****Principles of Biochemistry: Exam One

Name and briefly describe the four basic types of weak interactions encountered in biochemistry.

(1) Hydrogen bonds form between a donor group: a hydrogen atom attached to an electronegative atom, and an acceptor group (an electronegative atom). Common acceptors are oxygen, nitrogen, and sulfur. (2) Electrostatic ionic interactions occur between two atoms with opposite charges; the strength of interaction depends upon the distance between ions and the environment around them. (3) van der Waals interactions occur between nonpolar molecules and arise from temporary dipoles caused by fluctuation in electron clouds. If dipoles of opposite signs align at the appropriate distance, an interaction can occur. These interactions are quite weak, but collectively among several atoms, they have a strong cumulative effect. (4)The hydrophobic effect is driven by the tendency for hydrophobic molecules to pack together in solution. By packing closely, hydrophobic molecules decrease overall surface area, decreasing the number of water molecules forming ordered (entropically unfavorable) structures around the hydrophobic molecules.

Name the four noncovalent interactions that occur within and between biomolecules that facilitate life processes at the molecule level. Which of these noncovalent interactions directly or indirectly involve H2O.

(1) Hydrogen bonds, (2) ionic interactions, (3) van der Waals interactions, and (4) hydrophobic effects. Hydrogen bonds form directly between H2O and biomolecules and between H2O molecules themselves, whereas hydrophobic effects are indirectly caused by H2O due to "water-avoiding" interactions between nonpolar molecules.

Name and briefly describe the three proposed mechanisms of how globular proteins fold in aqueous environments.

(1) Hydrophobic collapse model: Hydrophobic residues form the interior of the protein due to the hydrophobic effect, causing a loosely defined tertiary structure called a molten globule. Then, proximal residues in the molten globule interact to form well-ordered secondary and tertiary structures through van der Waals interactions and hydrogen bonding. (2) Framework model: Initially, local secondary structures form independently. Then, local secondary structures interact to form tertiary structures. (3) Nucleation model: Random interactions lead to a localized region of correct three-dimensional structure, which facilitates the formation of the surrounding tertiary and secondary structures.

What are the two phenotypical consequences produced by protein-folding diseases?

(1) The degradation of a misfolded protein, known as a loss-of- function effect because the activity of the particular protein is missing. (2) Protein aggregation, known as a gain-of-function effect because these proteins add a process to the cell. Gain-of- function protein-folding phenotypes can result from missense mutations or from accumulation of misfolded wild type proteins.

Explain why secondary structures are so prevalent in proteins.

(1) They are formed from combinations of phi and psi angles that minimize steric hindrance (2) they allow maximum hydrogen bonding interactions in the polypeptide backbone.

Be able to compare the strength among the noncovalent interactions.

(Strong) Ionic interaction > Hydrogen bond > Hydrophobic effect > van der Waals interaction (Weak)

Which of the following would be the most ionized (under standard physiological conditions)? phosphoric acid (pKa = 2.1) acetic acid (pKa = 4.7) phenol (pKa = 9.9) lactic acid

(pKa = 3.9), phosphoric acid (pKa = 2.1)

A reaction with which of the following would most likely be endergonic?

+ΔG

A reaction with which of the following would most likely be endergonic? low EA high EA +ΔG -ΔG

+ΔG

Amino Acid interaction w/substrate

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An acid with a pKa of 8.0 is present in a solution with a pH of 6.0. What is the ratio of the protonated to the deprotonated form of the acid?

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Be able to convert between the Ka and the pKa.

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Be able to distinguish between and name molecule type when given a molecular formula.

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Be able to distinguish between and name types of bonds when given molecular formulas.

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Be able to explain the limitations on rotation in a polypeptide chain. (i.e. Which bonds in a polypeptide chain can rotate, which can't and why.)

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Be able to explain the unique properties of Gly, Cis and Pro.

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Be able to give the ionization reaction and equilibrium constant equation (Keq) of water.

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Be able to give the monomer and polymer for each of the major biological macromolecule types.

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Be able to list the polypeptides components that can participate in non-covalent interactions and what they can interact with.

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Be able to list what is always the same between DNA and RNA and what is always different.

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Be able to list what is always the same between amino acids and what is always different.

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Be able to list what is always the same between types of amino acids and what is always different.

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Be able to name the type of polynucleotide that often exists as two associated polynucleotide strands. Describe how the two polynucleotide strands associate/are held together.

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Be able to state if enzymes affect free energy of a reaction and why.

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Be able to use a Lineweaver-Burk (double reciprocal) Plot for a reaction to determine the Vmax and KM and distinguish between inhibitor types.

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Be able to use a Mechaelis Menton Plot for a reaction to determine the Vmax and KM, if the reaction was enzyme catalyzed, distinguish between inhibitor types and be able to identify an allosteric enzyme curve.

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Be able to use the Ka and pKa to deterimine the strength of an acid.

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Be able to write and use the equations for calculating average rate (or average velocity) of a reaction.

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Be able to write the equation relating between pH and pKa. Be able to use the equation to determine ion concentration ratios at given pHs and how to make a buffer (ex. #18 on page 32 of book).

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Be able to write the equilibrium constant equation for an acid (Ka).

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Define (Delta)G'

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Define Vmax and KM.

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Define amphiphilic and describe how the term applies to phospholipids.

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Define buffer and describe its importance in biological systems.

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Define conjugated carbohydrate and give an example of where it can be found in cells and its function there.

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Define endergonic, exergonic and spontaneity as it relates to chemical reactions.

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Define endosome

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Define enzyme and describe how it works (be sure to include what it does in both a general sense and also the step-wise cycle, the type of macromolecule it most often is and where on the enzyme specificity is conferred).

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Define free energy and change in free energy as it relates to a chemical reaction.

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Define polymer and monomer. Name and explain the chemical reactions that convert between them.

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Define polynucleotide and be able to name the chemical components of the monomer (the nucleotide) that connect and the component that is not directly involved in linking to make a polymer (polynucleotide).

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Define saturated, unsaturated and polyunsaturated.

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Define the following: substrate, active site, transition state, activation energy, apoenzyme, cofactor, coenzyme, holoenzyme.

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Define transition state and relate it to substrate-enzyme interactions.

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Describe changes to amino acids at varying pHs using the list of pKas (include the species most prevalent at acidic, neutral and basic pHs).

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Describe cooperativity in relation to enzymes.

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Describe four mechanisms of enzyme catalysis.

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Describe how the rate of reaction changes with varying relative concentrations of enzyme and substrate and relate to reaction order.

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Describe the chemical components of and be able to recognize the structure of nucleotides in general and apply to ATP, GTP, cAMP, ribonucleotides and deoxyribonucleotides.

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Describe the chemical components of and be able to recognize the structure of steroids, including cholesterol.

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Describe the composition and characteristics (including fuctions) of lipids.

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Describe the effects changing reactant concentration can have on the rate of the reaction. Include the terms collision theory, zero order, first order and second order.

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Describe the roles and chemical structures of DNA and RNA. Be able to recognize each when given structures.

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Describe the structural differences between DNA and RNA.

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Describe where in a chemical pathway allosteric enzymes are found.

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Differentiate between free energy and standard free energy. Be able to state where/in what situations each is useful.

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Differentiate between kinetics and thermodynamics.

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Explain how allosteric enzymes can be regulated by activators and inhibitors.

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Explain how large variety is generated from universally limited monomer types.

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Explain how reactions with positive standard delta Gs can still occur in cells.

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Explain what determines if an enzyme-substrate complex will form.

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Explain what is meant by "monomer types are conserved".

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Explain what is meant by "sterically possible" and "energetically favorable".

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For carbohydrates give the general characteristic, molecular formula and names on different levels of polymerization.

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For each of the following types of enzymes be able to describe the type of reaction that is catalyzed: oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase.

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Give the chemical reaction that creates peptides from amino acids (include the name of the reaction, what portions of the amino acids react and the bond and products formed).

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Give the chemical reaction that creates peptides from amino acids (include the name of the reaction, what portions of the amino acids react and the bond and products formed). Also be sure to know that the reaction requires energy.

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Give the functions of carbohydrates in general and be able to give the functions of glycogen, starch and cellulose specifically.

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Give the major function of triglycerides, phospholipids, steroids and cholesterol.

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Give the name of the strongest intermolecular interaction that could occur between the resist protein's shown amino acids and the drug substrate 1 as it is oriented in the drawing. (assume physiological pH)

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Given a list of buffers and pKas, be able to determine the buffer that will be best at a given pH.

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Given a polypeptide sequence be able to identify the charged groups at various pHs (using the aa pKa table). Assume the polypeptide is linear (i.e. no interactions between groups).

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Given a polypeptide sequence, be able to identify which groups could interact with each other.

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Given a polypeptide structure or protein structure be able to distinguish whereeach amino acid starts and ends.

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Given a polypeptide structure, protein structure or amino acid sequence be able to determine polarity using the terms amino-terminal residue, N-terminal, carboxyl-terminal residues, C-terminal.

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Given a polypeptide structure, protein structure or amino acid sequence be able to identify peptide bonds, carboxyl groups, amino groups, R groups/side chains, a-carbons.

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Given a structure be able to differentiate between a purine and a pyramidine.

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Given a value for (delta)G for a reaction, be able to determine whether reactants or products have more free energy (or if there is an equal amount in both), whether it will be spontaneous and whether it will be endergonic or exergonic.

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Given amino acid structures (at neutral pH) be able to determine which are polar uncharged, polar charged, non-polar, hydrophobic and hydrophilic.

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Given an example of an enzyme catalyzed reaction with chemical structures be able to determine the type(s) of catalysis that the enzyme used.

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Given kcat values for various enzymes be able to determine with is most and least efficient.

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Given molecules be able to predict the intermolecular forces that may exist between them.

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Given pKas name the amino acids that have ionizable side chains.

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Given structures of amino acids, water or other chemicals determine the interactions that are likely to occur between them.

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Given the amino acid sequence of a polypeptide be able to draw the structure at various pHs (use pKa table and structures as reference).

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Given the amino acid structures at physiological (~ neutral) pH, be able to identify those that are polar charged, polar uncharged, nonpolar and the unique properties of Gly, Cis and Pro.

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Given the pKa, be able to determine the ionization (or lack of) for a generic amino acid (with the R-group just represented by R) and specific amino acids.s

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In what situation (what relative concentrations of enzyme to substrate) is the Mechaelis-Menton Model most useful?

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Know levels of protein structure and interactions that create/stabilize each.

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List common buffers in biological systems.

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List the names and biological functions of the four major types of nucleotides.

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Name and define the major types of intermolecular forces. Include the types of molecules involved in each type and the relative strength of each.

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Name and define the primary types of lipids

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Name and describe the chemical reactions by which ATP stores and releases energy.

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Name and describe the chemical reactions by which GTP stores and releases energy.

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Name and describe the names of the levels of protein structure. For each level,include the types where applicable, and the interactions or bonds that determine/stabilize each.

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Name the chemical components of and be able to recognize the structure of an amino acid.

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Name the chemical components of and be able to recognize the structure of phospholipids.

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Name the chemical components of and be able to recognize the structure of triglycerides.

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Name the types of bonds, describe how they are formed and what characteristic of the atoms involved determines the type.

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On a free energy graph of a reaction with and without an enzyme be able to identify where activation energy is and where the change in free energy is.

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Relate standard free energy to equilibrium.

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Translate the following amino acid sequence into one-letter code: Glu-Leu-Val-Ile-Ser-Ile-Ser-Leu-Ile-Val-Ile-Asn-Gly-Ile-Asn-Leu-Ala-Ser-Val- Glu-Gly-Ala-Ser

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Water is said to be polar but uncharged. How is it possible?

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What is an electronegative atom, and why are such atoms important in biochemistry?

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What is the relation between the pKa of an acid and the strength of the acid?

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When there is a much greater enzyme concentration than substrate concentration what order is the reaction? What happens to the rate when more substrate is added? What happens when more enzyme is added?

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When there is a much greater substrate concentration than enzyme concentration what order is the reaction? What happens to the rate when more substrate is added? What happens when more enzyme is added?

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Which amino acid side chains are capable of ionization?

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Which amino acids have positively charged R groups at pH 7?

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Which of the following amino acids have R groups that have hydrogen-bonding potential? Ala, Gly, Ser, Phe, Glu, Tyr, Ile, and Thr.

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What is the function a cAMP?

-ATP minus both second and third phosphate groups -Acts as "second messenger"Acts as "second messenger"

What is the function of ATP?

-Cell's most important energy-transfer molecule •Briefly stores energy gained from exergonic reactions •Releases energy within seconds for physiological work

Explain what prions and prion disease.

-Extremely small proteinacious infectious particles - Misfolded protein triggers misfolding in correctly folded prions and misfolded prions accumulate in cell membrane of brain cells and kill the cells

Enzymes affect reactions by__________.

-Stabilizing the transition state -Decreasing energy of activation -Forming an energetically favorable complex between enzyme and substrate in the transition state

What are proteins functions?

-Structure -Communication -Membrane Transport -Catalysis -Recognition and Protection -Movement -Cell adhesion

How are triglycerides formed and broken down?

-each bond formed by dehydration synthesis -broken down by hydrolysis

What are the four major types of lipids?

-fatty acids -triglycerides -phospholipids -steroids

Which of the following indicates that the reaction is spontaneous?

-ΔG

Which of the following indicates that the reaction is spontaneous? +ΔG high EA more than one of the listed answers. -ΔG low EA

-ΔG

The polarity of the solvent and other environmental factors can affect the pKa of a weak acid. Suppose the alpha amino group of a protein has a pKa of about 8.0 when it is exposed to H20 on the outside of a protein. 1.) Would you expect the pKa to be higher or lower than 8 if the group were buried in the hydrophobic interior of the protein? Explain. 2.) This same alpha amino group in the hydrophobic interior of the protein has the opportunity to form an ionic bond in that hydrophobic environment with a carboxylate group in the side chain of a charged Asp residue. Under these conditions, how would the pKa of this alpha amino group compare with the pKa of the alpha amino group in the hydrophobic interior of the protein without a nearby Asp residue to form this ionic bond?

1.) It is energetically unfavorable for the alpha amino group to be charged in the hydrophobic interior, thus the pKa would be lower. The proton can be released, as H30+, before the amino group enters the interior during the folding process because the strong electrostatic attraction between the lone pair electrons in the N atom and the proton is outweighed by the unfavorable condition of a charge in a hydrophobic environment. 2.) The pKa for this alpha amino group would increase relative to the example in (a), and would be close to the pKa of around 8. This ionic bond neutralizes both the NH3+ charge and the COO- charge, reducing the effect of having a charged group in the hydrophobic environment. Ionic bonds are stronger in a hydrophobic environment because it is unfavorable to have unbalanced charges.

The total carbonate pool in blood plasma (blood without red blood cells) is 0.025 M and consists of both HCO3^- and CO2(aq). The pKa for the dissociation of H2CO3 to produce HCO3^- + H^- at 37 degrees C is 6.1. Because H2CO3 is readily produced in blood from dissolved CO2(aq) + H2O, in a reaction catalyzed by the enzyme carbonic anhydrase, CO2(aq) can be considered the conjugate acid and HCO3^- the conjugate base in the bicarbonate buffering system. 1.) What is the ratio of HCO3^- and CO2(aq) in blood plasma at pH 7.4? 2.) What are the individual concentrations of CO2(aq) and HCO3^- under these same conditions?

1.) Using the Henderson-Hasselbalch equation: pH = pKa + log [A-]/[HA] 7.4 = 6.1 + log [HCO3^-]/[CO2(aq)] 7.4 - 6.1 = 1.3 = log [HCO3^-]/[CO2(aq)] 10^1.3 = 10^[HCO3^-]/[CO2(aq)] [HCO3^-]/[CO2(aq)] = 20/1 2.) 0.025 M = 2.5 x 10^-2 M = [HCO3^-] + [CO2(aq)] (2.5 x 10^-2 M)/(20 + 1) = [CO2(aq)] = 1.19 x 10^-3 M [HCO3^-] = 2.5 x 10^-2 M - 1.19 x 10^-3 M = 2.38 x 10^-2 M

Asprin (acetylsalicyclic acid) has a pKa of 3.4. What is the ratio of [A-] to [HA] at pH of 7.4 (the pH of blood)?

10^4

define dipeptide

2 amino acids

define tripeptide

3 amino acids linked together

Be able to distinguish four general classes of tertiary protein structure.

4 classes of structure: - Alpha helix - Beta sheet - alpha/beta: intermixed alpha helix and beta strands - Aplha+beta: alpha helix adjacent to beta strands (alpha helix is in one region and beta sheets in another)

Be able to define protein domain.

A compact independent folding module within the polypeptide chain with a defined function Globular proteins fold into domains. Range from 25-30 to several hundreds of amino acids. Large proteins have 2 or more distinct domains of compacts folded region.

a five carbon (pentose) sugar, one or more phosphate groups, a nitrogen containing base.

A nucleotide consists of... (Choose ALL that apply.)

define nucleic acids

A polymer consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins, for all cellular structures and activities. The two types of nucleic acids are DNA and RNA.

Be able to describe the structure the fibrous protein collagen.

A right handed triple helix fiber formed by 3 left handed helices. Helix has distinct amino acid sequence. - Gly-X-Y (X usually Proline, Y usually 4-hydroxyproline). - Glycine lies near center of the triple helix. Key amino acids: Gly, Pro Forces: - No hydrogen bonds within individual helix. - Hydrophobic effects and h bonds stabilize between the individual helices; crosslinks stabilized between the triple-helix fibers. Examples: skin, bone, teeth, tendons, cartilage Collagen add on: Within triple-helix fiber: H-bonds between amide hydrogen in Gly in one chain and carbonyl oxygen in Pro, or OH group in 4-hydroxyproline Between triple helix fiber: hydroxylated lysine cross-links stabilize between triple helix fibers

Clamp Type of chaperon protein:

ATP binding induces conformational changes that allows unfolded protein to bind. ATP hydrolysis induces another conformational change that fold and release the protein. It clamps on and induces a change that lets it bind: then it induces another change that correctly folds and releases the protein. Example: heat shock proteins

Buffer preparation is an important skill in biochemistry. Prepare the buffer as described below. Acetic acid has a pKa of 4.8. How many milliliter (mL) of 0.3M acetic acid and 0.2M sodium acetate and water are required to prepare 1 liter of 0.1M buffer solution having a pH of 5.8? (15 points)

Acetic acid = HA = 0.3M, pKa=4.8 Sodium acetate = A- = 0.2M Buffer solution = 0.1M, 1L, pH=5.8 pH = pKa + log ([A-]/[HA]) 5.8 = 4.8 + log ([A-]/[HA]) [A-]/[HA] = anti-log(5.8-4.8) [A-]/[HA] = 10 Percentage of A- = 10/11 * 100% = 90.9% Percentage of HA = 1/11 * 100% = 9.1% Use this equation: Molarity = # of moles / Volume in L In 0.1M, 1L, pH=5.8 Buffer solution: Acetic acid: Molarity = 0.1 M * 9.1% = 0.0091 M # of moles = 0.0091 M * 1 L = 0.0091 moles Volume (L) = 0.0091 moles / 0.3 M = 0.0303 L = 30.3 mL (from 0.3M acetic acid) Sodium acetate: Molarity = 0.1 M * 90.9% = 0.0909 M # of moles = 0.0909 M * 1 L = 0.0909 moles Volume (L) = 0.0909 moles / 0.2 M = 0.4545 L = 454.5 mL (from 0.2M sodium acetate) At the end, you need to bring the volume up to 1L by adding H2O = 1000 - 30.3 - 454.5 = 515.2 mL

Glycosylation

Addition of carbs with enzymes

What are purines? How many rings?

Adenine and Guanine. 2 rings

Alanine

Ala

Which macromolecule(s) is/are likely to form hydrogen bonds with water? Explain your choice(s).

All four macromolecules (lipids, proteins, nucleic acids, and carbohydrates) have the potential to form hydrogen bonds with water. This is because they all contain either hydrogen donor and/or acceptor groups.

Explain how an alpha helix can be amphipathic.

Alpha helices are amphipathic when residues that are hydrophobic (or hydrophilic) are placed three to four amino acids away from each other. Because there are 3.6 amino acids per turn, amino acids that are three to four amino acids apart will lie on the same side of the helix.

Cyclic Carbon Three

Always H

Cyclic Carbon Two

Always OH

Be able to determine the L and D form of amino acids.

Always have amino group pointing away from you and on top. Carboxyl group oriented away from you and on the bottom. L form has the R-group on the left side, D form has the R-group on the right side. L and D forms are enantiomers

Be able to recognize functional groups.

Amino Hydroxyl Sulfhydryl Phosphoryl Carboxyl Methyl

Be able to explain the characteristics of protein folding.

Amino acid sequence alone determines folding Rapid (why it is so hard to study) Takes place through many intermediate states Follows the laws of thermodynamics → folded proteins will reach lower energy states → more stable Cooperative and sequential process → the formation of one part of a structure leads to the formation of the remaining parts of the structure Different domains fold independently → more efficient Some protein folding is assisted by the two types of chaperon proteins

Match the levels of protein structure with the descriptions below. Amino acid sequence from the N to C terminus. Commonly occurring folds found in proteins, such as 𝛼-helix or β-sheet. The overall three-dimensional structure of the protein chain. The arrangement of subunits in a multi-subunit protein.

Amino acid sequence from the N to C terminus = Primary Commonly occurring folds found in proteins, such as 𝛼-helix or β-sheet = Secondary The overall three-dimensional structure of the protein chain = Tertiary The arrangement of subunits in a multi-subunit protein = Quaternary

What is the monomer and polymer for protein?

Amino acid, protein

Choose the substance below that will have the strongest intermolecular interaction with (i.e. be most soluble in) water. Nitrogen (N2) Ammonia (NH3) Methane (CH4) Oxygen (O2)

Ammonia (NH3)

Choose the substance below that will have the strongest intermolecular interaction with (i.e. be most soluble in) water. Oxygen (O2) Nitrogen (N2) Ammonia (NH3) Methane (CH4)

Ammonia (NH3)

What does it mean for a molecule to be amphipathic? Why are amphipathic lipids important for life?

Amphipathic molecules contain hydrophobic and hydrophilic regions. Amphipathic lipids form biological membranes, whose hydrophobic core is relatively impermeable to polar molecules. This maintains separation of the inside of cells from the environment and allows compartmentalization within cells where specific reactions can occur.

What is a haloenzyme?

An enzyme with cofactor bound; active enzyme

Arginine

Arg

Asparagine

Asn

Aspartate

Asp

In glycoproteins, the carb moiety is always attached to the amino acid residues

Asparagine, Serine, or Theronine

Polar, Negatively Charged R Groups

Aspartate (Asp) and Glutamate (Glu)

Acidic amino acids

Aspartic acid & glutamic acid

10^4

Aspirin (acetylsalicyclic acid) has a pKa of 3.4. What is the ratio of [A-] to [HA] at pH of 7.4 (the pH of blood)?

A homopolymer of histidine residues (polyhistidine) is able to form an α-helical structure or is unfolded, depending in the pH of the solution. Predict whether the structure of polyhistidine would be α-helical or unfolded at pH values of 4 and 8. Explain your reasoning.

At pH 4, the homopolymer of His residues would be unfolded. This is because at pH 4, His residues carry positive charges. These charges would repel each other preventing the formation of alpha helix. At pH 8, the homopolymer of His residues would be alpha helical. This is because at pH 8, the His residues are neutral with no repulsion among themselves. Therefore, alpha helix can be form.

Stereoisomers

Atoms are connected in the same order but differ in spatial arragement

Explain the function of Beta turns.

Beta Turns: function to connect Beta strands to another Beta strands in the antiparallel sheet There are type 1 and type 2 turns - differs in the orientation of the carbonyl oxygen. Both of these turns consist of four amino acids in which the carbonyl oxygen of the first amino acid residue is hydrogen bonded to the nitrogen atom of the fourth amino acid residue

_________ contain hydrogen bonds between parallel or antiparallel or a combination of parallel and antiparallel.

Beta-sheets

_________ contain hydrogen bonds between parallel or antiparallel or a combination of parallel and antiparallel. Beta-sheets Both Alpha-helices and Beta-sheets Alpha-helices Neither Alpha-helices nor Beta-sheets

Beta-sheets

Lectin

Bind oligosaccharides

What is characteristic of uncompetitive inhibitors?

Bind only ES complexes and prevent product release •CanNOTbe overcome with high substrate/inhibitor ratios Max velocity perm lower very quickly

Define competitive inhibitor

Blockage of the action of an enzyme on its substrate by replacement of the substrate with a similar but inactive compound that can combine with the active site of the enzyme

Common polar covalent bonds:

C-O, O-H, and N-H.

Which of the following is most likely to be a carbohydrate? C55H98O6 C9H14N2O6P C12H24O12 C6H13NO2 C5H4N4

C12H24O12

What is the base formula for a carbohydrate?

CH2O

What is the general formula of a carbohydrate and what are their general functions?

CH2O quickly mobilized source of energy -all digested carbohydrates converted to glucose -oxidized to make ATP

What are the unique properties of cysteine?

Can bond with another cysteine molecule to form a disulfide link

What are the unique properties of proline?

Can create kinks in a polypeptide chain disrupting proteins secondary structure

Which of the macromolecules would you expect to be soluble in water? Why?

Carbohydrates (or amylose), nucleic acids (or DNA), and proteins (or peptide) would be soluble in water. These molecules have the polar groups all over their structure that allows the formation of hydrogen bonds with water, making them soluble.

Define mitochondria

Cell organelle that produces ATP.

· In the closely packed interior of the tertiary structure of an enzyme, an alanine residue was changed by mutation to a valine, leading to a loss of enzyme activity, although that residue was not directly involved in the catalytic function of the enzyme. However, activity was partially regained when an additional mutation at a different position in the primary structure changed an isoleucine residue to a glycine. Based on the structure of the amino acid side chains of alanine, valine, isoleucine, and glycine, explain how the first mutation Ala --> Val likely caused a loss of activity, and the second mutation in another region of the protein, Ile --> Gly resulted in a partial recovery of enzyme activity.

Changing an Ala to a Val would introduce a bulkier side chain, taking up more volume in the protein interior; the resulting structural adjustments in the tertiary structure must be serious enough to cause the enzyme to lose activity. The replacement of an Ile residue with a Gly allows a tertiary structure close enough to the original structure for partial enzyme activity.

Be able to describe the function/mechanism of two types of chaperon proteins.

Chaperon proteins: - Prevent aggregates - Protect or repair damaged protein caused by temperature increases → chaperons are also called heat shock proteins for this reason - Bind to misfolding proteins and uses ATP hydrolysis to facilitate correct folding Two Types: - Clamp Type -Chamber Type

Hydrogen Bond

Charge attraction + partial covalent bond

Explain how the pKa of an amino acid can differ within a folded protein compared to that of the free amino acid in water.

Chemical properties of nearby functional groups can alter the pK. of specific amino acids if it is energetically favorable. For example, because positive or negative charges in the hydrophobic interior are energetically unfavorable, the pKa value of a side chain may be altered to favor the neutral state over the charged state at physiological pH.

Be able to describe the general structure of amino acids.

Chiral carbon, amino group, r group, and carboxylate group Used in acid-base properties Varied chemical functionality

Glycosaminoglycans

Chondroitin sulfate, Keratan sulfate, & Hyaluronic acid

Ammonia (NH3)

Choose the substance below that will have the strongest intermolecular interaction with (i.e. be most soluble in) water.

Be able to determine the net charge of an amino acid at certain pH.

Compare ionizable groups pH values and the specific pH of the solution to determine how many groups are deprotonated and how many are still protonated to tell you overall charge

What are three ways in which quaternary structures can provide increased functionality for a protein?

Complexes can provide structural properties not present in individual subunits and can be a mechanism for regulation of protein function through conformational changes affecting subunit interfaces. Also, bringing functional components into proximity can increase efficiency of biochemical processes.

Explain the features of functional groups:

Contains electronegative atoms, i.e. O, N, S Are usually electrically charged or polar Make organic molecules amphipathic Create multifunctional molecules that increase functional diversity Provide sites for intra- and intermolecular interaction: - Hydrogen bonding - Ionic interaction

Bond strength, greatest to weakest

Covalent Ionic Hydrogen van der Waals interaction

Covalent bond definition:

Covalent bonds are formed by atoms sharing their valence shell electrons to completely fill each atom's outer most shell. · Not all covalent bonds are created equal. · The more pairs of electrons shared between the atoms, the stronger the bond strength and the shorter the distance. · Covalent bonds can be either polar or nonpolar depending on the electronegativity difference between two atoms (Polar = > 0.5, Nonpolar = < 0.5). Common polar covalent bonds: C-O, O-H, and N-H.

Tertiary, Primary

Covalent bonds are or can be an interaction in protein___________structures

Cysteine

Cys

Sulfhydryl group

Cysteine

What is transcription?

DNA -----> RNA

How does information flow?

DNA -> RNA -> Protein

I- cell disease

Defective phosphotransferase

Hurler's Disease

Deficient alpha-iduronidase

Be able to explain the differences between protein degradation and denaturation.

Degradation: Protein chain is destroyed with covalent bonds of primary sequence cleaved. Denaturation: Protein chain unfolded with covalent bonds of primary sequence unbroken. - Loss of structural integrity and activity. - Ex. Boiled egg- goes from clear to white when boiled

Be able to explain how misfolded proteins can lead to disease.

Degrades: reduces the level of functional protein (loss of function). - Ex: Cystic Fibrosis: gene is mutated, leads to misfolded protein, leads to a degraded protein with loss of function. Aggregated: Interfere with cellular processes (gain of function). - Ex: Huntington's Disease: gene is expanded, misfolded protein, aggregated protein: gain of function. Creutzfeldt-Jakob Syndrome: Gene encodes wildtype protein, protein is in the wrong conformation, aggregated protein: gain of function. Transmissible Spongiform Encephalopathies: Accumulation of misfolded proteins that form large aggregates in brain tissues - Prion proteins

Monomers link via what reaction?

Dehydration (condensation)

Give the full names of DNA and RNA.

Deoxyribosenucleicacid and Ribosenucleicacid

Epimers

Differ at one asymmetric carbon

The smallest monosaccharides

Dihydroxyacetone Glyceraldehyde

Strongest Molecular forces of Ala

Dispersion/van der Waals

Strongest Molecular forces of Val

Dispersion/van der Waals

What is the difference between motifs and domains?

Domains when separated from each other can still function but when the structures in motifs are separated from each other it disrupts the nature of the folding and therefore loses its function.

What are triglycerides function?

Energy storgae

What is covalent catalysis?

Enzyme active site contains strong nucleophile, which creates a temporary covalent bond with electrophilicregion of substrate

What is the monomer and polymer for lipids?

Fatty acid, lipid

Be able to compare and contrast fibrous and globular proteins.

Fibrous Proteins: - Long extended chains, with high tensile strength. - Composed on 1 type of secondary structure. - 3-4 particular amino acids. - Insoluble in water because long hydrophobic chains. Globular Proteins: - spherical 3D structures, compact. - Incorporate multiple types of secondary structure. - Charged/polar amino acids on surface. - Hydrophobic amino acids on the interior. - Soluble

Aldaric Acid

First and last carbon are oxidized

Aldonic acid

First carbon is oxidized

Define chloroplast.

Found in plant cells and conducts photosynthesis, contains its own DNA

Be able to determine the ionic state of an amino acid at certain pH.

Found in the properties of the common amino acids found in proteins chart

Be able to identify the buffering region(s) in a titration curve.

Found within one pH unit above and below the pka

A antigen

GalNAc

B antigin

Galactose transferase

van der Waals interaction example:

Gecko feet: The tips of the furs on a Geckos feet branch out. The molecule on these branches allows for van der Waals interactions to occur with the molecule on the wall. (Same reason why Spiderman can climb a wall)

Be able to explain the thermodynamics of protein folding.

Gibbs free energy (Delta G): the difference between folded and unfolded state must be favorable (LESS THAN ZERO) in order to drive the folding process. Enthalpy (DeltaH) the heat content of the system , favorable because more interactions (covalent or disulfide) in the folded state than in the unfolded state. LESS THAN ZERO - In unfolded states there are ionic bonds that haven't formed and hydrophobic residues are exposed to polar molecules which is why this state is not favorable. Entropy (Delta S): the degree of freedom of a system. Unfavorable from protein folding (less than 0). However, it is highly favorable with surrounding water (S>>>>>)). Overall: GREATER THAN ZERO Energy landscape model of protein folding: Unfolded: high gibbs free energy= energetically unfavorable Native state is the best of them all Oligomers can often dissociate back into monomers Aggregates and amyloid fibrils are super stable, larger reduction in gibbs free energy, but often come from mutations.

Glutamine

Gln

Briefly explain in terms of the thermodynamics of protein folding why the folded structures of water-soluble globular proteins have extensive secondary structure.

Globular proteins will have some polar backbone groups (amide NH and carbonyl O groups) buried inside the protein. When these groups are in the protein's interior, they have lost their favorable hydrogen bond interactions with H20. The enthalpy change (delta H) for this process would be unfavorable (breaking bonds) if new hydrogen bonds were not made within the protein by secondary structures (hydrogen bonding within alpha helices and between Beta strands to form Beta sheets).

Glutamate

Glu

When glucose acts as a reducing agent what does it get oxidized to?

Gluconic acid

Glycine

Gly

Nonpolar, Hydrocarbon R Groups

Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Proline (Pro), and Methionine (Met)

Explain why Gly and Pro are common in turns and loops.

Glycine is often the second or third residue in β turns because the Hydrogen- atom side chain allows glycine to adopt the unusual dihedral angles necessary to make tight turns. Proline is often in a β turn because the cyclic ring side chain fits perfectly to make a turn Turns will have Pro and Gly next to each other. This is because the turn caused by the proline kink needs to be followed by a small sidechain (the hydrogen is the smallest side chain) to avoid steric hindrance

Hydrophobic amino acids

Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine, Phenylalanine, & Tryptophan

Covalent bond example:

H2O: the hydrogen atom has 1 electron and the oxygen atom has 6 electrons. Two hydrogen atoms can completely fill the outermost shell of an oxygen atom by sharing the electrons. When one pair of electrons is shared, it forms a single, covalent bond.

Histidine

His

Polar, Positively Charged R Groups

Histidine (His), Lysine (Lys), and Arginine (Arg)

Be able to use the nomenclature of homo- and hetero- in multi-subunits proteins.

Homodimer - 2 identical subunits Heterodimer- 2 different subunits *Dimer is 2, Trimer is 3, Tetramer is 4*

Be able to describe the structure of a protein.

How many amino acids? How many domains? (count colors) What is the major secondary structure (of each domain)? (From 4 general classes) What type of motif (does each domain have)?

How do you describe the quaternary structure?

How many subunits? Are these subunits the same? How do you call them? How many amino acids? How many domains? What are the secondary structures of each domain? What are the motifs in each domain?

Hydrogen bond example:

Hydrogen bond between two water molecules. The O attached to the other H is the Hydrogen-bond acceptor. The Other O is the Hydrogen bond-donor.

Hydrogen bond definition:

Hydrogen bonds can form when a hydrogen that is covalently bonded to an electronegative atom (e.g. oxygen), is in proximity to another electronegative atom. · Second strongest Noncovalent interaction (partial charges). · All hydrogen bonds have a hydrogen-bond acceptor and a hydrogen-bond donor. · The strength of the hydrogen bond depends on the donor and the acceptor. · Linear bonds are stronger than angled bonds. · NH and OH form hydrogen bonds. Hydrogen bond depends on formation of partial charges between the H and O molecules - H partially positive, O partly negative Main attractive force holding protein Secondary Structures in place

What are the unique properties of glycine?

Hydrogen is the only atom in the side chain. Allowing it to be in hydrophobic or hydrophilic environment. Often resides where two polypeptides come into close contact

R-groups of the Phe and Val

Hydrogen-bonding is an attractive force between all of the following EXCEPT_____________

If you have an enzyme that speeds up a reaction in which water is used to split a molecule it should be categorized as a(n) _______________.

Hydrolase

If you have an enzyme that speeds up a reaction in which water is used to split a molecule it should be categorized as a(n) _______________. Oxidoreductase Hydrolase Lyase Isomerase Transferase

Hydrolase

Be able to describe the differences among the three proposed protein folding pathways.

Hydrophobic collapse: Hydrophobic residues first form the interior and then form the secondary and tertiary structures Framework model: Local secondary structures form independently and then leads to the tertiary structures Nucleation model: Localized tertiary structures lead to other secondary and tertiary structures

Hydrophobic effect definition:

Hydrophobic effects are due to the tendency of nonpolar molecules to pack close together away from water. · Second weakest Noncovalent interaction (nonpolar, more permanent). · Hydrophobic effect is one of the main factors behind: protein folding, protein-protein association, formation of lipid micelles, and enzyme-substrate complex formation. · When nonpolar molecules are in polar solvent, they are surrounded by water. This is energetically unfavorable because there is a reduce in water movement. These nonpolar molecules group together, which reduces the surface area surrounded by water. This allows for fewer water molecules needed to be ordered (can move around freely), which makes it more energetically favorable. Main attractive force holding protein Tertiary and Quaternary Structures in place

What makes phospholipids amphiphilic?

Hydrophobic fatty acid tails and hydrophilic phosphate heads

Phospholipids interact with each other via ____________ to make a lipid bilayer (part of the membrane).

Hydrophobic interactions Electrostatic interactions Dispersion forces

Be able explain stabilizing forces in protein tertiary structure.

Hydrophobic interactions (major stabilizing force) and van der waals: hydrophobic portions stay away from H2O by compacting which can cause van der waals forces between neutral side chains . Hydrophobic residues are buried inside of protein - Disrupted by detergents Hydrogen bonds: between the r groups. - Disrupted by heat Ionic interactions: charged polar side chains will attract or repel each other based on charge. Metal ions like zinc and iron can form electrostatic interactions with charged side chains. - Disrupted by ph changes Disulfide bridges between cysteine amino acids:cysteines close to each other causes a bond through the oxidation of the SH bond. - Disrupted by a reductive environment

Hemiacetal

Hydroxyl + Aldehyde

Ether

Hydroxyl + Hydroxyl

Hemiketal

Hydroxyl + Ketone

Ester

Hydroxyl + carboxylic acid

Acidosis

Hyperventilate

Be able to distinguish right-handed from left-handed.

If you go up the stairs, which hand would you put on the handrail? If the handrail is on your right, that's a right-hand helix, otherwise it's a left-handed helix.

Isoleucine

Ile

Be able to explain the function and importance of biological buffer systems.

Important in maintaining blood pH level. When blood pH falls below 7.4, acidosis. When blood pH level rises above 7.4, alkalosis. To counter acidosis: Removal of excessive protons as H2O. To counter alkalosis: Addition of protons through an increase of H2CO3.

Absorption of food in the stomach and intestine depends on the ability of molecules to penetrate the cell membranes and pass into the bloodstream. Because hydrophobic molecules are more likely to be absorbed than hydrophilic or charged molecules, the absorption of orally administered drugs may depend on their pKa values and the pH in the digestive organs. Aspirin (acetylsalicylic acid) has an ionizable carboxyl group (circled below; pKa = 3.5). Calculate the percentage of the protonated form of aspirin available for absorption in the stomach (pH = 2.5) and in the intestine (pH = 5.0). (5 points)

In the stomach, pH = 2.5: pH = pKa + log [deprotonated] / [protonated] 2.5 = 3.5 + log [deprotonated] / [protonated] [deprotonated] / [protonated] = anti-log (2.5-3.5) [deprotonated] / [protonated] = 0.1 / 1 percentage of protonated form = 1 / (0.1 + 1) * 100% = 90.91% ---------------------- In the intestine, pH = 5.0: pH = pKa + log [deprotonated] / [protonated] 5 = 3.5 + log [deprotonated] / [protonated] [deprotonated] / [protonated] = anti-log (5-3.5) [deprotonated] / [protonated] = 31.62/ 1 percentage of protonated form = 1 / (31.62 + 1) * 100% = 3.07%

Tertiary

Interactions between amino acid R-groups determine___________

Strongest Molecular forces of Glu

Ion-dipole

Non-covalent bonds

Ionic Hydrogen bonds Van der Waal interactions Hydrophobic interactions

Strongest Molecular forces of Asp

Ionic bond (ion-ion)

Select the answer below that correctly lists from strongest to weakest. Ionic interaction > van der Waals > electrostatic interaction Ionic interaction > dipole-dipole interaction > van der Waals force Electrostatic interaction > van der Waals force > Ionic interaction None of the answers listed are correct.

Ionic interaction > van der Waals > electrostatic interaction

Ionic interaction example:

Ionic interaction between a Sodium atom (a cation, Na+) and a Chloride ion (an anion, Cl-) to form Sodium chloride (NaCl): The sodium atom has one outermost electron, which can be transferred to the chlorine atom, which has 7 valence electrons. This transfer allows both atoms to become more stable and creates a positive sodium ion and a negative chloride ion. These opposite charged ions attract each other, creating an ionic interaction.

List the following from strongest to weakest. van der Waals, ionic interactions, dipole-dipole interactions

Ionic interactions > dipole-dipole interactions > van der Waals

Ionic interaction definition:

Ionic interactions occur between opposite charged atoms or groups. · Strongest Noncovalent interaction (full positive/negative charges). · AKA also called charge-charge interactions or salt bridges. · The electronegativity difference between two atoms must be >2 (often formed between the most and the least electronegative atoms).

Name the four types of noncovalent interactions that stabilize tertiary and quaternary structures of proteins.

Ionic interactions, hydrogen bonds, van der Waals interactions, an hydrophobic interactions.

Diastereoisomers

Isomers that are not mirror images

What is a phospholipid?

It is a lipid that has a phosphate group attached to the glycerol and only two fatty acid chains.

Ka =

Ka= (H+ *A-)/HA pKa= -logKa

Which chiral isomer is more prevalent in cells.

L- Amino Acids

Alduronic acid

Last carbon is oxidized

Stronger the acid, ___(more/less)___ ionization?

Less,

Leucine

Leu

Do carbohydrates or lipids have more energy (calories/gram)?

Lipids

What are the four major categories of biological macromolecules?

Lipids Nucleic acid Saccarides Proteins

Which macromolecule(s) is/are likely to form hydrophobic effects? Explain your choice(s).

Lipids would be likely to experience hydrophobic effects because it has long nonpolar hydrocarbon chains.

Which macromolecule(s) is/are likely to form ionic interactions with another molecule? Explain your choice(s) by identifying the functional groups that allow such interaction.

Lipids, proteins (or peptide), and nucleic acids (or DNA) could form ionic interactions with another molecule. The negatively charged phosphate groups on the lipids and nucleic acids and the negatively charged COO- (carboxylate) groups and positively charged NH3+ (amino) groups on the proteins allow them to form ionic interactions with an opposite charge on another molecule.

Explain the function of loops.

Loops: functions to connect a Beta sheet to and Alpha helix. Usually range from 6- 20 residues long. They are rigid due to the multiple weak interactions between the tightly packed atoms. They are usually on the surface of proteins and contribute to the specificity of protein-protein interactions.

Lysine

Lys

Basic Amino acids

Lysine, Arginine, & Histidine

Be able to explain why weak acids are important in biochemistry.

Many biological molecules or their components are weak acids (e.g. amino acids, DNA & RNA). The ionization state of weak acids regulates not only their function but also their interaction with other biological molecules. The structure and function of these molecules is often regulated by the pH of the solution.

Methionine

Met

What is metal ion catalysis?

Metal can stabilize ionic intermediates (transition state)

You observe that the final product of a metabolic pathway inhibits the enzyme catalyzing the first committed step. You observed ______________ of a __________________. negative feedback

Michaelis-Menton enzyme positive feedback, Allosteric enzyme negative feedback, Allosteric enzyme positive feedback, Michaelis- Menton enzyme, negative feedback, Allosteric enzyme

What is the monomer and polymer for carbohydrates?

Monosaccaride, polysaccarides

Alpha-alpha corner and Beta alpha beta loops motifs:

Most common motifs that provides 2 layers of secondary structure

Be able to define quaternary protein structure.

Multiple polypeptide chain interactions to form a functional protein (multisubunit complex).

Be able to explain how amino acids are arrange to form amphipathic α helix.

Must not have like charges in close proximity that will repel each other and prevent helix formation Every 3-4 amino acids (takes 3.6 amino acids to make an alpha helical turn) must be a hydrophobic or hydrophilic amino acid, creating a hydrophilic and a hydrophobic surface This can be visualized with a helical wheel diagram

van der Waals interaction

Mutual synchronization of fluctuation charges

Be able to identify the N- and C-terminus.

N terminus of an alpha helix has a partial positive charge and the C terminus has a partial negative charge caused by the dipoles in each peptide bonds.

Glycation

Non specific addition of sugar resides

What types of inhibitors can be overcome with high substrate/inhibitor levels?

Noncompetitive, uncompetitive

Be able to differentiate nucleophiles and electrophiles.

Nucleophiles: electron-rich (either negative charge or unshared pair of electrons) - Ex: O, N, S, C Electrophiles: Positively charged Nucleophiles attack electrophiles - Ex: water can act as both nucleophilic and electrophilic; lone pair on oxygen (nucleophile) attacks the H of another water (electrophile)

What is the monomer and polymer for nucleic acids?

Nucleotide, nucleic acids

Cyclic Carbon Four

OH on Glucose & H on Galactose

How many strands does RNA have and what is it's backbone made of?

One and a sugar-phosphate backbone

What is a polyunsaturated fatty acid?

One with a large number of double bonds.

What is an unsaturated fatty acid?

One with double bonds.

What is a saturated fatty acid?

One without double bonds.

Peptide bonds form between two amino acids (aa) when the ______________ form water leaving a covalent bond between ________. Oxygen of the first aa and Hydrogen of the second aa, Carbon and Oxygen Oxygen of the first aa and Hydrogen of the second aa, Carbon and Nitrogen Hydrogen of the first aa and Oxygen of the second aa, Carbon and Nitrogen Hydrogen of the first aa and Oxygen of the second aa, Carbon and Oxygen,

Oxygen of the first aa and Hydrogen of the second aa, Carbon and Nitrogen

Peptide bonds form between two amino acids (aa) when the ______________ form water, leaving a covalent bond between ________.

Oxygen of the first aa and Hydrogen of the second aa, Carbon and Nitrogen

Distinguish parallel and antiparallel β-sheets.

Parallel: the strands in the N to C terminus direction forms a hydrogen bond with an adjacent strand that is also in the direction of N to C Antiparallel: the strands in the N to C terminus direction forms a hydrogen bond with an adjacent strand that is in the direction of C to N - Antiparallel is stronger due to the perpendicular angle of the hydrogen bonds

What is a peptide bond and how is it formed?

Peptide bond: joins the carboxylic acid group of one ammoacid and the amine group of another amino acid; formed by condensation reactions catalyzed by the ribosome. The reaction is unfavorable and requires ATP hydrolysis.

Be able to explain the resonance structure and the properties of the peptide bond.

Peptide bonds are rigid and has partial double bond characteristics due to resonance structures. The resonance is in the C-N and C=O bonds. - This restricts and confines the bond to either cis or trans. Almost always trans, glycine is the only amino acid that readily accepts cis formation which helps in Beta turns. Proline also helps in beta turns due to its intrinsic curve. Peptide grows towards C-terminus.

Be able to draw the peptide bond formation between amino acids.

Peptide bonds form between the carbon from the carboxylic group of one amino acid and the nitrogen from the amino group of another. An oxygen from the carboxylic group and 2 hydrogens from the amino group form H2O as peptide bonds between amino groups form. This is a condensation reaction.

Oxygen of first amino acid and hydrogen of second amino acid, Carbon of first amino acid and nitrogen of second amino acid.

Peptide bonds form between two amino acids (aa) when the

Phenylalanine

Phe

Nonpolar, Aromatic R Groups

Phenylalanine (Phe), Tyrosine (Tyr), and Tryptophan (Trp)

Be able to explain the phi and psi angles and how these angles between amino acids are used to generate a Ramachandran plot.

Phi ϕ angles: The torsional angle between the amide nitrogen and the Cα Psi ψ angles: the torsional angle between the Cα and the carbonyl carbon energetically favored combinations of ϕ and ψ angles can be plotted as ϕ versus ψ angles in a Ramachandran plot. Ideal combinations that do not result in steric hindrance are darkly colored areas.

Explain the physical relevance of phi and psi angles.

Phi: The torsional angle between the alpha carbon and the amide nitrogen of an amino acid psi: The angle between the alpha carbon and the carbonyl carbon. The values of phi and psi affect the conformation of the peptide backbone.

Electrostatic interactions, Hydrophobic interactions, Dispersion forces

Phospholipids interact with each other via _________ to make a lipid bilayer (part of the membrane).

dehydration

Polymers are made by____________ reactions

Prion Protein Transmissible Spongiform Encephalopathy:

PrPC= normal prion protein - Alpha helix PrPSC: Scrapies protein, accumulate in brain cells and form plaques -- infectious - Beta strands so they aggregate into trimers and then stack

Be able to explain the forces between the protein subunits.

Primarily hydrophobic effects. Ionic interactions help the alignment of the subunits and provide specificity. Hydrogen bonds and van der Waals can also be used to maintain quaternary structure because they easily associate and dissociate which allows for regulation of protein function.

Be able to describe the structure the fibrous protein silk fibroin.

Primarily made of beta sheets Amino acids: Gly, Ala, Ser Forces: Within sheet, H bonds within antiparallel beta strands (between backbone NH and CO groups on separate strands) and, van der Waals interaction between separate beta sheets Example: Silk protein of insects and spiders

Covalent bonds are or can be an interaction in protein __________ structure. (Select all that apply) None of the options listed Tertiary Primary Secondary

Primary +Tertiary

Be able to define primary protein structure.

Primary protein structure is the amino acid sequence, which determines how the polypeptide backbone folds into an energetically stable 3-d structure.

Be able to compare and contrast the stabilizing forces in 1°, 2°, 3° & 4° protein structure.

Primary structure stabilizing forces: Peptide bonds (covalent bonds) Secondary structure stabilizing forces: Hydrogen bonds between atoms of the backbone Tertiary structure stabilizing forces: Hydrophobic effects is main Quaternary structure stabilizing forces: Hydrophobic effects and ionic interactions

Covalent bonds are or can be an interaction in protein __________ structure. (Select all that apply) Primary Secondary None of the options listed Tertiary

Primary, Tertiary

Proline

Pro

What is the chemical reaction which GTP is the main energy source?

Protein Synthesis

Define and differentiate between protein conformation and denaturation.

Protein conformation is when the protein is formed to the correct shape in order to preform its primary duty. Denaturation is when the protein is unfolded.

What are the enthalpic and entropic factors that lead to the stabilization of a protein upon protein folding?

Protein folding introduces favorable enthalpic changes because there are more interactions in the folded state than in the unfolded state. These changes result from noncovalent interactions (or disulfide bond formation) because covalent bonds other than disulfide bonds do not change during folding. It is entropically unfavorable because it restricts the number of conformations a polypeptide can take, but the folded protein causes an increase in the disorder of water molecules, which is entropically favorable.

Hydrophobic effect example:

Protein folding: Hydrophobic effects are the driven force for protein folding. The nonpolar amino acids tend to group together and stay inside of the folded protein, so that they can stay away from aqueous solution.

Be able to explain the reason why many proteins form multisubunit complexes.

Provide active sites (where proteins can carry out their functions) that are not present in individual subunits. More stable (lower delta G). Increase functionality and efficiency by linking functional component in close proximity. Provide a mechanism for regulation of protein function through conformational changes that alter the protein subunit interfaces.

Hydrogen-bonding is an attractive force between all of the following EXCEPT ____________. R-groups of Phe and Val R-groups of Ser and Trp Protein components to make secondary structure DNA double strands Polysaccharides in water

R-groups of Phe and Val

Hydrogen-bonding is an attractive force between all of the following EXCEPT ____________. R-groups of Phe and Val R-groups of Ser and Trp Protein components to make secondary structure Polysaccharides in water DNA double strands

R-groups of Phe and Val

What is translation?

RNA ------> protein

Define translation

RNA to protein

How are sugar alcohols obtained?

Reduced

Phosphoryl Functional Group

Replace the O- on the left side with an R

Be able to explain the ribonuclease A folding experiment and its contribution to the understanding of protein folding.

Ribonuclease A was used to study protein folding. It has Disulfide bridges that help prevent unfolding. First, you have this protein with the correct disulfide bridges, is active and fully folded. Urea ( a denaturing agent) and Beta-mercaptoethanol (BME, and reducing agent) are added to the RibonucleaseA. - Urea: disrupt noncovalent bonds - BME: break disulfide bridges through reduction This will result in an inactive protein that is unfolded with broken disulfide bonds. IF you remove urea and BME, the protein will refold properly with correct disulfide bonds. IF you remove BME and then Urea, there will be randomly formed disulfide bonds in the protein so it will be incorrectly folded. - This can be undone by adding trace BME and no Urea. This will allow the incorrect bonds to be broken and the correct bonds to be formed. Overall the contribution of this experiment was that the amino acid sequence alone determine the native conformation.

Constitutional isomers

Same molecular formula, differ connectivity

Ionic interaction>dipole-dipole interaction>van der Waals force

Select the answer below that correctly lists from strongest to weakest.

Serine

Ser

Polar, Uncharged R Groups

Serine (Ser), Threonine (Thr), Cysteine (Cys), Asparagine (Asn), and Glutamine (Gln)

Hydroxyl groups

Serine, Threonine, & Tyrosine

What is a steroids function?

Signaling molecule that changes protein production (regulate at transcription level)

Define endoplasmic reticulum

Smooth and Rough Rough endoplasmic reticulum contains ribosomes that translate RNA into proteins Smooth ER forms a tubular network

Be able to explain the difference between strong and weak acids.

Strong acid: acids that completely dissociate in water - Ex: HCl → H+ + Cl- - Single forward arrow: symbolized complete dissociation Weak acid: acid that partially dissociate in water - Ex: CH3COOH ⇋ H+ + CH3COO- - Partial half arrows show it can go back and forth

Be able to distinguish and explain the features of different protein motifs.

Super secondary structures consisting of a combination of alpha helices, sheets, and loops in close proximity. Associated with particular functions. Motifs: - Alpha-alpha corner - Beta alpha beta loops - Helix bundle - Beta barrel - Greek key fold - Rossman fold - Tim barrel

Be able to describe how each different factors below disrupt a native protein: Temperature pH Detergents Chaotropic agents

Temperature: - Disrupts H-bonds and van der Waal's interaction. (In high temp., the energy increases the movement of the molecules so that the interactions become unstable.) - Looking at the graph, T(m)= transition curve midpoint where 50% of the proteins are fully folded and 50% are fully denatured. pH: - Can disrupt ionic interaction. - pH affects the ionization state of charged amino acids that are important for protein folding. Detergents: - Disrupt hydrophobic effect because the hydrophobic tail can penetrate into the protein interior and disrupt the hydrophobic effects among the nonpolar amino acids. Chaotropic agents: - Urea and guanidinium chloride are excellent H-bond formers. - Disrupt H-bonds because they compete H bonding in protein structure. - Disrupt hydrophobic effect by disrupting regular water structures.

Describe effects of temperature and pH on enzymes.

Temperature= 20-50 rise 50-100 fall. PH some enzymes thrive in lower PH, some in higher.

Electrostatic AND hydrophobic interactions can participate in holding ____________ structure together in proteins.

Tertiary

Electrostatic AND hydrophobic interactions can participate in holding ____________ structure together in proteins. Primary None of the options listed Secondary More than one of the options listed Tertiary

Tertiary

Interactions between amino acid R-groups determine__________.

Tertiary

Interactions between amino acid R-groups determine__________. Tertiary none of the options listed Primary Secondary

Tertiary

Be able to calculate the pI for an amino acid.

The average of the two pKas between the zwitterion

Define the central dogma of biology.

The central dogma describes the fundamental information flow in biological systems. DNA is replicated to form new DNA, which is transcribed into RNA. The RNA is translated into protein.

Define secondary structure of proteins

The corkscrew-like twists or folds formed by hydrogen bonds between amino acids in a polypeptide chain.

Define peptide bond

The covalent linkage between two amino acid units in a polypeptide; formed by a dehydration reaction.

Be able to describe the basic structure of α helix.

The hydrogen bonds between the carbonyl oxygen and the hydrogen atom attached to the nitrogen is optimal with an N-O distance of 2.8A. There are 3.6 residues per 360 turn. The distance along each axis between turns is 5.4A All hydrogen bonding backbone atoms (except terminus) form hydrogen bonds within the helix. An average alpha helix in proteins are around 10-14 residues Sidechains are sticking outwards

Explain how H-bonds are formed in β-sheets.

The hydrogen bonds in pleated sheets form between the amino hydrogen and carbonyl oxygen of adjacent beta strands. (antiparallel is stronger due to its perpendicular angle)

Be able to explain why knowing the ionic state of amino acid side chain is important.

The ionic state of an amino acid influences protein folding which affects the 3-d structure of the protein. The ionic state influences the activity of the proteins.

What kind of scale is the pH scale? What values are considered acidic, neutral, and basic?

The pH scale is a logarithmic scale. A value of 0--6.5 is considered acidic; 7.5-14 is considered basic. Anything in between those two ranges (6.5-7.5) is considered pH neutral.

Define transcription

The process of copying the genetic code from DNA into the form of mRNA

Explain the position and the role of R group in β-sheets.

The r-groups are positioned up and down in an alternating pattern. Depending on the polarity and arrangements of the r-groups the beta sheets can have a hydrophilic and hydrophobic surface. - Hydrophilic r groups face the aqueous solvents. - Hydrophobic r groups face the inside of protein.

Be able to explain the position and the role of R group in alpha helix.

The r-groups in secondary structures face outwards in helices R-groups play a key role in determining the structure and function of the protein. Folding of polypeptides depend on the r-groups involved. - I.e. electrostatic repulsions between amino side chains in an alpha helix can cause the helix to unfold. Steric hindrance caused by bulky side chains close to each other can cause disruption in the formation of Hbonds.

how are pKa and Ka related?

The smaller the value of Ka, the larger the value of pKa, the weaker the acid.

Define the hydrophobic effect.

The tendency of nonpolar molecules to interact with one another in the presence of water. The interaction is powered by the increase in entropy of water molecules when the nonpolar molecules are removed from the watery environment.

Define tertiary structure of proteins

The unique and complex three-dimensional shape formed by multiple twists of the secondary structure of the protein as amino acids come together and form hydrogen bonds or covalent sulfur-sulfur bonds.

Why is delta S negative when a nonpolar molecule such as limonene is dissolved in water?

The water molecules hydrogen bond into a cage-like structure around the hydrophobic limonene, increasing the order of the water molecules. This is entropically unfavorable, and therefore delta S is negative.

Be able to explain the structure of a water molecule.

There is an unequal electron distribution. - Oxygen is more electronegative than hydrogen. The angle of H-O-H bonds is 104.5 H2O exhibits permanent dipole moments.

Explain feedback inhibition

This is when a product of one enzyme becomes the substrate of another and after it becomes what it needs to become it will stop binding to enzymes. Then when there are enough of the final products one will go to the initial enzyme and bond to it (not at its active site) and this will stop anymore reactions

Threonine

Thr

Tryptophan

Trp

Both reactions with negative and +ΔGo' can occur spontaneously in cells.

True

Both reactions with negative and positive deltaGo' can occur spontaneously in cells. True or False True False

True

How many stands in DNA?

Two

Anhydride

Two carboxylic acids

Be able to describe the structure the fibrous protein keratin.

Two right-handed helices combine to form overall left-handed helix Homodimer of 2 helical peptides that wrap around each other to form a coiled coil structure Key amino acid: Cys Forces: Hydrogen bonding within the individual helix, hydrophobic effects between 2 helices, disulfide bonds between the Cysteine residues Examples: hair, nails, wool, claws the disulfide bonds are formed between Cys residues between the Coiled-coil dimer

Tyrosine

Tyr

In this type of enzymatic inhibition, the inhibitor can only bind to the enzyme-substrate complex to form an enzyme-substrate-inhibitor complex.

Uncompetitive

A homopolymer of lysine residues (polylysine) can adopt an alpha-helical conformation or is unfolded, depending on the pH of the solution. Predict whether the conformation of polylysine would be alpha-helical or unfolded at pH values of 1, 7, and 11. Explain your reasoning.

Unfolded at pH 1 (the charge repulsion from the numerous positively charged alpha amino groups); mostly unfolded at pH7 (even though the pKa of the alpha amino groups in the alpha-helix would be lower than the normal about 10.8, it would not be as low as pH7, and therefore still mostly protonated); alpha helical at pH 11 (above the pKa of 10.8, so slightly more than half of the alpha amino groups would be deprotonated and uncharged).

Chamber Type of chaperon protein:

Upper and Lower chambers, each one made of 7 subunits for 14 total subunits. GroES and ATP bind to the GroEL rings, trapping the unfolded protein within the folding chamber. Conformational changes releases GroES and folded protein exits the lower chamber. ATP hydrolysis causes a conformational change in the upper chamber that facilitates protein folding and resets the lower chamber for another round. A new unfolded protein inters the lower camber and this moves on in the same cycle.

Explain the roles of urea and Beta-mercaptoethanol in Arifinsen's experiments on protein folding using the protein ribonuclease. What was the most important conclusion resulting from this experiment that earned Arifinsen the Nobel Prize?

Urea is a denaturing agent: It unfolds proteins by disrupting noncovalent interactions; Beta-mercaptoethanol is a reducing agent: It breaks disulfide bonds. With sufficient amounts of both urea and Beta- mercaptoethanol, ribonuclease protein was completely unfolded. The important conclusion was that the primary structure has all the information necessary to specify the tertiary structure.

Be able to calculate the volume needed to prepare buffer solutions using weak acids and conjugate bases.

Use henderson-hasselbalch equation to find the ratio of deprotonated to protonated ions or the concentration of conjugate base to acid - pH=pKa + log([A-]/[HA]) - Solving for [A-]/[HA] Find the percent [A-] and percent [HA] - % [HA]= [HA] /{[HA] + [A-]} x 100 - % [A-]= [A-]/ {[A-]+[HA]} x 100 *Follow the next steps if you are given the molarity of the buffer solution* If given a molarity of the buffer solution the % [A-] and % [HA] will tell you the molarity of the acid and conjugate base within the buffer solution. - Multiply the molarity of the buffer by the decimal form of the percent of each to give you the molarity of acid and base. Convert from molarity to mol by multiplying your molarity of each by the volume of buffer. Divide the moles of acid by the molarity of the stock solution of acid to give you volume of acid in the buffer. Divide the moles of base by the molarity of the stock solution of base to give you the volume of base in the buffer ***Subtract your acid and base volumes from the total volume of buffer to give you the volume of water needed***

Be able to calculate the percentage of a weak acid and its conjugate base at certain pH.

Use henderson-hasselbalch equation to find the ratio of protonated and deprotonated ions or the ratio of conjugate base and weak acid. - pH = pKa + log ([A-]/[HA]) Next find the percent protonated form which gives you % of weak acid. - % [HA]= [HA] /{[HA] + [A-]} x 100 Find the percent deprotonated from which gives you % of conjugate base. - % [A-]= [A-]/ {[A-]+[HA]} x 100

Valine

Val

Which macromolecules would you expect to have the greatest contribution from van der Waals interactions? Explain your choice(s).

Van der Waals interactions would be most prevalent in the lipids because of the nonpolar hydrocarbon chains. Nonpolar atoms are required to form van der Waals interactions.

How is large variety generated from small number of monomer types?

Varying sequence, types of bondings, site of bonds,

Be able to explain why water is a good solvent for hydrophilic substances but not a good solvent for hydrophobic substances.

Water can act as a hydrogen-bond donor AND a hydrogen-bond acceptor Due to this hydrogen-bond forming character, water is a good solvent for ionic and polar substances (hydrophilic) - Amino acids and peptides, Small alcohols, Carbohydrates. (These substances contain functional groups (all but methyl groups) that allow them to form hydrogen bonds with water.) Water forms hydration layer around hydrophobic substances that it cannot form hydrogen bonds to - Water is not a good solvent for hydrophobic substances because interaction between nonpolar atoms and water causes an unfavorable change in free energy (ΔG>0) - Cannot bond with hydrocarbons, aromatic rings, and amphipathic molecules

Be able to explain the ionization of water.

Water ionization constant @ 25 C: Kw= [H+][OH-]=1.0x10-14 M2 [H+] and [OH-] are reciprocally related Only small % of water ionizes most stay at H2O

Be able to explain how weak acids and bases behave in water.

Weak acids and bases partially dissociate in water - Partial dissociation forms either a conjugate base/acid Use pKa to determine the strength of weak acid; how much it will dissociate → become deprotonated Ka= (H+ *A-)/HA pKa= -logKa

Why are weak bonds important in biochemistry

Weak bonds allow for flexibility in biological molecules due to their transient nature. However, these weak interactions provide great strength in numbers.

Briefly explain how proteins manage to "neutralize" the polarity of main-chain carbonyl O and amide NH groups that have to be buried in the hydrophobic interior of the protein when the protein folds.

When the amide and carbonyl groups are involved in hydrogen bonding, such as in alpha-helix and Beta-sheet structures, this serves to minimize the effects of these polar groups.

Glu

Which of the following amino acids are considered polar charged at physiological pH? (You may use the structures below, which will be provided on the exam and are under the modules section for your reference, to answer this question.)

Choice C above

Which of the following best represents the structure of an amino acid

C12H24O12

Which of the following is most likely to be a carbohydrate?

phosphoric acid (pKa=2.1)

Which of the following would be the most ionized (under standard physiological conditions)?

Be able to construct titration curves for weak acids.

Y-axis should be labeled: pH range and spacing between numbers should be consistent X-axis should be labeled OH- equivalents and spacing between numbers should be consistent Label the title of the chart Titration Curve for X molecule Label the pKa value at the ionizable group points, values from the chart provided by Kenny - This value tells you where 50% of that ionizable group is protonated and 50% is deprotonated Graph starts at 0,0 Graph flattens out at the pKa values for the ionizable groups then jumps up sharply to the next one

How would you describe a Mechaelis Menton enzymatic reaction in which there is no change in the rate of the reaction with addition of substrate?

Zero order

How would you describe a Mechaelis Menton enzymatic reaction in which there is no change in the rate of the reaction with addition of substrate? First order None of the given choices apply Second order Zero order

Zero order

Be able to define zwitterion and isoelectric point.

Zwitterion- A molecule carrying both positive and negative charges with a zero net charge Isoelectric point (PI): A point on the pH range where the average charge on the molecule sums to exactly zero.

What is Keq?

[product]/[reactants]

Tertiary

_________ structures of a protein can be held together by BOTH electrostatic AND hydrophobic interactions.

What is a triglyceride?

a lipid made of one glycerol and three fatty acids

Define cytoskeleton

a microscopic network of protein filaments and tubules in the cytoplasm of many living cells, giving them shape and coherence.

Define zwitterion and describe how the term applies to amino acid

a molecule or ion having separate positively and negatively charged groups.

Define oligopeptide

a peptide whose molecules contain a relatively small number of amino-acid residues.

Name the chemical components of an amino acid.

a α-carbon, amino group, carboxyl group

32. A reaction with which of the following would most likely be endergonic? a. +ΔG b. -ΔG c. low EA d. high EA

a. +ΔG

The basic structure of collagen consists of ___ _____ -handed helices, which form a _____ -handed _____- helix fiber. Select one: a. 3; left; right; triple b. 3; right; left; triple c. 2; left; right; double d. 2; right; left; double

a. 3; left; right; triple

39. The following image shows an enzyme-catalyzed isomerization reaction in glycolysis. What type(s) of catalysis mechanism is/are shown? a. Acid-base catalysis b. Covalent catalysis c. Metal ion catalysis d. Orientation catalysis e. More than one of the above

a. Acid-base catalysis

Which one of the following statements comparing alpha keratin and silk fibroin is true? Select one: a. Both fibers are heavily stabilized by hydrogen bonds. b. Both are primarily 𝛼-helical in character. c. Both fibers are intracellularly located. d. Both have covalently cross-linked strands.

a. Both fibers are heavily stabilized by hydrogen bonds.

6. Select the answer below that correctly lists from strongest to weakest. a. Ionic interaction, dipole-dipole interaction, van der Waals force b. Electrostatic interaction, van der Waals force, Ionic interaction c. Ionic interaction, van der Waals, electrostatic interaction d. None of the above

a. Ionic interaction, dipole-dipole interaction, van der Waals force

Which statement regarding protein secondary structures is correct? Select one: a. Protein 𝛼-helices and β-strands differ in that 𝛼-helices are stabilized by intrahelical hydrogen bonds, whereas β-strands are stabilized by hydrogen bonds across adjacent strands. b. Protein 𝛼-helices alternate with β-strands in stabilizing protein structure. c. β-strands allow 𝛼-helices to interact with one another. d. Protein 𝛼-helices are left-handed, whereas β-sheets are right-handed in arrangement.

a. Protein 𝛼-helices and β-strands differ in that 𝛼-helices are stabilized by intrahelical hydrogen bonds, whereas β-strands are stabilized by hydrogen bonds across adjacent strands.

Which statement about the 𝛼-helix is true? Select one: a. The amide backbone dipoles line up in one direction. b. The helical backbone structure is stabilized by ionic interactions. c. There are about five amino acids per helical turn. d. The center of the helix is an open channel.

a. The amide backbone dipoles line up in one direction.

34. Both reactions with negative and positive ΔGo' can occur spontaneously in cells. a. True b. False

a. True

At what point does the isoelectric point or pI occur? Select one: a. at the pH when all negative charges on a zwitterion counter the positive charges. b. when the molecule has a single electric charge. c. at pH = 7.0. d. when all of the acidic protons are neutralized with base.

a. at the pH when all negative charges on a zwitterion counter the positive charges.

Which gives rise to a favorable entropic (∆S) driving force for protein folding? Select one: a. the decrease in ordered water molecules as hydrophobic amino acids pack together b. the limiting of possible conformations as the protein folds c. the lining up of hydrogen bonds as the protein folds d. the stabilization caused by favorable electrostatic interactions of amino acid side chains

a. the decrease in ordered water molecules as hydrophobic amino acids pack together

The interaction between nonpolar molecules is best characterized as Select one: a. van der Waals interactions. b. a hydrogen bond. c. ionic interactions. d. a covalent bond.

a. van der Waals interactions.

What is the dominant secondary structure found in hair keratin? Select one: a. 𝛼-helices b. disulfide bonds c. β-sheets d. loop structures

a. 𝛼-helices

Enzymes affect reactions by__________.(Choose all that are true.) Decreasing energy of activation Forming an energetically favorable complex between enzyme and substrate in the transition state Stabilizing the transition state

all

Phospholipids interact with each other via ____________ to make a lipid bilayer (part of the membrane).(Choose all answers that apply.) Dispersion forces Electrostatic interactions Hydrophobic interactions

all

Glycogen

alpha 1-4, & alpha 1-6

Starch

alpha 1-4, & alpha 1-6

Where is the alpha carbon located? What groups are attached?

amino group (NH2), carboxyl group (COOH) and radical group (R group)

Define allosteric enzyme (include it's roles).

an enzyme that contains a region to which small, regulatory molecules ("effectors") may bind in addition to and separate from the substrate binding site and thereby affect the catalytic activity

Define lipids

any of a class of organic compounds that are fatty acids or their derivatives and are insoluble in water but soluble in organic solvents. They include many natural oils, waxes, and steroids.

Amide groups (NH2)

asparagine & glutamine

30. Which of the following indicates that the reaction is spontaneous? a. +ΔG b. -ΔG c. low EA d. high EA

b. -ΔG

7. Asprin (acetylsalicyclic acid) has a pKa of 3.4. What is the ratio of [A-] to [HA] at pH of 7.4 (the pH of blood)? a. 4 b. 10^4 c. -4 d. 10^-4 e. None of the above

b. 10^4

Which substance do you expect to have the strongest intermolecular interaction with (i.e. be most soluble in) water? Methane, CH4. b. Ammonia, NH3. c. Carbon dioxide, CO2. d. Nitrogen, N2.

b. Ammonia, NH3.

17. Below are pairs of amino acids that interact with each other via their R groups to maintain protein structure. Which will experience a change in their interaction (either a gain, loss or change specific type of interaction) when placed in a basic environment? a. Val-Ala b. Asn-Cys c. Gln-Ser d. Asp-Arg e. More than one of the above

b. Asn-Cys

37. What portion(s) of the graph below would be altered if an enzyme specific to the reaction was added? a. A b. B c. C d. D e. E f. More than one of the above

b. B

21. _______________ contain hydrogen bonds between parallel or antiparallel chains. a. Alpha-helices b. Beta-sheets c. Both alpha-helices and beta-sheets

b. Beta-sheets

Which of the following are negatively charged amino acids at pH = 7? Select one: a. Cys, Asn. b. Glu, Asp. c. Gln, Asn. d. Thr, Tyr.

b. Glu, Asp.

28. In which of the following do proteins move to the pH at which they have a net zero charge? a. Gel filtration chromatography b. Isoelectric focusing c. Afinity Chromatography d. Ion Exchange Chromatography e. More than one of the above

b. Isoelectric focusing

An 𝛼-helix has the sequence: NH3+-Ser-Glu-Gly-Asp-Trp-Gln-Leu-His-Val-Phe-Ala-Lys-Val-Glu-COO-. The carbonyl oxygen (in the peptide bond) of the histidine residue is hydrogen bonded to the amide nitrogen of Select one: a. Asp. b. Lys. c. Trp. d. Ala.

b. Lys.

29. Mass spectrometry distinguishes one amino acid from another based on ____________. a. Distance between peaks b. Mass c. pH d. pI

b. Mass

Which of the following statements about β-sheet structures is true? Select one: a. All amino acid side chains in antiparallel and parallel β-sheet structures point to one side of the sheet. b. The individual strands of all β-sheet structures are connected by turns, helices, or loops. c. All β-sheet structures form a spiraling backbone chain. d. Antiparallel β-sheets have a larger number of stabilizing H-bonds between backbone amides than parallel β-sheets.

b. The individual strands of all β-sheet structures are connected by turns, helices, or loops.

Using the figure below, which of the following best describes the titration curve? Select one: a. The equivalence point for the titration is pH = 7. b. The pKa for this weak acid is 4.76. c. This is a titration of a weak base by NaOH. d. The midpoint of the titration is pH = 7.

b. The pKa for this weak acid is 4.76.

What is a current hypothesis that explains the infectious nature of prion diseases? Select one: a. The small molecule denaturants found in infected cells are passed on to healthy cells. b. The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins. c. Unfavorable environmental factors negatively influence healthy cells. d. The virus responsible for prion diseases is transmissible.

b. The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins.

What is the difference between clamp-type and chamber-type chaperone proteins? Select one: a. One type is found extracellularly and one intracellularly. b. They are shaped differently. c. One folds proteins, whereas the other just protects them from unfolding. d. One uses ATP and the other does not.

b. They are shaped differently.

If an unknown solution has low pKa value, it can be said with certainty that it is Select one: a. a weak acid. b. a strong acid. c. pure water. d. a nonpolar solution.

b. a strong acid.

It is important for cells to degrade misfolded proteins. If misfolded proteins are not degraded, the misfolded proteins may Select one: a. waste excessive ATP in attempts to refold them. b. aggregate and interfere with normal cellular function. c. be excreted from the cell rather than recycled for building blocks. d. eventually refold, but not until excessive and sometimes fatal levels of cellular energy are spent.

b. aggregate and interfere with normal cellular function.

Which stabilizing force in protein tertiary structures is a covalent bonding force? Select one: a. van der Waals bonding b. disulfide bonding c. ionic bonding d. hydrophobic interactions

b. disulfide bonding

Limonene is a nonpolar molecule. The water molecules around it form Select one: a. hydrogen bonds with limonene and entropy increases. b. hydrogen bonds with themselves and entropy decreases. c. covalent bonds with limonene and entropy increases. d. ionic bonds with themselves and entropy decreases.

b. hydrogen bonds with themselves and entropy decreases.

33. ___________ is the abbreviation for change in free energy under standard conditions while ___________ is the abbreviation for a change in free energy under NON-standard conditions, such as those in a cell. a. ΔG, ΔGo' b. ΔGo', ΔG

b. ΔGo', ΔG

Cellulose

beta 1-4

Chitin

beta 1-4

What is a characteristic of an reversible inhibitor?

bind loosely to the enzyme

What is characteristic of noncompetitive inhibitors?

bind somewhere other than active site and change the shape of the enzyme so that the substrate will no longer fit the active site •CanNOTbe overcome with high substrate/inhibitor ratios Max velocity of enzyme cannot be reached (I.e. Vmaxis reduced)

What is a characteristic of an irreversible inhibitor?

bind tightly to the enzyme

Define noncompetitive inhibitors

binds to site other than substrate binding site

Amylopectin (starch)

branched

Phenylalanine key features

bulky side chain, very hydrophobic

23. Edman degradation sequences polypeptides in a step-wise manner by identifying ______ amino acid(s) at a time from the ______ end of the polypeptide. a. A single, C- terminus b. Groups of, C- terminus c. A single, N-terminus d. Groups of, N-terminus

c. A single, N-terminus

Which of the following is true? Select one: a. A basic solution does not contain H+. b. A neutral solution contains [H2O] = [H+]. c. An acidic solution has [H+] > [OH-]. d. A neutral solution does not contain any H+ or OH-.

c. An acidic solution has [H+] > [OH-].

27. You need to know the total amount of protein in your sample so you can design your experiment. Which of the following techniques will give you the information you need? a. SDS-PAGE ' b. FRET c. Bradford Assay d. Western blot

c. Bradford Assay

41. Polymers are made by _______________ reactions. a. Hydrolysis b. Replacement c. Dehydration d. Redox

c. Dehydration

25. You are trying to find an unknown protein with a specific activity from a cell lysate. Which of the following techniques would allow you identify the fraction that contains the protein you are interested in? a. Isoelectric focusing b. SDS-PAGE c. Functional assay d. Chromatography e. Centrifugation

c. Functional assay

4. Which of the following amino acids are considered polar charged at physiological pH. a. Ser b. Phe c. His d. Glu

c. His, d. Glu

36. If you have an enzyme that speeds up a reaction in which water is used to split a molecule it should be categorizes as a _______________. a. Oxidoreductase b. Transferase c. Hydrolase d. Lyase e. Isomerase

c. Hydrolase

18. Select the statement that correctly describes the carbon labeled with an *. See attached a. It is the alpha-carbon of the third amino acid b. It is a carboxyl carbon of the fourth amino acid c. It is an alpha-carbon of the fourth amino acid d. it is a carboxyl carbon of the third amino acid e. none of the above are correct

c. It is an alpha-carbon of the fourth amino acid

38. The following image shows an enzyme-catalyzed ATP hydrolysis reaction in glycolysis. What type(s) of catalysis mechanism is/are shown? a. Acid-base catalysis b. Covalent catalysis c. Metal ion catalysis d. Orientation catalysis e. More than one of the above

c. Metal ion catalysis

Which statement about amino acids is true? Select one: a. All naturally occurring amino acids in proteins are chiral. b. Most naturally occurring amino acids in proteins are D-amino acids. c. Most common natural amino acids in proteins are L-amino acids. d. Naturally occurring amino acids in proteins occur as a mixture of enantiomers.

c. Most common natural amino acids in proteins are L-amino acids.

16. Which of the following best represents the structure of an amino acid in basic solution (pH = 11)? a. R-CH(+NH2)-COO- b. R-CH(NH2)-COOH c. R-CH(NH2)-COO- d. R-CH(+NH3)-COOH e. R-CH(+NH3)-COO-

c. R-CH(NH2)-COO-

12. Electrostatic AND hydrophobic interactions can participate in holding ____________ structure together in proteins. a. Primary b. Secondary c. Tertiary d. More than one of the above e. None of the above

c. Tertiary

13. Interactions between amino acid R-groups determine__________. a. Primary b. Secondary c. Tertiary d. More than one of the above e. None of the above

c. Tertiary

19. Which of the following are hydrophobic amino acids? a. Ser b. Thr c. Trp d. His e. Met

c. Trp, e. Met

Given a solution with pH > pKa, what are the relative concentrations of A- and HA? Select one: a. [HA] = [A-] = 1 b. [HA] = [A-] c. [HA] < [A-] d. [HA] > [A-]

c. [HA] < [A-]

In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT Select one: a. hydrophobic effects. b. hydrogen bonds. c. covalent bonds. d. ionic bonds.

c. covalent bonds.

At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer? Select one: a. leucine-aspartate b. phenylalanine-lysine c. glutamate-lysine d. Glutamate-aspartate

c. glutamate-lysine

Below is an image of the top view of the triple-helix fiber of collagen. What is the identity of the amino acid labeled X (X is the 3 in the middle)? Select one: a. hydroxylated lysine b. 4-hydroxyproline c. glycine d. Proline

c. glycine

31. Which of the following indicates that a reaction will occur quickly? a. +ΔG b. -ΔG c. low EA d. high EA

c. low EA

Hydrophobic interactions between nonpolar molecules result from the Select one: a. tendency to maximize water's interaction with nonpolar molecules. b. strong attractions between nonpolar molecules. c. water becoming more ordered around the nonpolar molecule. d. water ionically bonding to the nonpolar molecule.

c. water becoming more ordered around the nonpolar molecule.

What is a conjugated carbohydrate? What is one function?

carbohydrate covalently bound to lipid (glycolipid) or protein (glycoproteins) - markers on the external surface of a cell membrane

Amide

carboxylic acid + amine

Define (delta)G

change in free energy

Classify all of the amino acids into the categories charged, hydrophobic, hydrophilic, and aromatic.

charged: aspartate, glutamate, lysine, arginine, histidine hydrophobic: glycine, alanine, proline, valine, leucine, isoleucine, methionine hydrophilic: serine, threonine, cysteine, asparagine, glutamine aromatic: phenylalanine, tyrosine, tryptophan

What is characteristic of competitive inhibitors?

compete with the enzyme for active sites •Can be overcome with high substrate/inhibitor ratios Max velocity of enzyme is reached only with higher substrate concentrations

Rossman fold motif

complex protein fold in which there are alternating alpha helices and beta strands. Found in proteins that bind nucleotides such as dehydrogenases.

Greek key fold motif

consists of 4 or more beta strands linked together to form a beta sheet structure; many channel proteins contain this motif to allow it to pass through hydrophobic cell membrane

Tim barrel motif

consists of alternating alpha helix and beta strand in the structure. Is found in large metabolic enzymes

Helix bundle motif

contains 4 or more alpha helices that provides hydrophobic pockets or hydrophilic channels in membrane protein to allow movement of hydrophilic molecules across membranes

Beta barrel motif

contains multiple twisted beta strand forming a beta sheet barrel structure. It forms an antiparallel beta sheet and forms a channel to allow polar molecules to pass through cellular membranes

Proline key features

cyclic structure with restricted confirmation, cannot form H-bonds in polypeptide, and found at protein turns because of shape

What is the maximum number of covalent bonds a carbon atom can make? a. 2 b. 8 c. 6 d. 4

d. 4

Which of the following statements regarding protein domains is true? Select one: a. A domain is a region absent of 𝛼-helices and β-sheets. b. Multiple domains require multiple subunits and a quaternary structure. c. Each protein has one unique domain. d. A domain can be composed of smaller structural units called motifs.

d. A domain can be composed of smaller structural units called motifs.

11. Phospholipids interact with each other via ____________ to make a lipid bilayer (part of the membrane). a. Electrostatic interactions b. Hydrophobic interactions c. Dispersion forces d. All of the above e. None of the above

d. All of the above

35. Enzymes affect reactions by__________. a. Forming an energetically favorable complex between enzyme and-substrate in the transition state b. Stabilizing the transition state c. Decreasing energy of activation d. All of the above e. None of the above

d. All of the above

40. A protein is cleaved into peptides and the amino acid sequence is determined using Edmand degradation. The data generated is shown below. Select the correct amino acid sequence of the full protein from the choices below. Data: Asp-Arg-Val Ile-His-Pro Pro-Phe Arg-Val-Tyr Val-Tyr-Ile a. Asp-Arg-Val-Ile-His-Pro-Pro-Phe-Arg-Val-Tyr-Val-Tyr-Ile b. Asp-Arg-Val-Ile-His-Pro-Phe-Arg-Val-Tyr-Val-Tyr-Ile c. Asp-Arg-Val-Tyr-Ile-His-Pro d. Asp-Arg-Val-Tyr-Ile-His-Pro-Phe

d. Asp-Arg-Val-Tyr-Ile-His-Pro-Phe

5. Which of the following is most likely to be a carbohydrate? a. C6H13NO2 b. C5H4N4 c. C9H14N2O6P d. C12H24O12 e. C55H98O6

d. C12H24O12

22. Which of the following uses charged beads (a matrix) to slow the flow of proteins of the opposite charge, thereby separating proteins based on charge? a. Gel filtration chromatography b. Isoelectric focusing c. Affinity Chromatography d. Ion Exchange Chromatography e. More than one of the above

d. Ion Exchange Chromatography

14. Covalent bonds can be an interaction in protein __________ structure. a. Primary b. Secondary c. Tertiary d. More than one of the above e. None of the above

d. More than one of the above

10. Peptide bonds form between two amino acids (aa) when the ______________ form water, leaving a covalent bond between ________. a. Hydrogen of the first aa and Oxygen of the second aa, Carbon and Oxygen b. Oxygen of the first aa and Hydrogen of the second aa, Carbon and Oxygen c. Hydrogen of the first aa and Oxygen of the second aa, Carbon and Nitrogen d. Oxygen of the first aa and Hydrogen of the second aa, Carbon and Nitrogen

d. Oxygen of the first aa and Hydrogen of the second aa, Carbon and Nitrogen

20. What is the highest level of structure in the protein below? a. Primary b. Secondary c. Tertiary d. Quarternary

d. Quarternary

Polymers are made by _______________ reactions. a. Hydrolysis b. Replacement c. Dehydration d. Redox

d. Redox

24. All of the following are true of 2-hybrid systems EXCEPT: a. They are used to determine if proteins interact b. When the two proteins bind the bait and prey are brought together c. When proteins interact a reporter protein is produced d. You know you have protein interaction if green light is given off when purple light is shined onto the cells e. All are true, no exceptions.

d. You know you have protein interaction if green light is given off when purple light is shined onto the cells

The proteins collagen, silk fibroin, and hair keratin have all of the following in common, EXCEPT that they Select one: a. are fibrous proteins. b. are composed of repeating amino acid sequences. c. play important structural roles in biology. d. are composed of 𝛼-helical structures.

d. are composed of 𝛼-helical structures.

The amino acid with a neutral side chain at neutral pH is Select one: a. aspartate. b. arginine. c. glutamate. d. asparagine.

d. asparagine.

Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure? Select one: a. nucleation model b. hydrophobic collapse model c. mutant globule d. framework model

d. framework model

Which interaction largely stabilizes protein secondary (2°) structures? Select one: a. hydrophobic effect. b. van der Waals interactions. c. disulfide bonds. d. hydrogen bonds.

d. hydrogen bonds.

8. Which of the following would be the most ionized? a. phenol (pKa = 9.9) b. acetic acid (pKa = 4.7) c. lactic acid, (pKa = 3.9) d. phosphoric acid (pKa = 2.1)

d. phosphoric acid (pKa = 2.1)

In a hydrogen bond between a water molecule and another water molecule, Select one: a. the hydrogen atom forms an ionic bond with a carbon on the other water. b. a hydrogen ion on the water molecule forms an ionic bond with the oxygen ion on the other water. c. a hydrogen on the water molecule forms a covalent bond to a hydrogen atom on the other water. d. the hydrogen bond typically forms between the oxygen atom of the water and the hydrogen on the other water.

d. the hydrogen bond typically forms between the oxygen atom of the water and the hydrogen on the other water.

The amino acid with the most hydrophobic side chain is Select one: a. asparagine. b. threonine. c. aspartate. d. valine.

d. valine.

Which of the following is the equation to calculate the average rate of a reaction?

d[product]/dt

Which of the following is the equation to calculate the average rate of a reaction? d[reactant]/dt k[reactant]n d[product]/dt

d[product]/dt

Polymers are made by ___________ reactions.

dehydration

Polymers are made by ___________ reactions. hydrolysis dehydration redox replacement

dehydration

What does the reaction order tell us?

describe how the concentration of the reactant affects the rate of the reaction

A nucleotide consists of _______________ a. one or more phosphate groups. b. a five carbon (pentose) sugar. c. a nitrogen containing base. d. a carboxyl group e. A, B & C

e. A, B & C

15. Hydrogen-bonding can be important in maintaining which of the following in proteins? a. Primary structure b. Secondary structure c. Tertiary Structure d. Quarternary Structure e. More than one of the above

e. More than one of the above

9. Hydrogen-bonding is an attractive force between all of the following EXCEPT a. DNA double strands b. Protein components to make secondary structure c. Polysaccharides in water d. R-groups of Ser and Trp e. R-groups of Phe and Val

e. R-groups of Phe and Val

What is the function of starch?

energy storage in plants

What is the function of glycogen?

energy storage polysaccharide in animal cells •Large and highly branched

What is the enzyme-substrate complex?

enzyme binds to its substrate

What is orientational catalysis?

enzymes hold substrates in the optimal position of the reaction

What is meant by "monomer types are conserved"?

eukaryotes, prokaryotes, and specialized cells use the same monomer types

Acetal linkage

hemiacetal + hydroxyl

Valine/Leucine key features

highly hydrophobic

Isoleucine key features

highly hydrophobic and additional stereocenter at second carbon

How are polymers broken down?

hydrolysis

Define carbohydrates

hydrophilic organic molecule (sugar or sweet)

What is an apoenzyme?

inactive enzyme that requires cofactor for activation

What is the function of GTP?

involved in energy transfer, Can donate phosphate group to other molecules

What is the function of cellulose?

it is the structural component of plant cell walls

What determines a protein's function?

its structure (conformation)

What is a steroid?

lipids characterized by a carbon skeleton consisting of four fused rings

What is the isoelectric point of a protein? What is the specific term that describes amino acids at this point?

lsoelectric point of a protein: The pH at which it carries no net charge term: zwitterions

Sulfur containing hydrophobic amino acid

methionine

Enantiomers

mirror images at all chiral carbons

What is a prion?

misfolded protein

What is Amphipathic?

molecule that contains a hydrophobic region (hydrocarbon) & hydrophilic region (functional group)

What are the three types of carbohydrates?

monosaccharides, disaccharides, polysaccharides

You observe that the final product of a metabolic pathway inhibits the enzyme catalyzing the first committed step. You observed ______________ of a __________________.

negative feedback, Allosteric enzyme

What is a cofactor?

non-protein molecule necessary to activate apoenzyme(make it an holoenzyme)

What is the turnover number?

number of substrate molecules an enzyme converts to a product per second

A nucleotide consists of... (Choose ALL that apply.) one or more phosphate groups. a five carbon (pentose) sugar. a nitrogen containing base. a carboxyl group.

one or more phosphate groups. a five carbon (pentose) sugar. a nitrogen containing base.

A nucleotide consists of...

one or more phosphate groups. a nitrogen containing base. a five carbon (pentose) sugar.

Define lysosomes

organelle that breaks down organelles that are no longer useful

How are sugar acids obtained?

oxidation

to form a disulfide bond you _____ cystine

oxidize

Be able to define pH and pKa.

pH is the negative logarithm of the concentration of H+ → which is the acidity or basicity of an aqueous solution (pH = -log[H+]) - pH tells the extent of dissociation of a solution pKa is the negative logarithm of Ka → which is the constant for acid dissociation - The lower the pKa, the stronger the weak acid

Be able to solve weak acid problems with the Henderson-Hasslebalch equation.

pH= pKa + log([A-]/[HA]) Tells how much of the weak acid will become deprotonated Shows direct relationship between the pH of a solution and the ratio of the deprotonated form [A-] to the protonated form [HA] of some ionizable group.

Buffers work best when ...

pH=pKa

Explain the relationship between pH, pKa and ionization.

pKa = −log Ka pH = pka + log ([A-]/[HA])

pKa =

pKa= -logKa

What are the three components of nucleotides?

phosphate group, pentose sugar, nitrogenous base

Which of the following would be the most ionized (under standard physiological conditions)? acetic acid (pKa = 4.7) lactic acid, (pKa = 3.9) phenol (pKa = 9.9) phosphoric acid (pKa = 2.1)

phosphoric acid (pKa = 2.1)

Describe the basic structure β-strand.

polypeptide chains adjacent to each other held together by hydrogen bonds between the backbone The distance between 2 amino acids is 3.2-3.4 -> they are almost fully extended

Be able to identify the cis and trans configuration of a polypeptide.

polypeptides are usually in trans 6 configuration.

Define primary structure of proteins

sequence of amino acids in a polypeptide chain

What are the hydroxyl containing amnio acids

serine, threonine, & tyrosine

neutral hydrophilic amino acids

serine, threonine, & tyrosine

Glycine key features

small and flexible, used in turns in proteins and non-chiral alpha carbon

Alanine key features

small, chemically inactive, large portion of proteins

What are phospholipids function?

structural foundation of cell membrane

___________ is the abbreviation for change in free energy under standard conditions while ___________ is the abbreviation for a change in free energy under NON-standard conditions

such as those in a cell. ΔG, ΔGo' ΔGo', ΔG , ΔGo', ΔG

What is cholesterol?

the 'parent' steroid from which the other steroids are synthesized

If the pH is > pKa then

the group is mostly de-protonated

If the pH is < pKa of a group by 1 unit, then

the group is mostly protonated

Be able to explain how H-bonds are formed in alpha helix.

the hydrogen bonds that form in an α helix between the carbonyl oxygen (residue n) and the hydrogen atom attached to the nitrogen in the peptide bond located four amino acids away (n + 4).

In this type of enzymatic inhibition

the inhibitor can only bind to the enzyme-substrate complex to form an enzyme-substrate-inhibitor complex. None of the given choices Irreversible Uncompetative Noncompetitive Competitive ,Uncompetative

𝛂 helix:

the most common elements of secondary structure in proteins is the right-handed 𝛂 helix. Stabilized by numerous intrastrand hydrogen bonds and it rotates around an imaginary central rod in a right-hand direction. Right hand helix: favorable and abundant Left hand helix: unfavorable, less stable, short, and infrequent *proline can disrupt the alpha helix because its rotation is restricted due to its r-group and its amino group does not have an H available for hydrogen bonding.*

Define replication

the process of copying DNA

Be able to define secondary protein structure.

the regular repetitive arrangement of local regions of the polypeptide backbone. There are three major structures: β strands, α helices, and β turns. (backbone interactions)

Define cell membrane

the semipermeable membrane surrounding the cytoplasm of a cell.

Be able to define tertiary protein structure.

the spatial location of all the atoms in the polypeptide chain. The overall 3-D arrangement of polypeptides. (interactions between secondary structure and conformations of side chains). - A protein becomes functional when it is folded into its tertiary structure.

Define kcat .

the turnover number, the number of times each enzyme site converts substrate to product per unit time.

What are the pyridines? How many rings?

thymine, cytosine, and uracil. 1 ring

Amylose (starch)

unbranched

Methionine key features

unreactive sulfur makes up thioester side chain, 1st amino acid in polypeptides

van der Waals interaction definition:

van der Waals interactions occur between neutral molecules/atoms by temporary dipole moments because of fluctuation in electron clouds. · Weakest Noncovalent interaction (nonpolar, transient). · Interactions between nonpolar molecules. · Strong repulsion is when atoms are too close. Weak attraction is when atoms are farther apart. · Maximum van der Waals attraction occurs at a distance slightly greater than the sum of the van der Waals radii of the two atoms.

Tyrosine/Tryptophan key features

very hydrophobic, amphipathic and found at transition from exterior to interior of a protein

Define uncompetitive inhibitors

when an enzyme inhibitor binds only to the complex formed between the enzyme and the substrate

define polypeptide.

~ A molecule formed from more than 2 amino acids bonded by peptide bonds

Define protein

~ Proteins are large macromolecules consisting of more than one amino acid chain

Define peptide

~ Short chains of more than two amino acids bonded in a chain

Covalent bond features

· Not all covalent bonds are created equal. · The more pairs of electrons shared between the atoms, the stronger the bond strength and the shorter the distance. · Covalent bonds can be either polar or nonpolar depending on the electronegativity difference between two atoms (Polar = > 0.5, Nonpolar = < 0.5). · Common polar covalent bonds: C-O, O-H, and N-H.

Hydrogen bond features:

· Second strongest Noncovalent interaction (partial charges). · All hydrogen bonds have a hydrogen-bond acceptor and a hydrogen-bond donor. · The strength of the hydrogen bond depends on the donor and the acceptor. · Linear bonds are stronger than angled bonds. · NH and OH form hydrogen bonds. Hydrogen bond depends on formation of partial charges between the H and O molecules - H partially positive, O partly negative Main attractive force holding protein Secondary Structures in place

Hydrophobic effect features:

· Second weakest Noncovalent interaction (nonpolar, more permanent). · Hydrophobic effect is one of the main factors behind: protein folding, protein-protein association, formation of lipid micelles, and enzyme-substrate complex formation. · When nonpolar molecules are in polar solvent, they are surrounded by water. This is energetically unfavorable because there is a reduce in water movement. These nonpolar molecules group together, which reduces the surface area surrounded by water. This allows for fewer water molecules needed to be ordered (can move around freely), which makes it more energetically favorable. Main attractive force holding protein Tertiary and Quaternary Structures in place

Ionic interaction features:

· Strongest Noncovalent interaction (full positive/negative charges). · AKA also called charge-charge interactions or salt bridges. · The electronegativity difference between two atoms must be >2 (often formed between the most and the least electronegative atoms).

van der Waals interaction features:

· Weakest Noncovalent interaction (nonpolar, transient). · Interactions between nonpolar molecules. · Strong repulsion is when atoms are too close. Weak attraction is when atoms are farther apart. · Maximum van der Waals attraction occurs at a distance slightly greater than the sum of the van der Waals radii of the two atoms.

___________ is the abbreviation for change in free energy under standard conditions while ___________ is the abbreviation for a change in free energy under NON-standard conditions, such as those in a cell.

ΔGo', ΔG

Valine (Val), Leucine (Leu), and Isoleucine (Ile) details

• Branched hydrocarbon side chain. • Highly hydrophobic. • Ile has an additional stereocenter (at *).

Phenylalanine (Phe), Tyrosine (Tyr), and Tryptophan (Trp) details

• Bulky aromatic side chain. • Very hydrophobic, but Phe is more hydrophobic. • Tyr and Trp are amphipathic and are often found at the transition of exterior and interior of a protein. • Tyr and Trp absorb UV light at 280 nm, can be used to measure protein concentration.

Proline (Pro) details

• Forms cyclic structure with restricted conformation. • Cannot form H-bonds in a polypeptide. • Usually found at the turns of polypeptide chain.

Asparagine (Asn) and Glutamine (Gln) details

• Highly hydrophilic because the side chains can form hydrogen bonds. • Their side chains can act as both H-bond donor or acceptor.

Alanine (Ala) details

• Methyl group side chain. • Relatively small. • Chemically inactive. • Flexible. • Gly + Ala = 15% in proteins.

Serine (Ser), Threonine (Thr), and Cysteine (Cys) details

• Ser & Thr have a hydroxyl group, can be phosphorylated to regulate enzyme function. • Thr has a second stereocenter (at *). • Cys has a sulfhydryl group, can form disulfide bridge in folded protein. • They are hydrophilic and good nucleophiles playing key roles in enzyme activity.

Aspartate (Asp) and Glutamate (Glu) details

• Side chains are negatively charged --> highly hydrophilic. • Asp and Glu are dicarboxylic amino acid. • These charges are important for protein separation.

Histidine (His), Lysine (Lys), and Arginine (Arg) details

• Side chains are positively charged --> highly hydrophilic. • His carries a positive charge at pH 6, function as both a hydrogen donor and acceptor at neutral pH. • These charges are important for protein separation.

Methionine (Met) details

• Thioester sidechain makes it hydrophobic. • Sulfur is unreactive. • 1st amino acid in a polypeptide.

Glycine (Gly) details

• α-carbon is not chiral. • Smallest. • Chemically inactive. • Flexible and able to form sharp turns in proteins.