Biochemistry Fundamentals: Carbohydrates, Lipids, Proteins, and Nucleic Acids

Study Guide - Smart Notes

Tailored notes based on your materials, expanded with key definitions, examples, and context.

Carbohydrates

Classification and Structure of Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, and serve as a primary energy source for living organisms. They are classified based on their structure and the number of sugar units present.

Monosaccharides: Simple sugars with a single polyhydroxy aldehyde or ketone unit (e.g., glucose).
Disaccharides: Composed of two monosaccharide units joined by a glycosidic bond (e.g., sucrose).
Polysaccharides: Large polymers of monosaccharides (e.g., starch, glycogen, cellulose).

Monosaccharides are further classified by:

Aldose: Contains an aldehyde group.
Ketose: Contains a ketone group.
Number of carbons: Triose (3C), tetrose (4C), pentose (5C), hexose (6C).

Chirality and Isomerism

Chiral Molecule: A molecule that is non-superimposable on its mirror image.
Chiral Carbon: A carbon atom bonded to four different groups.
Enantiomers: Mirror-image isomers of chiral molecules.
D- and L- Isomers: Determined by the position of the -OH group on the chiral carbon farthest from the carbonyl group in Fischer projections.

Example: D-glucose vs. L-glucose differ in the configuration at all chiral centers.

Cyclic Forms and Anomerism

Monosaccharides can cyclize to form ring structures (Haworth projections) in solution.
These cyclic forms are in equilibrium with their open-chain (Fischer projection) forms.
Anomers: Isomers differing at the new chiral center formed during ring closure (α and β forms).

Example: α-D-glucose vs. β-D-glucose differ in the orientation of the -OH group on the anomeric carbon.

Polysaccharides and Glycosidic Bonds

Glycosidic Bond: Covalent bond joining monosaccharide units (e.g., α(1→4) linkage).
Starch: Plant polysaccharide; amylose (unbranched, α(1→4)), amylopectin (branched, α(1→4) and α(1→6)).
Glycogen: Animal storage polysaccharide; highly branched (similar to amylopectin).
Cellulose: Linear polymer with β(1→4) glycosidic bonds; not digestible by humans.

Table: Major Glucose Polysaccharides

Name	Structure	Glycosidic Bond	Branching
Amylose	Unbranched coil	α(1→4)	No
Amylopectin	Branched coil	α(1→4), α(1→6)	Yes
Glycogen	Highly branched coil	α(1→4), α(1→6)	Yes (more than amylopectin)
Cellulose	Linear	β(1→4)	No

Additional info: Branched polysaccharides provide more ends for enzymatic breakdown, allowing rapid glucose release.

Lipids

Classification and Properties of Lipids

Lipids are a diverse group of hydrophobic biomolecules, insoluble in water, and serve as energy storage, structural components, and signaling molecules.

Fatty Acids: Long hydrocarbon chains with a carboxylic acid group.
Waxes: Esters of fatty acids and long-chain alcohols.
Triacylglycerols (Triglycerides): Esters of glycerol and three fatty acids; main storage form of fat.
Steroids: Four fused carbon rings; cholesterol is the most abundant steroid.

Fatty Acids: Types and Properties

Saturated: No double bonds; higher melting points; solid at room temperature (animal fats).
Monounsaturated: One double bond.
Polyunsaturated: Multiple double bonds; lower melting points; liquid at room temperature (plant oils).
Omega-3 and Omega-6: Classified by the position of the first double bond from the methyl end.

Example: Oleic acid (monounsaturated), linoleic acid (polyunsaturated, omega-6).

Reactions of Triacylglycerols

Hydrogenation: Addition of H2 to unsaturated fatty acids, converting double bonds to single bonds (used to make margarine).
Cis vs. Trans: Hydrogenation can produce trans fats, which have higher melting points and are less healthy.
Hydrolysis: Splitting of ester bonds by water, producing glycerol and fatty acids.
Saponification: Base-catalyzed hydrolysis of triacylglycerols, producing soap and glycerol.

Equation for Saponification:

Phospholipids and Cell Membranes

Glycerophospholipids: Main component of cell membranes; contain a polar head and two nonpolar fatty acid tails.
Form lipid bilayers with hydrophobic tails inward and hydrophilic heads outward.
Lipoproteins: Transport cholesterol and other lipids in the bloodstream.

Amino Acids, Proteins, and Enzymes

Structure and Classification of Amino Acids

Amino acids are the building blocks of proteins, each containing a central (α) carbon, an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).

Classification: Based on side chain properties: nonpolar, polar, acidic, or basic.
Essential Amino Acids: Nine amino acids that must be obtained from the diet.
At physiological pH (7.4), amino acids exist as zwitterions: and .

Peptides and Protein Structure

Peptide Bond: Amide bond linking the carboxyl group of one amino acid to the amino group of another.
Dipeptide: Two amino acids joined by a peptide bond.
Polypeptide: Chain of many amino acids.
Protein: One or more polypeptide chains folded into a functional structure.
Written from N-terminus (left, ) to C-terminus (right, ).

Levels of Protein Structure

Primary: Sequence of amino acids.
Secondary: Local folding (α-helix, β-pleated sheet) stabilized by hydrogen bonds.
Tertiary: Overall 3D shape stabilized by hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.
Quaternary: Association of multiple polypeptide chains.

Table: Forces Stabilizing Protein Structure

Level	Type of Bond/Interaction
Primary	Covalent (peptide bonds)
Secondary	Hydrogen bonds
Tertiary	Hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bridges
Quaternary	Same as tertiary (between subunits)

Protein Denaturation

Loss of native structure due to changes in pH, temperature, or chemical exposure.
Disrupts secondary, tertiary, and quaternary structure, leading to loss of function.

Enzymes and Catalysis

Enzymes: Biological catalysts that speed up reactions by lowering activation energy.
Active Site: Region where substrate binds and reaction occurs.
Enzyme-Substrate Complex: Temporary association during catalysis.
Enzyme Inhibitors: Molecules that decrease enzyme activity by blocking or altering the active site.
Enzyme activity is sensitive to pH and temperature (optimal at 37°C and pH 7.4).

Nucleic Acids and Protein Synthesis

Structure of Nucleic Acids

Nucleic acids (DNA and RNA) are polymers of nucleotides, which store and transmit genetic information.

Nucleotide: Composed of a pentose sugar, phosphate group, and nitrogenous base.
DNA: Deoxyribonucleic acid; double helix; bases A, T, C, G.
RNA: Ribonucleic acid; single-stranded; bases A, U, C, G.

Base Pairing and Structure

DNA strands held together by hydrogen bonds between complementary bases: A=T (2 H-bonds), C≡G (3 H-bonds).
RNA uses uracil (U) instead of thymine (T).

DNA Replication and Transcription

Replication: DNA makes an exact copy of itself during cell division.
Transcription: DNA sequence is copied into mRNA in the nucleus.
Translation: mRNA is decoded by ribosomes to synthesize proteins in the cytoplasm.

Types of RNA:

mRNA (messenger RNA): Carries genetic code from DNA to ribosome.
tRNA (transfer RNA): Brings amino acids to ribosome during translation.
rRNA (ribosomal RNA): Structural and catalytic component of ribosomes.

Genetic Code and Mutations

Genetic Code: Sequence of three bases (codon) on mRNA specifies an amino acid.
Mutations are changes in DNA sequence that can lead to nonfunctional proteins and genetic diseases.

Viruses and Disease

Viruses infect cells by injecting their genetic material, hijacking the host's machinery for replication.
Some viruses can cause cancer by disrupting normal cell regulation.

Identification of Biomolecules

Recognizing Biomolecules by Structure

Monosaccharide: Single ring or chain with multiple -OH groups.
Disaccharide: Two monosaccharide units joined by a glycosidic bond.
Polysaccharide: Long chains of monosaccharide units (e.g., starch, glycogen, cellulose).
Fatty Acid: Long hydrocarbon chain with terminal carboxylic acid; can be saturated or unsaturated.
Triacylglycerol: Glycerol backbone with three fatty acid esters.
Wax: Ester of a fatty acid and a long-chain alcohol.
Steroid: Four fused carbon rings.
Amino Acid: Central carbon with amino, carboxyl, hydrogen, and R group.
Polypeptide/Protein: Chain of amino acids; may show α-helix or β-sheet structure.
DNA Nucleotide: Deoxyribose, phosphate, and nitrogenous base (A, T, C, G).
RNA Nucleotide: Ribose, phosphate, and nitrogenous base (A, U, C, G).
DNA Double Helix: Two antiparallel strands coiled into a helix.