Biochemistry Quiz: Amino Acids and Structures

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Questions and Answers

What unique feature does histidine possess that allows it to be positively charged near neutral pH?

A hydroxyl group

An imidazole group (correct)

A carboxyl group

A methyl group

Which two amino acids are typically negatively charged at physiological pH?

Arginine and Lysine

Aspartic acid and Glutamic acid (correct)

Cysteine and Methionine

Serine and Threonine

What is the role of ionizable groups in amino acids?

They determine the primary structure of proteins.

They can only donate protons.

They facilitate ionic bonds and reactions. (correct)

They stabilize the polypeptide backbone.

What is the abbreviation for glutamine?

Gln Signup and view all the answers

In terms of bond strength during protein folding, which type of interaction is the strongest?

Covalent bonds Signup and view all the answers

How many amino acids have readily ionizable side chains?

7 Signup and view all the answers

What is typically ignored during the process of amino acid folding?

Hydrogen bonding along the backbone Signup and view all the answers

Which of the following amino acids does NOT have the first three letters of its name as its abbreviation?

Asparagine Signup and view all the answers

How many bonds does carbon commonly form with other atoms?

4 bonds Signup and view all the answers

What occurs to the orientation of atoms around carbon when two carbon atoms are joined by a double bond?

All bonds around those carbons are in the same plane Signup and view all the answers

Which of the following is true about isomers?

Isomers have different structures and properties Signup and view all the answers

Which of the following sugars are isomers?

L and D glucose, mannose and glucose Signup and view all the answers

What are the seven functional groups that give rise to biological molecules?

Hydroxyl, carboxyl, amine, carbonyl, phosphate, sulfhydryl, and methyl Signup and view all the answers

What does the term amino acid indicate about its molecular structure?

It contains a carboxyl group and an amine group Signup and view all the answers

Which of the following statements is correct about the properties of water?

Water exhibits cohesion and temperature moderation Signup and view all the answers

What is the primary role of buffers in biological fluids?

Buffers maintain constant pH levels Signup and view all the answers

What is the primary reason L amino acids are utilized in protein synthesis?

L amino acids are slightly more soluble than a racemic mixture of D and L amino acids. Signup and view all the answers

In their dipolar form, what is the ionization status of the amino group and the carboxyl group of amino acids?

Amino group is protonated and carboxyl group is deprotonated. Signup and view all the answers

At what approximate pH does the dipolar form of an amino acid cease to exist?

pH 9 Signup and view all the answers

Which category of amino acids can be synthesized by the human body?

Both nonessential and conditional amino acids. Signup and view all the answers

What is a common characteristic of all 20 standard amino acids?

They all contain an α-carbon. Signup and view all the answers

How do amino acids change as the pH of the solution increases?

The amino group remains protonated while the carboxyl group dissociates first. Signup and view all the answers

What role do the R groups play in α-amino acids?

They provide the unique properties of each amino acid. Signup and view all the answers

What happens to the solubility of amino acids at different pH levels?

Solubility varies based on the amino acid's charge state. Signup and view all the answers

What prevents rotation about the peptide bond in polypeptides?

The double-bond character of the bond Signup and view all the answers

Which configuration of a peptide bond is more common and why?

Trans, due to steric clashes Signup and view all the answers

What stabilizes beta sheets?

Hydrogen bonding between polypeptide strands Signup and view all the answers

What primarily stabilizes the alpha helix structure in proteins?

Hydrogen bonds between peptide N-H and C=O groups Signup and view all the answers

What is the typical distance between adjacent amino acids along a beta strand?

3.5 Å Signup and view all the answers

How many amino acids are typically found in one turn of an alpha helix?

3.6 Signup and view all the answers

Which statement about the structure of the alpha helix is true?

The CO group of each amino acid forms a hydrogen bond with the NH group four residues ahead Signup and view all the answers

In terms of structure, how do adjacent beta sheets typically align?

They can align in either parallel or antiparallel orientations. Signup and view all the answers

Which of the following amino acid types predominantly makes up the interior of myoglobin?

Nonpolar residues Signup and view all the answers

Which type of secondary structure is characterized by a tightly coiled backbone?

Alpha helix Signup and view all the answers

What determines the catalytic structure of ribonuclease?

The amino acid sequence Signup and view all the answers

What is the overall course of the polypeptide chain in a protein called?

Tertiary structure Signup and view all the answers

Which structure represents the secondary structure of proteins?

Alpha helices and beta sheets Signup and view all the answers

What is the rise along the helix axis for each amino acid in an alpha helix?

1.5 Å Signup and view all the answers

Which amino acids are less likely to form stable alpha helices due to branching?

Valine, Threonine, and Isoleucine Signup and view all the answers

Which of the following describes the hydrophobic effect in protein folding?

Hydrophobic residues are excluded from water. Signup and view all the answers

What type of interactions stabilize the secondary structure in proteins?

Hydrogen bonds and van der Waals interactions Signup and view all the answers

Which statement is true regarding protein folding?

Folding involves progressive stabilization of intermediates Signup and view all the answers

Which molecule plays a critical role in myoglobin's ability to bind oxygen?

Protoporphyrin IX Signup and view all the answers

What is formed when two amino acids combine?

Dipeptide Signup and view all the answers

What role do the two histidine residues in myoglobin play?

They are involved in binding iron and oxygen. Signup and view all the answers

What aspect of amino acids restricts their structural possibilities during bonding?

Rotational ability of bonds Signup and view all the answers

Where are hydrophobic amino acids like valine most likely found in a protein structure?

In the interior of the protein Signup and view all the answers

Which level of protein structure involves multiple polypeptides?

Quaternary structure Signup and view all the answers

Study Notes

Nutritional Biochemistry - Amino Acids and Proteins

The course is DIET413/BHCS1019
Dr Nathaniel Clark FHEA RNutr MRSB is the lecturer
Contact details are provided

Last Time - Quiz Questions

Carbon commonly forms 4 bonds with other atoms.
When carbon forms a double bond with another carbon, the orientation of atoms changes.
An isomer is a molecule with the same chemical formula but a different arrangement of atoms. There are three main types of isomers.
Two examples of isomeric sugars were not specified.
Seven functional groups give rise to biological molecules; the particular molecules rich in these groups were not listed.
The term "amino acid" indicates a molecule with both an amino group and a carboxyl group.

Previously (1)

Matter is composed of elements in pure form or in combinations (compounds).
Essential elements of life include carbon, oxygen, hydrogen, and nitrogen, which account for 96% of these elements.
Atomic number is the number of protons in an atom.
Isotopes of an element differ in the number of neutrons.
Electrons orbit the nucleus in specific energy levels.
Strong chemical bonds include covalent (atoms share electrons) and ionic (atoms transfer electrons).
Weak chemical bonds include van der Waals interactions and hydrogen bonding.
Chemistry underlies the understanding of biology.

Previously (2)

Water's polarity leads to hydrogen bonding.
Water's properties (cohesion, temperature moderation, and solvent properties) are vital for life.
Water molecules can transfer H+ to form hydronium (H3O+) and hydroxide (OH-) ions.
pH measures the concentration of H+.
Buffers maintain the pH of biological fluids.
A buffer comprises an acid-base pair in reversible equilibrium with hydrogen ions.

Previously (3)

Carbon's valence allows it to form up to four bonds.
Double bonds alter molecular configuration.
Carbon forms the structural backbone of most organic molecules, allowing for complexity and diversity of living matter.
In hydrocarbons, only carbon and hydrogen atoms are present.
Isomers have the same chemical formula but different spatial arrangements (structural, geometric, or enantiomers).
The properties of organic molecules depend on their carbon skeleton and attached components.
There are 7 functional groups.

Learning Outcomes

Describe the general structure of amino acids.
Explain variable amino acid side chains.
Understand primary, secondary, tertiary, and quaternary protein structure.
Understand the forces causing the folding of amino acids into proteins.

What is the Role of Protein?

The role of protein was not detailed.

Proteins Main Functions

Proteins have diverse functions based on their structure. Diagrams illustrating these functions were present.

What can you tell me about this structure?

The structure shown is a general representation of an amino acid. Amino acids consist of an amino group, a carboxyl group, a central carbon atom (α-carbon), and a variable R group.

The 20 Amino Acids

Amino acids, the building blocks of proteins, have a central chiral carbon atom.
The R group varies between amino acids.
They have L or D forms (different spatial arrangements).

L Amino Acids

Only L-amino acids are used in proteins.
L-amino acids are slightly more soluble than D-amino acids.
This solubility difference might account for the predominance of L-amino acids in primordial soup.

Amino Acid Ionisation

Amino acids exist as dipolar ions, or zwitterions in solutions at neutral pH.
The amino group is protonated, while the carboxyl group is deprotonated.
The ionization state varies depending on pH.

Activity (Page 13)

The graph illustrated the varying ionization states of amino acids at different pH levels.

Amino Acids

The 20 amino acids have varying side chains in size, shape, charge, hydrogen bonding, hydrophobic character, and chemical reactivity.
All proteins are constructed from the same 20 amino acids.
Nine of these are essential amino acids (obtained from diet).
Five are non-essential (synthesized in the body).
Six are conditional; these are essential at certain life stages or in disease states.

Clinical relevance - disorders

Interference with normal amino acid metabolism can lead to various disorders.
Errors in metabolic processes, such as tyrosine metabolism, can result in changes to biochemistry.
Inborn errors of metabolism, such as phenylketonuria, are examples of genetic defects affecting metabolic pathways.

R Groups

Amino acids are classified into 4 groups based on the characteristics of their R groups:
- Hydrophobic non-polar
- Polar neutral
- Positively charged
- Negatively charged

Structures

An overview of amino acid side chain structures.
Questions on identifying a-carbons, those without a-carbons, and amino acids with two chiral carbons.
Questions to determine the properties of the side chains.
Polar, non-polar, basic, and acidic are the categories for side chain properties.

Hydrophobic Amino Acids

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, and others are among the hydrophobic amino acids.
Larger aliphatic side chains cluster together to avoid water.
Aliphatic chain in proline differs from the others.

Hydrophobic Amino Acids (2)

Phenylalanine and tryptophan have more simple aromatic side chains.
Phenylalanine is purely hydrophobic, while tryptophan has aromatic characteristic with an NH group.

Polar Amino Acids

Serine, threonine, tyrosine (contain hydroxyl -OH).
Which of these 3 polar amino acids is closely aligned with hydrophobic side chains?
Asparagine and glutamine contain carboxamide groups instead of carboxylic acid groups.
Cysteine contains a sulfhydryl group, which is highly reactive compared to hydroxyl.
Pairs of sulfhydryl groups may come together to form disulphide bonds, thus stabilizing some proteins.

Positively Charged Amino Acids

Lysine and arginine have long chains with positively charged terminal groups at neutral pH.
Lysine has a primary amino group.
Arginine has a guanidinium group
Histidine has an imidazole group which can be either charged or uncharged, depending on its local environment.

Histidine's Involvement in Fat Metabolism

Histidine is involved in fat metabolism. Diagram shows its role.

Negatively Charged Amino Acids

Aspartic acid and Glutamic acid have acidic side chains.
Aspartate and glutamate are often called 'negatively charged' at physiological pH.

Ionizable Groups

Seven amino acids have readily ionizable side chains.
These side chains can donate or accept protons, facilitating reactions and ionic bonds.

Amino Acid Abbreviations

Abbreviations are used in scientific papers. The abbreviations use the first 3 letters except for some (Asn, Gln, Ile, Trp).

Amino Acid Fold

How amino acids fold into a protein.
The factors important to protein folding.
Considering the main chain hydrogen bonding capability of amino acids.

Polypeptide Versus Protein

Definitions for polypeptides versus proteins.
Large proteins (e.g., titin) contain large amounts of amino acids.
Shorter chains (e.g., insulin) of amino acids are called oligopeptides
Structure can determine if molecule is peptide or protein.

Size Comparison (by weight)

Mean molecular weight of amino acid residues (100 Daltons).
Most protein molecular weights fall between 5500 and 220,000.
Proteins can be expressed in kilodaltons (kDa).
Example sizes (titin, insulin, glucose).

Polypeptide Chains Flexibility

Peptide bonds are planar and thus limit rotation.
Rotation in other bonds (adjacent to peptide bonds) enables protein folding flexibility.

Secondary Structure

Polypeptide chains fold into regular secondary structures like alpha helices and beta sheets.
These structures result from hydrogen bonds between adjacent N-H and C=O groups.

The Alpha Helix

This describes the structure of and forces involved in the formation of the α-helix.

The Alpha Helix (2)

The rise and rotation per turn of a-helix structure was described and the factors stabilizing it.

Beta Sheets

Different types of β-sheets are possible.

Beta Sheets (2)

Alternative arrangements where amino acids point in opposite directions for hydrogen bonds. The various arrangements of β-sheets are described.

Quaternary Structure

Polypeptide chains can assemble into quaternary structures like dimers and other forms, which contains multiple subunits (a dimer consists of two identical subunits).
Explains human hemoglobin as example of more complex quaternary structure, with its alpha and beta subunits.

Amino Acid Sequence

Explains how the structure of proteins is determined from amino acid sequence through a series of intermediates.

Summary

Summary of amino acid structure and function.
Key points about amino acid categories and their roles in protein structure.

Questions (Quiz)

Questions on amino acid chemical groups.
Questions on amino acid side chain classification.

Before Next Time

List of topics for the next lecture (various structural components of biochemistry, such as isomer, chiral molecules, different types of carbohydrates).
List of resources for additional reading on these topics in relevant textbooks.

Practical Assessment (Tomorrow)

Practical scheduled, workbook is linked (to be reviewed prior to the session).

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Description

Test your knowledge on amino acids, their properties, and the fundamental concepts of protein chemistry. This quiz covers various aspects such as ionizable groups, functional groups, and isomers in biological molecules. Perfect for biochemistry students looking to reinforce their understanding of macromolecules.