Princeton Biology Review CH3 Biologically Important Molecules

The 1, 2, or 3 phosphate units join to the carbon ________ of the ribose ring of a nucleotide.

5

Energy extracted from the oxidation of foodstuffs is immediately stored in the phospho-anhydride bonds of ____________. This energy is later used to power cellular processes.

ATP Adenosine TripPhosphate

__________ is the Universal short-term energy storage molecule.

ATP Adenosine TripPhosphate

KHAN ACADEMY ------TYPES AND FUNCTIONS OF PROTEINS------ ____________ act as catalysts in biochemical reactions, meaning that they speed the reactions up. Each one recognizes one or more substrates, the molecules that serve as starting material for the reaction it catalyzes. Different ones participate in different types of reactions and may break down, link up, or rearrange their substrates.

Enzyme

___________ refers to the disruption of a proteins shape without breaking peptide bonds and can only be done so by extremes of pH, by extremes of temperatures, by changes in salt concentration (tonicity) or by Urea.

Denaturation

_________ refers to the initial folding of a polypeptide chain into shapes stabilized by hydrogen bonds between backbone NH and CO groups. A. Primary Structures B. Secondary Structures

Secondary Structures

___________ serves as energy storage for carbohydrates in PLANTS and is composed of thousands of glucose units.

Starch

The purine or pyrimidine base of a nucleotide is joined to a carbon number _______ of the ribose ring.

1

When a fatty acid is introduced into an aqueous solution and a Micelle is formed, the _________ are HYDROPHILIC and polar with charged groups and the tails are HYDROPHOBIC and nonpolar. A. Tails B. Heads

1. Heads 2. Tails

What three PHYSIOLOGICAL ROLES do Lipids have? 1. 2. 3.

1. In Adipose cells (fat cell) they help store fat energy = TRIGLYCERIDES 2. In Cellular membranes they constitute a barrier between intracellular and extracellular environments = PHOSPHOLIPIDS 3. Serve as the building block for the hydrophobic steroid hormone = CHOLESTEROL

What are the three main reasons Anhydride bonds (a compound that has two acyl groups bonded to the same oxygen atom) store so much energy and therefore is extremely favorable to hydrolysis? 1. 2. 3.

1. When linked together, their negatives charges repel each other STRONGLY 2. ORTHOPHOSPHATE has more resonance forms and thus a lower free energy than linked phosphates 3. ORTHOPHOSPHATE has a more favorable interaction with the biological solvent than linked phosphates

Proteins can only be denatured by which FOUR means? 1. 2. 3. 4.

1. extremes of pH 2. extremes of temperature 3. extremes of tonicity 4. Urea

How does the shape of an unsaturated fatty acid differ from the that of a saturated fatty acid?

AN unsaturated fatty acid is BENT or KINKED this is due to the CIS DOUBLE BOND (Saturated Fatty acids do not have ANY double bonds)

KHAN ACADEMY Albumin is a protein that is found in eggs. Which of the following describes the structure of albumin? A. A molecule containing carbon, hydrogen, and oxygen in a 1:2:1 ratio B. A chain of amino acids folded and twisted into a molecule C. Three fatty acids attached to one glycerol molecule D. A series of nitrogenous bases attached to a sugar-phosphate backbone

A chain of amino acids folded and twisted into a molecule Albumin is a protein. Proteins are made up of one or more chains of amino acids called a polypeptides.

KHAN ACADEMY Which describes a carbohydrate? A. A molecule containing carbon, hydrogen, and oxygen in a 1:2:1 ratio B. A chain of amino acids folded and twisted into a molecule C. Three fatty acids attached to one glycerol molecule D. A series of nitrogenous bases attached to a sugar-phosphate backbone

A. A molecule containing carbon, hydrogen, and oxygen in a 1:2:1 ratio

The formation of atherosclerotic plaques is due to high levels of __________________. A. Blood Cholesterol B. Membrane Cholesterol

A. Blood Cholesterol

There are two types of covalent bonds between amino acids in proteins. This strong bond forms between two cysteine R-groups and helps stabilize a protein. A. Disulfide Bridge B. Peptide Bond

A. Disulfide Bridge

At low temperatures cholesterol ____________ fluidity because the ring structure of cholesterol does not allow for tight phospholipid tail packing. A. Increases B. Decreases

A. Increases

In cellular membranes, this lipid constitutes a barrier between intracellular and extracellular environments. A. Phospholipids B. Triglycerides C. Cholesterol

A. Phospholipids

A fatty acid with non-carbon-carbon double bonds is said to be ___________ with hydrogen because every carbon atom in the chain is covalently bound to the maximum number of hydrogens. A. Saturated B. Unsaturated

A. Saturated

______________ are the more efficient energy storage molecules due to their hydrophobicity that allows them to pack closer together and due to the fact that they contain more energy,. A. Triacylglycerols B. Carbohydrates

A. Triacylglycerol's

Which two are linear in structure? A. Triglycerides B. Phospholipids C. Steroids D. Cholesterol

A. Triglycerides B. Phospholipids

In a ______________ secondary structure, two or more segments of a polypeptide chain line up next to each other held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet. The strands of this structure may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other). A. β pleated sheet B. α helix

A. β pleated sheet

KHAN ACADEMY ____________ share a basic structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group, a carboxyl group, and a hydrogen atom.

Amino Acids

_____________ are composed of long unsubstituted alkanes that end in a carboxylic acid and is normally 14-18 carbons long. A. Proteins B. Lipids C. Fatty Acids D. Steroids

C. Fatty Acids

Phenylketonuria (PKU) is an autosomal recessive disorder that results from a deficiency of the enzyme phenylalanine hydroxylase. This enzyme normally converts phenylamine into tyrosine. PKU results in intellectual disability, growth retardation, fair skin and eczema and a distinct must body odor. Which of the following is most likely true? A. Treatment should include a decrease in tyrosine in the diet B. The musty body odor is likely caused by a disorder in the aromatic amino acid metabolism C. Patients with PKU should increase the amount of phenylalanine in their diet D. PKU can be acquired by consuming too much aspartame (an artificial sweetener that contains high levels of phenylalanine)

B. A defect in phenylalanine hydroxylase would result in a build-up of phenylalanine. This would lead to an excess of phenylalanine byproducts such as phenylacetate, phenylacetate and phenylpyruvate and a decrease in tyrosine. Therefore, patients with PKU should increase the amount of tyrosine in their diet. So A would be wrong They should increase tyrosine as well as eliminate phenylalanine from their diet (C is wrong) PKU is genetically acquired disorder as mentioned in the passage, and thus it is not acquired by consuming too much phenylalanine. (Choice D is wrong) It is true that phenylalanine and its derivative are aromatic amino acids and that the high levels of these compounds lead to the distinct musty body odor.

Cholesterol ____________ the permeability of membranes by filling in the holes between the fatty acid tails. A. Increases B. Decreases

B. Decreases

There are two types of covalent bonds between amino acids in proteins. ONE of them is the _________ that links amino acids together into polypeptide chains. A. Disulfide Bridge B. Peptide Bond

B. Peptide Bond

In adipose cells, this lipid helps store fat energy. A. Phospholipids B. Triglycerides C. Cholesterol

B. Triglycerides

A fatty acids that has one or more double bonds in the tail and whose double bonds are almost always Z or Cis. A. Saturated B. Unsaturated

B. Unsaturated

Increasing the amount of cholesterol in plasma membrane would lead to an increase in: A. Membrane Permeability B. Atherosclerotic Plaques C. Membrane Fluidity at low temperatures but a decrease in membrane fluidity at high temperatures D. membrane fluidity at high and low temperatures

C The plasma membrane can be up to 50% composed of sterols. Sterols help stabilize the membrane at both spectrums of the temperature. At low temperatures, cholesterol increases fluidity because the ring structure of cholesterol does not allow for tight phospholipid tail packing. At high temperatures, cholesterol decreases membrane fluidity (the OH group of cholesterol prevents phospholipid dispersion) (C and D are wrong) Cholesterol decreases the permeability of membranes by filling in the holes between the fatty acid tails (A is wrong) The formation of atherosclerotic plaques, while related to cholesterol, is due to high levels of blood cholesterol, not membrane cholesterol

KHAN ACADEMY Which of these describes the formation of secondary protein structures? A. Several amino acids are joined together via peptide bonds. B. A protein binds with a substrate, lowering the activation energy of a reaction C. Amino acids fold into repeating patterns due to hydrogen bonding of the peptide backbone. D. A protein is exposed to extremely high heat, causing it to lose its secondary structure and be left with only its primary structure.

C. Amino acids fold into repeating patterns due to hydrogen bonding of the peptide backbone.

______________ is a special lipid that serves as the building block for hydrophobic steroid hormones. A. Phospholipids B. Triglycerides C. Cholesterol

C. Cholesterol

Which two are ringed in structure? A. Triglycerides B. Phospholipids C. Steroids D. Cholesterol

C. Steroids D. Cholesterol

KHAN ACADEMY Which of these describes a lipid? A. A molecule containing carbon, hydrogen, and oxygen in a 1:2:1 ratio B. A chain of amino acids folded and twisted into a molecule C. Three fatty acids attached to one glycerol molecule D. A series of nitrogenous bases attached to a sugar-phosphate backbone

C. Three fatty acids attached to one glycerol molecule

Because the process of oxidation (producing CO2) releases a large amount of energy, _____________ generally serves as the principal energy source for cellular metabolism.

Carbohydrates

___________ serve as the PRIMARY energy source for cellular metabolism.

Carbohydrates

How is cholesterol transported?

Carried in the blood packaged with Fats and Proteins called LIPOPROTEINS.

KHAN ACADEMY Which of the following are functions of proteins? Choose 2 answers A. Cell signaling B. Encoding genetic information C. Catalyzing chemical reactions D. Energy storage

Cell Signaling + Catalyzing Chemical Reactions Many Proteins are involved in cell signaling. For example, Hormones' are proteins that act as chemical signals, controlling specific processes such as growth, development, metabolism and reproduction. Some proteins are enzymes, enzymes act as catalysts, speeding up chemical reactions

Why is ATP known as a "high energy" structure at neutral pH? A. It exhibits a large decrease in free energy when it undergoes hydrolytic reactions B. The phosphate ion released from ATP hydrolysis is very reactive C. It causes cellular processes to proceed at faster rates D. Adenine is the best energy storage molecule of all the nitrogenous bases

Choice A is the best answer because it directly addresses the energetics of ATP hydrolysis. B discuses the reactivity of the release phosphate ion and not the structure of ATP itself, so it can be eliminated C can be eliminated because it describes the rate of cellular processes not the energy of ATP. D can be eliminated because the structure of adenine is not related to why ATP is a good energy storage molecule

Steroid Hormones are made from ____________.

Cholesterol

Which of the following best describes the secondary structure of a protein? A. Various folded polypeptide chains joining together to form a larger unit B. The amino acid sequence of the chain C. the polypeptide chain folding upon itself due to hydrophobic/hydrophilic interactions D. Peptide bonds hydrogen-bonding to one another to create a sheet-like structure

D The secondary structure of proteins is the initial folding of the polypeptide chain into a helices or b pleated sheets. A can be eliminated because it describes the formation of a quaternary protein B can be eliminated because it describes the primary protein structure C can be eliminated because it describes the tertiary protein structure

A genetic regulator is found to contain a lysine residue that is important for its binding to DNA. If a mutation were to occur such that a different amino acid replaces the lysine at that location, which of the following resulting amino acids would likely be the least harmful to its ability to bind DNA? A. Glycine B. Glutamate C. Aspartate D. Arginine

D While knowing the structures of the different amino acids is unlikely to be important for the MCAT, knowing which of the amino acids are a basic and which are acidic is likely to be relevant. In this case, since lysine is basic (and therefore best at binding the negatively charged DNA), one can assume that a mutation resulting in another basic amino acid would cause the lease change in its ability to bind DNA. Therefore, a mutation from lysine to arginine would cause the least harm. A mutation from lysine to glutamate or aspartate would cause the most harm (since they're both acidic) Glycine is a neutral amino acid (wrong)

KHAN ACADEMY Which of the following is an example of protein denaturation? A. Several amino acids are joined together via peptide bonds. B. A protein binds with a substrate, lowering the activation energy of a reaction C. Amino acids fold into repeating patterns due to hydrogen bonding of the peptide backbone. D. A protein is exposed to extremely high heat, causing it to lose its secondary structure and be left with only its primary structure.

D. A protein is exposed to extremely high heat, causing it to lose its secondary structure and be left with only its primary structure. Denaturation occurs when a protein unfolds, losing its higher-order structure, but NOT ITS PRIMARY structure. Changes in temperature or pH are common causes of proteins denaturation.

KHAN ACADEMY Which of these describes a nucleic acid? A. A molecule containing carbon, hydrogen, and oxygen in a 1:2:1 ratio B. A chain of amino acids folded and twisted into a molecule C. Three fatty acids attached to one glycerol molecule D. A series of nitrogenous bases attached to a sugar-phosphate backbone

D. A series of nitrogenous bases attached to a sugar-phosphate backbone

KHAN ACADEMY ___________ encode genetic information A. Proteins B. Carbohydrates C. Lipids D. Nucleic Acids

D. Nucleic Acids

At high temperatures, cholesterol __________ membrane fluidity (the OH group of cholesterol prevents phospholipid dispersion. A. Increases B. Decreases

Decreases

The structural determinants of membrane fluidity are 1. 2. 3.

Degree of saturation Tail Length Amount of Cholesterol

Odd and Even numbered fatty acids chains CAN be made in humans cells. T/F

FALSE they are synthesized two carbons at a time from acetate THERFORE can only be even numbered.

KHAN ACADEMY A person whose body makes only sickle cell hemoglobin will suffer symptoms of sickle cell anemia. These occur because the ________acid-to-________amino acid change makes the hemoglobin molecules assemble into long fibers. The fibers distort disc-shaped red blood cells into crescent shapes.

Glutamate acid - Valine amino acid change

___________ serves as energy storage for carbohydrates in ANIMALS and is composed of thousands of glucose units.

Glycogen

KHAN ACADEMY ------TYPES AND FUNCTIONS OF PROTEINS------ __________ are long-distance chemical signals released by endocrine cells (like the cells of your pituitary gland). They control specific physiological processes, such as growth, development, metabolism, and reproduction. While some are steroid-based (see the article on lipids), others are proteins.

Hormones

Which of the following may be considered an example of tertiary protein structure? I. Van der Waals interactions between two Phe R-Groups located far apart on a polypeptide II. Hydrogen bonds between backbone amino and carboxyl groups III. Covalent disulfide bonds between cysteine residues located far apart on a polypeptide

I. = is a great example of a tertiary bond II. = describes a secondary structure X III. = is a tertiary disulfide bond

KHAN ACADEMY The conformation, or shape, of a protein determines its function. There are four orders of protein structure: primary, secondary, tertiary, and quaternary. Which of the following statements is accurate regarding these protein structures? A. Interactions between the R groups in amino acids form tertiary structure. B. Proteins in a quaternary structure consist of a simple polypeptide chain C. Secondary structures are formed by multiple polypeptide chains. D. The two types of primary structure are \alphaαalpha helices and \betaβbeta pleated sheets.

Interactions between the R groups in amino acids form tertiary structure. Tertiary structure is primarily due to R group interactions between the amino acids that make up the protein. This gives proteins with tertiary structure a three-dimensional shape. R group interactions involved in tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces.

If a single polypeptide folds once and forms a beta-pleated sheet with itself, would this be parallel or antiparallel beta-pleated sheet?

It would be antiparallel because one participant in the B-pleated sheet would have a C to N direction, while the other would be running N to C. (imagine the folding process, they will run against each other -- anti-parallel)

A human space explorer crash-lands on a planet where the native inhabitants are entirely unable to digest glycogen but are able to digest cellulose. Consequently, they make their clothing out of glycogen-based material. The starving space explorer eats one of the native's shirts and the natives are amazed. Which of the following are true? I. The explorer can digest alpha-glycosidic linkages. II. The natives can digest alpha-glycosidic linkages. III. The native inhabitants can digest starch. A. I only B. I and III only C. II and III only D. I, II and III only

Item I is true: Humans can digest Alpha-glycosidic linkages, such as those found in glycogen. IF the native's shirts are made of glycogen our space explorer should have no trouble consuming and digesting them Item II is false: Cellulose contains Beta-Glycosidic linkages. If the natives can digest cellulose, but not glycogen, then they cannot digest Alpha-Glycosidic Linkages (D is wrong) Item III is false: Starch also contains Alpha-Glycosidic linkages. If the natives cannot digest glycogen, then they likely cannot digest start either (B is wrong)

_______ are enzymes that hydrolyze fats.

Lipases

Phospholipids also minimize their interactions with water by forming an orderly structure called a _______________ which is stabilized by Van der Waals forces. A. Micelle B. Lipid Bilayer

Lipid Bilayer

____________ are oily/fatty substances that play a role in fat store energy, in construction of cellular membrane barriers, and the formation of cholesterol.

Lipids

Carbon-Carbon bonds and hydrogen bonds are __________. A. Polar B. Non-Polar

Non-Polar Do NOT dissolve in water

What two ways is cholesterol obtained/synthesized?

OBTAINED in the diet SYNTHESIZED via the liver

Carbohydrates can be broken down to CO2 in a process called ________________. (also known as combustion or burning)

Oxidation

The bond that determines the primary location of a structure is the ______________. This is because it is the bond that links one amino acid to the next in a polypeptide.

Peptide Bond

KHAN ACADEMY DNA ---> Transcription ---> mRNA ---> Translation + tRNA + Amino Acids ----> _______

Protein

What is the difference between a disulfide bridge involved in quaternary structure and one involved in tertiary structure?

Quaternary disulfides are bonds that form between chains that aren't linked by peptide bonds. Tertiary disulfides are bonds that form between residues in the same polypeptide.

Would saturated or an unsaturated fatty acid residue have more van der Waals interactions with neighboring alkyl chains in a bilayer membrane?

The bent shape of the unsaturated fatty acids means that it doesn't fit in as well and has less contact with neighboring groups to form van der Waals interactions. Phospholipids composed of saturated fatty acids make the membrane more solid (its almost parallel shape can pack easier and closer together than its bent shape)

IF fatty acids are mixed into water, how are they likely to associate with each other?

The long hydrophobic chains will interact with each other to MINIMIZEW contact with water, exposing the charged carboxyl group to eh aqueous environment.

How are Triacylglycerols able to pack closer together than carbohydrates?

They are HYDROPHOBIC therefor can pack CLOSER TOGETHER carbs are relatively hydrophilic and carry a great amount of water molecules hydrogen bonded to their hydroxyl groups

How do free fatty acids interact in aqueous solution?

They form a structure called a MICELLE.

KHAN ACADEMY DNA ---> ______ ---> mRNA ---> Translation + tRNA + Amino Acids ----> Proteins

Transcription

KHAN ACADEMY DNA ---> Transcription ---> mRNA ---> _____ + ______ + _______ ----> Proteins

Translation + tRNA + Amino Acids

A peptide bond is formed between the CARBOXYL group of one amino acid and the A-AMINO group of another amino acid with the loss of __________.

WATER (Condensation reaction, any of a class of reactions in which two molecules combine, usually in the presence of a catalyst, with the elimination of water or some other simple molecule. The combination of two identical molecules is known as self-condensation.)

Why are fatty acids transformed into TRIACYLGYCEROL when stored?

because fatty acids are reactive chemicals

KHAN ACADEMY DNA ---> Transcription ---> ________ ---> Translation + tRNA + Amino Acids ----> Proteins

mRNA

KHAN ACADEMY The amino acids of a polypeptide are attached to their neighbors by covalent bonds known as a ______________

peptide bond

Each nucleotide contains

sugar, phosphate, base

In an ________ secondary protein structure, the carbonyl (C=O) of one amino acid is hydrogen-bonded to the amino H (N-H) of an amino acid that is four down the chain. This pattern of bonding pulls the polypeptide chain into a curled ribbon structure, with each turn of the helix containing 3.6 amino acids. The R groups of the amino acids stick outward from the α helix, where they are free to interact. A. β pleated sheet B. α helix

α helix