Biochemistry: Proteins and Amino Acids

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Questions and Answers

What is the primary reason proteins can be classified as heteropolymers?

They consist of a diverse range of amino acids. (correct)

They are always composed of identical repeating units.

They only function in specific cellular pathways.

They are formed from a single type of amino acid.

In addition to polypeptides, what other components can be incorporated into proteins to increase their complexity?

Only amino acids

Nucleic acids only

Carbohydrates, lipids, and metal ions (correct)

Enzymes and substrates

How do the structures of proteins (primary, secondary, tertiary, and quaternary) relate to their function?

Only the primary structure determines protein function.

The structure does not impact the function at all.

The arrangement and interactions of amino acids define functional roles. (correct)

Higher structures are only important for structural proteins.

Which statement accurately describes the importance of amino acids in proteins?

Only a specific subset of 20 amino acids is typically utilized in mammalian proteins. Signup and view all the answers

What role do proteins play in living systems concerning their abundance?

They account for up to 50% of the dry weight of most cells. Signup and view all the answers

What is the primary function of proteins that enables their complexity?

To carry out numerous functions like structural roles and enzymatic activity. Signup and view all the answers

Which amino acid is NOT essential for adult humans?

Arginine Signup and view all the answers

In which part of the amino acid is the R group found?

On the alpha carbon. Signup and view all the answers

How are the carbons in an amino acid typically designated in biochemical nomenclature?

Starting from the alpha carbon and proceeding through the R group. Signup and view all the answers

Which amino acid has a unique structure among alpha-amino acids?

Proline Signup and view all the answers

Which amino acid configuration is predominantly found in human proteins?

L-configuration Signup and view all the answers

What characterizes the R groups of the 20 amino acids?

They determine the amino acid's unique chemical and physical properties. Signup and view all the answers

What is the characteristic UV absorption wavelength for amino acids with aromatic side chains?

280 nm Signup and view all the answers

Which post-translational modification stabilizes collagen fibers through hydrogen bonding?

Hydroxylation Signup and view all the answers

Which of the following amino acids is classified as essential?

Valine Signup and view all the answers

How does the complexity of protein structure affect its function?

A complex structure allows proteins to perform diverse functions. Signup and view all the answers

Which amino acid modification is primarily responsible for gene expression regulation?

Methylation Signup and view all the answers

Vitamin K deficiency affects which process in amino acids, resulting in clotting issues?

Carboxylation Signup and view all the answers

At neutral pH, amino acids predominantly exist as what type of ions?

Zwitterions Signup and view all the answers

In eukaryotes, which amino acids can be phosphorylated?

Serine, Threonine, Tyrosine Signup and view all the answers

What type of amino acids are considered intermediates in the biosynthesis of Arginine and the urea cycle?

Uncommon amino acids Signup and view all the answers

Which amino acid is commonly associated with the formation of disulfide bonds?

Cysteine Signup and view all the answers

What distinguishes acidic amino acids from other types of amino acids?

An extra carboxyl group and negative charge Signup and view all the answers

Which of the following amino acids can switch between positive and neutral charge at physiological pH?

Histidine Signup and view all the answers

What is the primary characteristic of glycine's structure compared to other amino acids?

It has a side-chain that is a hydrogen atom. Signup and view all the answers

Which term best describes amino acids with aliphatic side chains?

Hydrophobic Signup and view all the answers

What defines the optical properties of most common amino acids?

An asymmetric center at the α-carbon Signup and view all the answers

Which amino acid is characterized by a lack of hydrogen bonds leading to the formation of kinks in protein structure?

Proline Signup and view all the answers

Which statement about asparagine and glutamine is true?

They are amides of aspartate and glutamate. Signup and view all the answers

What characterizes the peptide bond in terms of its rotation?

It exhibits partial double-bond character, restricting rotation. Signup and view all the answers

Which statement about polypeptides is incorrect?

Polypeptides can only exhibit tertiary structure. Signup and view all the answers

Which of the following interactions is primarily responsible for the formation of secondary structures in proteins?

Hydrogen bonds Signup and view all the answers

In protein structure, what best describes the quaternary structure?

It is the assembly of multiple polypeptide subunits. Signup and view all the answers

How do amino acids function in biological systems?

They can act as both proton donors and acceptors. Signup and view all the answers

During the synthesis of peptide bonds, which type of reaction occurs?

Condensation reaction Signup and view all the answers

Which structure of a protein is considered the simplest and serves as a foundation for understanding higher-order structures?

Primary structure Signup and view all the answers

What stabilizes the α helix structure of proteins?

Hydrogen bonds Signup and view all the answers

What is the basic structural composition of haemoglobin?

Four subunit polypeptides consisting of two alpha and two beta units. Signup and view all the answers

Which of the following is a characteristic of collagen?

It consists of multiple polypeptide chains that are supercoiled. Signup and view all the answers

What role do loops play in protein structure?

They join adjacent secondary structures and perform key biological functions. Signup and view all the answers

Which statement about protein denaturation is accurate?

It can occur due to temperature, pH, and certain chemicals. Signup and view all the answers

Which of the following best describes conjugated proteins?

Proteins associated with other chemical components. Signup and view all the answers

How are proteins modified after their initial synthesis?

Specific chains of amino acids are altered through various modifications. Signup and view all the answers

What is the significance of conformational changes in proteins?

They are crucial for the functionality of enzymes and binding processes. Signup and view all the answers

Which category of amino acids is considered essential?

Amino acids that must be obtained from dietary sources. Signup and view all the answers

Study Notes

Proteins

Proteins are heteropolymers of amino acids.
They are the most abundant and functionally diverse molecules in living systems.
Proteins account for up to 50% of the dry weight of most cells.
Twenty different amino acids are commonly found in mammalian proteins.

Biomolecules

Biomolecules are organic molecules formed by living organisms.
They are primarily composed of carbon, hydrogen, oxygen, and nitrogen.
Four major classes of biomolecules are lipids, proteins, carbohydrates, and nucleic acids.

Learning Outcomes

Students will describe the various functions of proteins in the body.
They will outline the structure of amino acids.
Students will explain how amino acids are joined into peptides through peptide bonds.
Understanding primary, secondary, tertiary, and quaternary protein structure is essential to grasping protein function.

Amino Acids

Amino acids are classified by their R-group.
The R-group can range from a simple hydrogen atom (as in glycine) to complex structures with many functional groups attached.
The 20 common amino acids have different physical and chemical characteristics due to their unique R-group structures.
Amino acids can be categorized further as polar, nonpolar, charged, or uncharged, all affecting their roles in protein structure and function.

Amino Acid Structure

Amino acids have a central carbon atom (α-carbon).
Attached to this central atom are an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a side chain (R-group).
The R-group (variant) distinguishes one amino acid from another in composition and properties. This accounts for their unique properties and roles in protein structure and function.
This general structure is common to all amino acids besides one: proline. In Proline the R group also bonds back to the amino group.

Amino Acid Classification

Amino acids are classified based on their R-group properties (polarity, charge, etc.).
Common classifications include non-polar aliphatic, aromatic, polar uncharged, acidic, basic, and small.

Amino Acids with Nonpolar Side Chains

Many nonpolar side chains have hydrocarbon structures as part of their R-groups.
These hydrocarbons contribute to their hydrophobic character and interactions within proteins.
Examples of these amino acids include Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan.

Non-polar Aliphatic Amino Acid

The side chain in nonpolar aliphatic amino acids is bonded to the amino nitrogen.
Proline amino acid has a secondary amino acid (imino acid).
The cyclic structure affects the resulting peptide conformation.

Uncharged Polar Side Chains

These amino acids have polar but uncharged side chains.
The polar nature contributes to their hydrophilic interaction with water.
Serine, threonine, cysteine, tyrosine, asparagine, and glutamine are examples.
Form hydrogen bonds.

Disulfide Bonds

Two cysteine molecules can form a disulfide bond, a covalent S-S linkage.
The disulfide bond helps stabilize many extracellular proteins like albumin.

Acidic Side Chains

These amino acids have extra carboxyl groups.
Examples include aspartate and glutamate.
The extra carboxyl group contributes to the negative charge at neutral pH.

Amides of Aspartate and Glutamate

Asparagine and glutamine are amides of aspartate and glutamate, respectively.
They are polar, uncharged amino acids.

Basic Side Chains

Histidine, lysine, and arginine have basic side chains.
These side chains can change their charge based on the surrounding pH; at neutral pH, they exhibit a positive charge allowing hydrogen bonding.
They often play key roles in enzyme active sites, catalyzing reactions by forming and breaking bonds.

Amino Acids with Special Properties

Glycine's R-group is a hydrogen atom.
It can fit into hydrophobic and hydrophilic environments.
It increases the flexibility of the polypeptide chain.
Proline has an amino group that forms part of a ring structure.
The ring structure causes bends and kinks in the polypeptide chain; restricts rotation around the alpha-carbon.
Cysteine contains a sulfhydryl group and can form disulfide bridges by linking to another cysteine.

Optical Properties of α-amino Acids

Most amino acids have an asymmetric α-carbon which can exist as two mirrored isomers (D and L).
Naturally occurring proteins only utilize the L-configuration.
D-amino acids are found in some peptides found in bacterial cell walls.

Spectral Properties of Amino Acids

Individual amino acids do not absorb visible light.
Aromatic amino acids (tyrosine, tryptophan, phenylalanine) absorb UV light.
UV absorption characteristics help quantify protein concentration.

Amino Acid Modification

Amino acids can be chemically altered after synthesis.
These modifications are called post-translational modifications.
Additions include hydroxyl, phosphoryl, and methyl groups, among others.

Hydroxylation / Hydroxylysine and Hydroxyproline

Additional hydroxyl groups can stabilize collagen fibres (hydroxyproline and hydroxylysine).
Deficiency in vitamin C hinders hydroxylations.

Methylation

Some proteins can attach methyl groups to amino acids.
Histone methylation regulates gene expression.

Carboxylation

Carboxylation adds carboxyl groups to glutamic acid.
For instance, in prothrombin (clotting factor).
Vitamin K deficiency prevents this and contributes to clotting problems.

Phosphorylation

Phosphorylation adds a phosphate group.
This can alter protein activity in various pathways.
Phosphorylation sites commonly observed are on Serine, Threonine, Tyrosine.

Uncommon Amino Acids

Additional amino acids exist but aren't protein building blocks.
These amino acids function as intermediates in specific metabolic pathways. Examples include Orntihine and Citrulline.

Amino Acids are Zwitterions

At neutral pH, the carboxyl group loses a proton, and the amino group gains a proton.
This leads to a net zero charge with a net positive charge on the amino end, and a net negative charge on carboxyl end.

Ionization

Amino acid ionization varies with pH changes.
These ions act as proton donors (acids) or acceptors (bases) maintaining pH balance.

Polypeptides

Amino acids join via peptide bonds in a condensation reaction.

Peptide Bond

A peptide bond is a chemical bond formed between the carboxyl group of one amino acid and the amino group of another.
Peptide bonds form a linear sequence of amino acids.
The peptide bond has a partial double bond character which restricts rotation.

Polypeptides have Polarity

Polypeptides have an N-terminus (amino acid end) and a C-terminus (carboxyl acid end).

Polypeptide Size Variation

Polypeptide size differs significantly between proteins.

Protein Structure

Proteins have four levels of structure.
Primary: Sequence of amino acids.
Secondary: Local folding patterns (alpha-helices, beta-sheets).
Tertiary: Overall 3D shape of the protein.
Quaternary: Structure of multiple polypeptide units.

Loops, Turns and Bends

Loops, turns, and bends are segments that connect secondary structure regions.
They often play roles in protein function.
Many are on the surface of the protein.

Proteins with Chemical Groups

Some proteins contain chemical groups beyond amino acids.
These are called Prosthetic groups
Examples include heme in hemoglobin and various lipids.

Dynamic Changes Within Proteins

Conformational Changes are essential for protein function.
These facilitate binding and catalytic activities. Changes are vital for enzymes.

Protein Denaturation

Denaturation disrupts protein structure.
Denaturation can be caused by altered PH, Temperature extremes, and chemicals like urea.
Denatured proteins often lose their function. The structure is disrupted, not just slightly altered.

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Description

This quiz covers various aspects of proteins and amino acids, including their classification as heteropolymers and the significance of different amino acids in protein structure and function. Explore the primary, secondary, tertiary, and quaternary structures of proteins as well as the roles they play in living systems and their unique characteristics.