chains organized into a double helix. b. Both molecules contain adenine, guanine and cytosine, but DNA also contains thymine and RNA also contains uracil. c. They contain different sugars. d. The first and second listed responses correctly describe differences between DNA and RNA. e. The first three listed responses correctly describe differences between DNA and RNA.

e. The first three listed responses correctly describe differences between DNA and RNA.

In making a fat, three fatty acid molecules are each joined to glycerol by an ________________, a bond formed by a dehydration reaction between a hydroxyl group and a carboxyl group.

ester linkage

The two strands are held together by ________________ between the paired bases.

hydrogen bonds

Nucleic Acids

polymers made of monomers called nucleotides.

Peptide bond

the covalent bond between multiple amino acids to form a polypeptide.

Antiparrallel strands

when the two sugar-phosphate backbones of the nucleotides run in opposite 5'→3' directions from each other. (5' 3' -3' 5')