Biochemistry: Proteins, Lipids, and Nucleic Acids

Comprehensive vocabulary flashcards covering proteins, amino acid organization, lipid classes, membranes, nucleic acid structure, replication, and molecular genetics based on the review lecture.

Proteins

Macromolecules formed by chains of amino acids that carry out four primary functional categories: catalytic acceleration of reactions, transport of molecules, mechanical structural support, and cellular signaling and biological regulation.

Amino Acid Basic Structure

A molecular structure organized around an $\alpha$-carbon bonded to four components: an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable side chain ($R$ group).

$R$ Group (Side Chain)

The variable side chain attached to the central $\alpha$-carbon of an amino acid that determines its unique chemical properties, such as polarity, hydrophobic or hydrophilic behavior, and acidic or basic nature.

Zwitterion

The dipolar ionic form of an amino acid in water at cellular pH, where the amino group accepts a proton acquiring a positive charge and the carboxyl group loses a proton acquiring a negative charge.

Peptide Bond

A covalent chemical bond formed between two amino acids via a condensation reaction between the carboxyl group of one and the amino group of another, releasing a molecule of water ($H_2O$).

Primary Structure

The linear sequence of amino acids joined together by peptide bonds, determined directly by genetic information.

Secondary Structure

The local spatial arrangement of the polypeptide backbone, stabilized mainly by hydrogen bonds between backbone groups, primarily forming $\alpha$-helices and $\beta$-pleated sheets.

$\alpha$-Helix

A common compact, helical secondary protein structure stabilized primarily by hydrogen bonds between the groups of the polypeptide backbone.

$\beta$-Pleated Sheet

An extended secondary protein structure with a zigzag disposition, stabilized mainly by hydrogen bonds between groups of the peptide backbone.

Proline (in Secondary Structure)

An amino acid with a rigid cyclic structure that limits backbone rotation and lacks an amide hydrogen, thereby disrupting the formation of hydrogen bonds required for an $\alpha$-helix.

Tertiary Structure

The overall three-dimensional folding conformation of a single polypeptide chain, determined by interactions among $R$ groups and between $R$ groups and the environment.

Quaternary Structure

The spatial association and organization of two or more independent polypeptide chains into a single functional protein complex.

Weak Interactions in Proteins

Non-covalent forces—including hydrophobic interactions, hydrogen bonds, Van der Waals forces, and electrostatic interactions (salt bridges)—that stabilize the three-dimensional conformation while providing flexibility.

Protein Denaturation

The loss of a protein's native three-dimensional conformation caused by factors such as changes in temperature, pH, or exposure to chemical agents, which often results in the loss of biological activity.

Fibrous Proteins

Proteins characterized by elongated polypeptide chains, repetitive structural organization, predominantly structural functions, and generally low solubility in water.

Globular Proteins

Proteins with compact, approximately spherical conformations with polar, hydrophilic residues on the exterior and hydrophobic residues buried inside, typically rendering them soluble in water.

Enzymes

Biological catalysts, generally proteins, that accelerate specific chemical reactions without being consumed or permanently altered during the process.

Four Stages of Enzymatic Catalysis

The sequential catalytic mechanism consisting of: 1. Substrate binding to the active site; 2. Catalysis by lowering activation energy; 3. Release of products; and 4. Regeneration of the free enzyme.

Protein Misfolding

Incorrect folding of a polypeptide that can lead to loss of function, insolubility, and the formation of toxic protein aggregates capable of accumulating in cells and causing disease.

Molecular Chaperones

Proteins that assist nascent or partially denatured proteins in folding correctly and prevent the formation of non-functional protein aggregates.

Protein Kinases

Regulatory enzymes that transfer phosphate groups from ATP to specific amino acid residues (such as serine, threonine, or tyrosine) of target proteins, altering their biological activity.

Lipids

Biomolecules characterized by hydrophobic behavior or the presence of hydrophobic regions, functioning in energy storage, membrane formation, thermal insulation, organ protection, and cellular signaling.

Fatty Acid Structure

A molecule consisting of three main structural regions: a terminal carboxyl group ($-COOH$), an apolar hydrocarbon chain primarily made of methylene groups ($-CH_2-$), and a terminal methyl group ($-CH_3$).

Saturated Fatty Acids

Fatty acids lacking double bonds between carbon atoms in their hydrocarbon chain, enabling their straight chains to pack tightly together.

Unsaturated Fatty Acids

Fatty acids containing one or more double bonds in their hydrocarbon chain; cis double bonds introduce bends (kinks) that hinder tight packing and lower the melting point.

Omega ($\omega$) Nomenclature

A naming convention for fatty acids indicating the position of the first double bond counted starting from the terminal methyl end ($-CH_3$).

Triacylglycerols

Lipids composed of a glycerol molecule joined by ester linkages to three fatty acids, functioning as the primary concentrated form of metabolic energy storage in cells.

Phospholipids

Amphipathic membrane lipids possessing a polar region containing phosphate and hydrophobic regions of fatty acid chains.

Amphipathic

A property of molecules possessing both a polar (hydrophilic) region that interacts with water and an apolar (hydrophobic) region that avoids contact with water.

Lipid Bilayer

The fundamental structural arrangement of cell membranes in aqueous media, formed by phospholipids with hydrophilic heads facing the water and hydrophobic tails tucked into the interior.

Lipid Rafts

Dynamic microdomains in cell membranes enriched in specific lipids (such as sphingolipids and cholesterol) and proteins, functioning in membrane organization and cellular signaling.

Saponifiable Lipids

Lipids containing fatty acids linked by bonds susceptible to alkaline hydrolysis, including triacylglycerols, phospholipids, sphingolipids, and waxes.

Non-Saponifiable Lipids

Lipids that do not contain fatty acids linked by hydrolyzable ester bonds, including steroids and terpenes.

Saponification

The alkaline hydrolysis of ester linkages in lipids, producing glycerol and fatty acid salts (soaps) when performed on triacylglycerols.

Cholesterol

A steroid lipid found in cell membranes that modulates membrane physical properties, regulates fluidity and stability, and serves as a precursor for steroid hormones.

Low-Density Lipoproteins (LDL)

Lipoproteins responsible for transporting cholesterol toward peripheral tissues; high levels can promote cholesterol deposition in arterial walls.

High-Density Lipoproteins (HDL)

Lipoproteins that mediate reverse cholesterol transport by carrying cholesterol away from peripheral tissues to the liver for processing.

Chylomicrons

Lipoproteins that carry dietary lipids, especially triacylglycerols, from the intestine to peripheral tissues such as adipose and muscle tissues.

$\beta$-Oxidation

The catabolic pathway occurring in mitochondria and peroxisomes where fatty acid chains are progressively broken down into two-carbon units, producing acetyl-CoA and reducing equivalents.

DNA (Deoxyribonucleic Acid)

The nucleic acid molecule that stores genetic information in living organisms, encoding instructions for RNA synthesis and protein production.

Nucleotide

The basic building block of nucleic acids, composed of a five-carbon pentose sugar, a nitrogenous base, and a phosphate group.

DNA vs. RNA Structure

DNA contains deoxyribose, thymine, is typically double-stranded, and has high long-term stability; RNA contains ribose, uracil, is typically single-stranded, and is more susceptible to degradation.

Complementary Base Pairing

The specific hydrogen bonding between nitrogenous bases in DNA: adenine pairs with thymine ($A-T$) via two hydrogen bonds, and guanine pairs with cytosine ($G-C$) via three hydrogen bonds.

Antiparallel Strands

The arrangement of the two sugar-phosphate backbones in DNA oriented in opposite directions: one strand runs $5' \rightarrow 3'$ and the complementary strand runs $3' \rightarrow 5'$.

2'-Deoxyribose Stability

The structural absence of a hydroxyl group on the $2'$ carbon of deoxyribose in DNA, which substantially reduces susceptibility to hydrolytic cleavage compared to ribose in RNA.

Central Dogma of Molecular Biology

The framework describing the directional flow of genetic information in biological systems: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{protein}$, through transcription followed by translation.

Gene

A segment of DNA that contains the instructions necessary to produce a functional RNA and, in coding genes, direct protein synthesis, including regulatory sequences that govern expression.

Messenger RNA (mRNA)

A type of RNA that carries genetic coding sequences from DNA in the form of three-nucleotide codons to the ribosome for protein synthesis.

Transfer RNA (tRNA)

An adapter RNA that carries specific amino acids to the ribosome and matches them to mRNA codons using its complementary anticodon sequence.

Ribosomal RNA (rRNA)

An RNA component of the ribosome structure that catalyzes the formation of peptide bonds during protein synthesis.

Codon

A sequence of three nucleotides in messenger RNA that specifies a particular amino acid or signals the termination of translation.

Degenerate Genetic Code

The feature of the genetic code whereby multiple different codons can encode the same amino acid, buffering against functional consequences of nucleotide substitutions.

Semiconservative Replication

The mode of DNA replication where the two original strands separate to act as templates, resulting in daughter double helices consisting of one original parental strand and one newly synthesized strand.

DNA Polymerase

An enzyme that synthesizes a complementary DNA strand by adding incoming nucleotides to the $3'$ end of a growing chain, carrying out synthesis exclusively in the $5' \rightarrow 3'$ direction.

Leading Strand

The newly synthesized DNA strand formed continuously in the $5' \rightarrow 3'$ direction, aligned with the forward movement of the replication fork.

Lagging Strand

The newly synthesized DNA strand produced discontinuously as a series of Okazaki fragments in the direction opposite to replication fork progression.

DNA Helicase

An enzyme that unzips the double helix by breaking hydrogen bonds between base pairs, separating the two strands to allow access by replication machinery.

DNA Ligase

An enzyme that joins breaks in the phosphodiester backbone of DNA, covalently linking Okazaki fragments on the lagging strand to create an unbroken strand.

Polymerase Chain Reaction (PCR)

A laboratory technique used to amplify a targeted DNA sequence across thermal cycles comprising three steps: denaturation of strands, annealing of primers, and extension by DNA polymerase.

Thymine (in DNA Repair)

The standard pyrimidine base of DNA whose methyl group distinguishes it from uracil produced by spontaneous cytosine deamination, facilitating DNA surveillance and damage repair.

Cloning Vector

A DNA vehicle used to carry a foreign DNA fragment into a host cell for propagation, maintenance, and replication of that genetic material.

Nucleosome

The fundamental repeating subunit of eukaryotic chromatin, consisting of a segment of DNA wrapped around an octamer of histone proteins.

Differential Gene Expression

The process by which cells sharing the same genome activate or repress distinct sets of genes, producing different subsets of RNAs and proteins tailored to cell-specific functions.