Biochemistry 1.1
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Questions and Answers

What is the central carbon atom in amino acids commonly referred to as?

  • Beta-carbon
  • Amino-carbon
  • Alpha-carbon (correct)
  • Gamma-carbon

    • What is the primary difference between serine and cysteine?

  • Cysteine contains a sulfur atom in its thiol group. (correct)
  • Serine has an additional methyl group attached.
  • Serine has a thiol group instead of a hydroxyl group.
  • Cysteine has an oxygen atom in its structure.

    • Which groups are directly bonded to the α-carbon in proteinogenic amino acids?

  • Amino and carboxyl groups (correct)
  • Carbonyl and keto groups
  • Phosphate and sulfhydryl groups
  • Hydroxyl and methyl groups

    • Which amino acid is nearly identical to serine but includes an extra methyl group?

    <p>Threonine (B)</p> Signup and view all the answers

    Which of the following amino acids is considered nonproteinogenic?

    <p>GABA (B)</p> Signup and view all the answers

    What characterizes an amino acid's zwitterionic form in a physiological environment?

    <p>It has no overall electric charge. (A)</p> Signup and view all the answers

    What role do the R-groups or side chains play in amino acids?

    <p>They determine the identity and unique properties of the amino acid (B)</p> Signup and view all the answers

    What distinguishes valine from threonine?

    <p>Threonine has an extra methyl group. (B)</p> Signup and view all the answers

    Which amino acid is considered the simplest due to its side chain structure?

    <p>Glycine (B)</p> Signup and view all the answers

    Which amino acid has an amino group located on its γ-carbon?

    <p>β-Alanine (D)</p> Signup and view all the answers

    Which amino acid connects its side chain to both the alpha carbon and the backbone nitrogen?

    <p>Proline (C)</p> Signup and view all the answers

    How are the proteinogenic amino acids categorized?

    <p>By the unique properties of their R-groups (B)</p> Signup and view all the answers

    Which of the following correctly describes alanine's side chain?

    <p>It has a methyl group. (A)</p> Signup and view all the answers

    What is the one-letter code for cysteine?

    <p>C (A)</p> Signup and view all the answers

    What happens to the amino acid structure when it is dissolved in aprotic solvents?

    <p>It maintains an electrically neutral form (B)</p> Signup and view all the answers

    Which amino acid structure contains a thiol group?

    <p>Cysteine (B)</p> Signup and view all the answers

    Why is it important to memorize the structures of each amino acid?

    <p>To recognize their unique properties when forming proteins. (C)</p> Signup and view all the answers

    What functional group does serine contain in its side chain?

    <p>A hydroxyl group (C)</p> Signup and view all the answers

    Which amino acid is specifically noted for playing an important role as an inhibitory neurotransmitter?

    <p>GABA (A)</p> Signup and view all the answers

    Isoleucine has the same molecular formula as which other amino acid?

    <p>Leucine (A)</p> Signup and view all the answers

    What is the one-letter code for threonine?

    <p>T (D)</p> Signup and view all the answers

    What is the three-letter code for glycine?

    <p>Gly (D)</p> Signup and view all the answers

    Which amino acid has a side chain derived from alanine?

    <p>Serine (B)</p> Signup and view all the answers

    What is the one-letter code for alanine?

    <p>A (B)</p> Signup and view all the answers

    What is the one-letter code for aspartate?

    <p>D (D)</p> Signup and view all the answers

    Which of the following amino acids contains a carboxylic acid group in its side chain?

    <p>Aspartic Acid (B)</p> Signup and view all the answers

    What is the predominant charge of aspartate under physiological conditions?

    <p>Negative (D)</p> Signup and view all the answers

    Which amino acid is neutral due to the structure of its side chain at physiological pH?

    <p>Asparagine (D)</p> Signup and view all the answers

    What distinguishes glutamic acid from aspartic acid?

    <p>Number of carbon atoms (A)</p> Signup and view all the answers

    Which amino acid's three-letter code highlights the amide functional group?

    <p>Asn (C)</p> Signup and view all the answers

    Which of the following statements is true regarding the one-letter codes for aspartate and glutamate?

    <p>They are alphabetically sequential in the coding (B)</p> Signup and view all the answers

    Which amino acid contains a methyl thioether group?

    <p>Methionine (A)</p> Signup and view all the answers

    What characterizes the structure of lysine at physiological pH?

    <p>It carries a positive charge at the end of a four-carbon chain. (D)</p> Signup and view all the answers

    How can you remember the one-letter code for lysine?

    <p>It is adjacent to L in the alphabet. (D)</p> Signup and view all the answers

    Which amino acid is structurally identical to phenylalanine except for the presence of a hydroxyl group?

    <p>Tyrosine (A)</p> Signup and view all the answers

    What is the one-letter code for phenylalanine?

    <p>F (C)</p> Signup and view all the answers

    Which amino acid has a guanidinium group in its structure?

    <p>Arginine (C)</p> Signup and view all the answers

    What type of amino acids are primarily found in proteins within living cells?

    <p>L-amino acids (A)</p> Signup and view all the answers

    What do the designations L and D in amino acids indicate?

    <p>Stereochemical configuration relative to L- and D-glyceraldehyde (B)</p> Signup and view all the answers

    Which amino acid is known to have an R-configuration at its α-carbon due to its sulfur side chain?

    <p>L-cysteine (A)</p> Signup and view all the answers

    If one amino acid rotates plane-polarized light clockwise, what can be inferred about its configuration?

    <p>It is a D-amino acid (A)</p> Signup and view all the answers

    Which amino acid has a chiral center in its side chain with an R-configuration?

    <p>L-threonine (B)</p> Signup and view all the answers

    What is the relationship between the rotation of plane-polarized light and the L/D designation of amino acids?

    <p>Some L-amino acids rotate light clockwise (B)</p> Signup and view all the answers

    Which of the following amino acids is primarily present in pathological conditions and is not prevalent in healthy humans?

    <p>Allothreonine (B)</p> Signup and view all the answers

    What does the R/S system refer to in the context of amino acids?

    <p>Stereochemical configuration at the α-carbon (C)</p> Signup and view all the answers

    Flashcards

    Amino Acids

    The basic building blocks of proteins, responsible for the diverse functions of proteins within a cell.

    Proteinogenic Amino Acids

    The 20 unique amino acids that make up all proteins in living organisms. Each has a specific structure and properties.

    Amino Acid Backbone

    A common structural core shared by all proteinogenic amino acids. It includes an amino group, a carboxyl group, a central carbon atom, and a hydrogen atom.

    Alpha-Carbon (α-Carbon)

    The central carbon atom in an amino acid, directly linked to the carboxyl group. The alpha-carbon is often referred to as the "chiral center" due to its four different attachments.

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    R-group or Side Chain

    A chemical group uniquely attached to the alpha-carbon in each amino acid, contributing to its distinct properties.

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    β-Alanine

    A non-proteinogenic amino acid with the amino group on the beta-carbon. It plays a structural role in coenzyme A.

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    γ-Aminobutyric Acid (GABA)

    A non-proteinogenic amino acid with the amino group on the gamma-carbon. It serves as an important inhibitory neurotransmitter.

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    Neutral Form of Amino Acid

    The form an amino acid takes when dissolved in aprotic solvents like DMSO. It exists with all atoms in an electrically neutral state.

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    Zwitterion

    An amino acid that exists in a state where the carboxyl group loses a proton (H+) and the amino group gains a proton, resulting in a neutral overall charge.

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    Methyl Group

    A chemical group composed of a carbon atom bonded to three hydrogen atoms.

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    Carboxyl Group

    A chemical group consisting of a carbon atom double-bonded to an oxygen atom and single-bonded to a hydroxyl group.

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    Amino Group

    A chemical group containing a nitrogen atom bonded to two hydrogen atoms.

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    Glycine

    The simplest amino acid with only a hydrogen atom as its side chain.

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    Serine

    An amino acid with a hydroxyl group (OH) as its side chain.

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    Side Chain

    The unique chemical structure that differentiates one amino acid from another.

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    What is the difference between serine and alanine?

    Serine is similar to alanine, but with an --OH group replacing one H atom in the --CH3 group.

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    What makes cysteine different from serine?

    Cysteine has a sulfur atom in its hydroxyl group, making it a thiol (--SH) group instead of a hydroxyl group.

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    What is the difference between threonine and serine?

    Threonine is like serine but has an extra methyl group.

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    How does valine differ from threonine?

    Valine is almost identical to threonine, but has a methyl group in place of the hydroxyl group.

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    What is the difference between leucine and valine?

    Leucine is similar to valine, but with an extra methylene group connected to the α-carbon.

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    How does isoleucine differ from leucine?

    Isoleucine has the same molecular formula as leucine, but the atoms are arranged differently. In leucine, both methyl groups are attached to the same carbon, while in isoleucine they are attached to different carbons.

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    What makes proline unique among amino acids?

    Proline's side chain connects to the backbone in two places: the α-carbon and the backbone nitrogen, forming a five-membered ring.

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    What type of amine does proline have?

    Proline has a secondary amine instead of a primary amine due to the ring structure.

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    What is glutamine?

    Glutamine is an amino acid with a side chain containing a carboxamide group (-CONH2).

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    What is methionine?

    Methionine is an amino acid with a side chain containing a methyl thioether group (-CH2-S-CH3).

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    Why is the one-letter code for methionine 'M'?

    Methionine's one-letter code is 'M' because it has a methyl group.

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    What is lysine?

    Lysine is an amino acid with a side chain containing a primary amino group (-NH2) at the end of a carbon chain.

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    Why is the one-letter code for lysine 'K'?

    Lysine's one-letter code is 'K' because it follows 'L' in the alphabet, and 'L' is used for leucine.

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    What is arginine?

    Arginine is an amino acid with a side chain containing a guanidinium group, which is a positively charged nitrogen-rich group.

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    Why is the one-letter code for arginine 'R'?

    Arginine's one-letter code is 'R' because it sounds like "R-ginine" and 'A' is already used for alanine.

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    What is phenylalanine?

    Phenylalanine is an amino acid with a phenyl group (-C6H5) attached to its side chain.

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    What is Aspartic Acid?

    Aspartic acid is a non-essential amino acid with a four-carbon dicarboxylic acid side chain. Its side chain is typically deprotonated under physiological conditions, carrying a negative charge. This deprotonated form is often referred to as aspartate.

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    What are the codes for Aspartic Acid?

    The three-letter code for aspartic acid is Asp. However, since 'A' is already used for alanine, a different one-letter code is needed. The one-letter code for aspartic acid is D, which can be remembered as representing asparDate or asparDic acid.

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    How is Asparagine different from Aspartate?

    Asparagine is similar to aspartate, but instead of a carboxyl group, it has an amide group. This side chain amide does not ionize and remains neutral under physiological conditions.

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    What are the codes for Asparagine?

    The three-letter code for asparagine is Asn, highlighting the --NH2 of the amide. The one-letter code is N, which can be remembered as the code for asparagiNe.

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    How is Glutamic Acid similar to Aspartic Acid?

    Glutamic acid is very similar to aspartic acid, but with an extra methylene group, giving it five carbons in total. Just like aspartic acid, glutamic acid tends to lose a proton from its side chain when in water and is commonly called glutamate.

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    What are the codes for Glutamic Acid?

    The three-letter code for glutamic acid is Glu. Because G is the one-letter code for glycine, E is the chosen one-letter code for glutamic acid because it comes after D (aspartate) alphabetically.

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    How is Glutamine similar to Glutamate?

    Glutamine is similar to glutamate, but with an amide group instead of a carboxyl group. Since 'Glu' is the three-letter code for glutamate, Gln is used for glutamine, highlighting the --NH2 of the amide.

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    What is the naming convention for amino acids with amide groups?

    Both asparagine and glutamine are named using the suffix '-ine' because they have an amide group. This is a common naming convention in chemistry.

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    R/S System

    The system uses (R) and (S) designations to describe the spatial arrangement of groups attached to the chiral center.

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    ʟ/ᴅ System

    A convention for naming amino acids based on their structural similarity to either ʟ-glyceraldehyde or ᴅ-glyceraldehyde.

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    Cysteine

    An amino acid with a sulfur atom in its hydroxyl group, making it a thiol (--SH) group instead of a hydroxyl group.

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    Study Notes

    Amino Acid Structure

    • Amino acids are the fundamental building blocks of proteins, crucial for nearly all cellular functions.
    • The 20 proteinogenic amino acids are the building blocks for all proteins in organisms.
    • Each amino acid has a unique structure, determining its properties and interactions with other molecules.
    • Amino acids share a common structure, the backbone, made up of an amino group and a carboxyl group, attached to a central alpha-carbon.

    Amino Acid Backbone

    • The backbone consists of an amino group and a carboxyl group (also known as a carboxyl group).
    • The alpha-carbon (α-carbon) is the central carbon atom directly adjacent to the carboxyl group.
    • The R-group, or side chain, differentiates each amino acid. This is the variable part of the structure and dictates the specific properties of each amino acid.

    Side Chains (R-groups)

    • The R-group is attached to the α-carbon.
    • The R-group determines the unique properties of each amino acid.
    • Some amino acids have multiple carbon atoms between the amino and carboxyl group. These are non-proteinogenic amino acids and are not typically found in proteins, but still play important roles.

    Zwitterion Form

    • In aqueous environments (like inside cells, typically near pH 7.4), amino acids often exist as zwitterions.
    • A zwitterion has both a positive and a negative charge, balancing out the overall charge to neutral.
    • In this form, the carboxyl group has lost a proton, while the amino group has gained a proton.

    Amino Acid Classification

    • Amino acids are classified based on the chemical properties of their R-groups categorized by polarity, including polar, nonpolar, acidic, and basic.
    • The polarity influences how the amino acids interact with water and other molecules.

    Three-Letter and One-Letter Codes

    • Amino acids are commonly abbreviated using three-letter codes (e.g., Gly for glycine) and one-letter codes (e.g., G for glycine).
    • Memorizing both codes is essential for understanding protein sequences and structures.

    Specific Amino Acid Examples (with structures)

    • Glycine (Gly/G): Simplest amino acid, with a hydrogen atom as its side chain.
    • Alanine (Ala/A): A methyl group (-CH3) as its side chain.
    • Serine (Ser/S): Contains a hydroxyl group (-OH) on a methylene group.
    • Cysteine (Cys/C): Contains a sulfur atom (-SH) instead of an oxygen atom.
    • Threonine (Thr/T): Similar to serine but with an extra methyl group.
    • Valine (Val/V): Similar to threonine but with a methyl group instead of a hydroxyl group.
    • Leucine (Leu/L): Similar to valine with an extra methylene group.
    • Isoleucine (Ile/I): Same molecular formula as leucine, but the methyl groups are attached to different carbons.
    • Proline (Pro/P): A cyclic structure, unique among amino acids and attaches to the main chain backbone (amino group) in two places.
    • Aspartic Acid (Asp/D)/Aspartate: A dicarboxylic acid with a carboxyl group attached to the methylene group; typically in its deprotonated form (aspartate);
    • Asparagine (Asn/N): Very similar to aspartate, but has an amide group instead of the carboxylic acid group.
    • Glutamic Acid (Glu/E)/Glutamate : Similar to aspartate, but with an extra methylene group; commonly exists as glutamate.
    • Glutamine (Gln/Q): Similar to glutamate but with an amide group
    • Methionine (Met/M): Contains a sulfur atom (methylthioether) attached to the side chain.
    • Lysine (Lys/K): Contains a chain of four methylene groups attached to the a-carbon with an amino group.
    • Arginine (Arg/R): Contains three methylene groups and a guanidinium group.
    • Phenylalanine (Phe/F): Contains a phenyl group attached to the methylene group.
    • Tyrosine (Tyr/Y): Similar to phenylalanine but with a hydroxyl group on the benzene ring.
    • Histidine (His/H): Contains a five-membered aromatic ring (imidazole).
    • Tryptophan (Trp/W): Contains two aromatic rings (the indole ring) in its side chain.

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