Proteins: Structure and Functions – Study Notes

Proteins Structure & Functions

Introduction

Proteins are fundamental macromolecules in all living cells, second only to water in abundance. They constitute about 15% of a cell’s overall mass and are composed primarily of carbon, hydrogen, oxygen, and nitrogen, with some proteins also containing sulfur. Proteins perform a wide variety of functions essential for life, including catalysis, structure, transport, and regulation.

Amino Acids

Structure of Amino Acids

Amino acids are the basic building blocks of proteins. Each amino acid consists of:

• Carboxyl group ($-COOH$ or $-COO^-$)

• Amino group ($-NH_2$ or $-NH_3^+$)

• Alpha carbon (central carbon atom)

• R group (side chain unique to each amino acid)

The general structure can be represented as:

$\mathrm{H_2N{-}C^{\alpha}(R){-}COOH}$

Classification of Amino Acids

There are twenty (20) standard proteinogenic amino acids found in the genetic code. Amino acids are classified based on the properties of their R group:

• Non-polar amino acids

• Polar neutral amino acids

• Acidic amino acids

• Basic amino acids

Non-Polar Amino Acids

Non-polar amino acids have hydrophobic side chains and are not attracted to water molecules. They contain one amino group, one carboxyl group, and a nonpolar side chain.

• Examples: Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), Phenylalanine (Phe, F), Tryptophan (Trp, W), Proline (Pro, P)

• Tryptophan is considered a borderline member due to its indole ring.

Polar Neutral Amino Acids

Polar neutral amino acids have side chains that are neither acidic nor basic at physiological pH. Their R groups can form hydrogen bonds with water, making them more soluble.

• Examples: Serine (Ser, S), Threonine (Thr, T), Tyrosine (Tyr, Y), Asparagine (Asn, N), Glutamine (Gln, Q), Cysteine (Cys, C)

Polar Acidic Amino Acids

Polar acidic amino acids have side chains containing a second carboxyl group, which is part of the R group. At physiological pH, the side chain bears a negative charge due to loss of a proton.

• Examples: Aspartic acid (Asp, D), Glutamic acid (Glu, E)

Basic Amino Acids

Polar basic amino acids have side chains containing a second amino group. At physiological pH, the side chain bears a positive charge due to acceptance of a proton.

• Examples: Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H)

Summary Table: Amino Acids, Abbreviations, and One-Letter Codes

Amino acid	Three-letter	Abbreviation	One-letter
Alanine	Ala	A
Arginine	Arg	R
Asparagine	Asn	N
Aspartic acid	Asp	D
Cysteine	Cys	C
Glutamine	Gln	Q
Glutamic acid	Glu	E
Glycine	Gly	G
Histidine	His	H
Isoleucine	Ile	I
Leucine	Leu	L
Lysine	Lys	K
Methionine	Met	M
Phenylalanine	Phe	F
Proline	Pro	P
Serine	Ser	S
Threonine	Thr	T
Tryptophan	Trp	W
Tyrosine	Tyr	Y
Valine	Val	V

Essential & Non-Essential Amino Acids

Essential amino acids are required for growth and normal body functions but cannot be synthesized by the body and must be obtained from the diet. Non-essential amino acids can be synthesized by the body.

Essential	Non-Essential
Histidine	Alanine
Isoleucine	Arginine*
Leucine	Asparagine
Lysine	Aspartic acid
Methionine	Cysteine
Phenylalanine	Glutamic acid
Threonine	Glutamine
Tryptophan	Glycine
Valine	Proline
	Serine
	Tyrosine*

*Arginine and Tyrosine are considered semi-essential, depending on developmental stage or health status.

Summary

• Proteins are vital macromolecules composed of amino acids.

• Amino acids are classified by the properties of their side chains (R groups).

• Essential amino acids must be obtained from the diet, while non-essential amino acids can be synthesized by the body.

• Understanding amino acid structure and classification is foundational for studying protein structure and function.

Additional info: The notes above expand on the brief points in the slides, providing definitions, examples, and tables for clarity and completeness.