Biochemistry Quiz on Molecules and Processes

Key Points

• Understand biochemical reactions in water (10%)
• Describe cell organization (8%)
• Detail amino acids and peptides (6%)
• Identify proteins, protein purification, and enzymes (14%)
• Describe biological membranes (6%)
• Understand nucleic acid structure and information conveyance (3%)
• Detail nucleic acid biosynthesis and replication (8%)
• Explain RNA biosynthesis (4%)
• Describe genetic message translation (6%)
• Understand viruses, cancer, and immunology (6%)
• Describe energy and electron transfer in metabolism (10%)
• Identify carbohydrate metabolism storage mechanisms (16%)
• Describe glycolysis (3%)

Carbohydrates

• Sugars are small carbohydrates (literally hydrates of carbons)
• Monosaccharides are smaller units polymerizing to form polysaccharides

Nomenclature

• Carbohydrate names are based on the number of carbons:
  • 3 carbons = triose
  • 4 carbons = tetrose
  • 5 carbons = pentose
  • 6 carbons = hexose
• All carbohydrates have an aldose or ketose functional group

Fisher Projection Formulas

• These are 3D representations (vertical bonds away, horizontal bonds toward viewer)
• Show stereocenters and exist as enantiomers (mirror images)
• Vertical lines represent bonds behind the plane
• Horizontal lines represent bonds in front of the plane
• D-stereoisomer has -OH on right
• L-stereoisomer has -OH on left
• n chiral centers = 2^n stereoisomers

Important Monosaccharides

• D-Glucose: stored at 65-110 mg/dL in blood, excess stored as glycogen or fat
• D-Fructose: ketohexose, sweetest monosaccharide
• D-Galactose: 6C aldohexose found in lactose
• Galactosemia: accumulation of galactose due to enzyme deficiency

Haworth Projections

• Cyclic hemiacetals, rings
• Create an anomeric carbon stereocenter (alpha or beta, based on OH position)
• Alpha has -OH down, beta has -OH up

Mutarotation

• Change in specific rotation due to equilibration of alpha and beta anomers in aqueous solutions
• Alpha can turn into beta

Formation of Glycosides

• Treatment of a monosaccharide with an alcohol produces an acetal
• Water is lost to form an acetal
• A cyclic acetal is a glycoside
• A glycosidic bond forms from anomeric carbon to an —OR group

Reduction to Alditols

• Reduces the CHO group of a monosaccharide to CH2OH
• Sorbitol is a sugar substitute
• Xylitol is used as a sweetening agent

Oxidation to Aldonic Acids

• Aldehyde group oxidizes to an aldonic acid
• Reducing sugars have an altered H to O-

Oxidation of Uronic Acids

• Enzyme oxidation forms uronic acid (CH2OH to COOH)

Phosphoric Esters

• Phosphoric acid reacts with alcohols
• A phosphate group is added to the sugar, a first step in glycolysis

Important Disaccharides

• Sucrose: glucose + fructose, a table sugar, non-reducing sugar
• Lactose: glucose + galactose, present in milk
• Maltose: 2 glucose units, alpha 1,4 glycosidic bond

Polysaccharides

• Starch and glycogen: polymers of alpha-glucose, used for energy storage (glycogen in animals, starch in plants)
• Cellulose: beta-glucose polymers, form plant cell walls, straight chains
• Acidic Polysaccharides: contain carboxyl and sulfuric ester groups, important in connective tissue (e.g., hyaluronic acid, heparan)

Lipids

Classification by Function

• Store energy (fats release more energy than carbs)
• Part of membranes
• Chemical messengers (e.g., hormones)

Classification by Structure

• Simple lipids
• Complex lipids
• Steroids
• Prostaglandins, thromboxane, leukotrienes

Fatty Acids

• Fatty acids are linked to alcohols via condensation reactions to form ester linkages
• Long, unbranched carbon chains with a carboxyl group
• Amphipathic (insoluble in water)
• Saturated vs. unsaturated (double bonds)
  • Saturated have no double bonds, straight chains; unsaturated have double bonds, kinked chains
• 3 most common: palmitic, stearic, oleic acids

Triglyceride Structure

• Glycerol backbone with 3 fatty acid chains linked by ester bonds
• Important form of stored energy

Physical State (Fats vs. Oils)

• Fats (saturated) : have straight chains, higher melting points
• Oils (unsaturated): have kinked chains, lower melting points

Complex Lipids

• Phospholipids (alcohol, 2 fatty acids, phosphate): components of membranes (e.g., glycerophospholipids, sphingolipids)
• Glycolipids (alcohol, fatty acid, carbohydrate): important in nerve cells

Phospholipids

• Phosphoglycerides: glycerol backbone, 2 fatty acids, phosphate group, esterified to alcohol
• Sphingolipids: sphingosine backbone, 1 fatty acid, phosphate group

Phosphatidylinositols

• Alcohol inositol bound by phosphate
• Signaling molecules in communication

Sphingolipids

• Backbone is sphingosine
• Combination with fatty acid called ceramide
• Can include phosphocholine or phosphoethanolamine

Glycolipids

• Complex lipids containing carbohydrates and ceramides
• Example: Cerebrosides(ceramide with mono or oligosaccharides)

Steroids

• Compounds with a fused 3 cyclohexane and 1 cyclopentane ring
• Not necessarily esters
• Example: Cholesterol (modulator of membrane fluidity, most abundant steroid)

Lipoproteins

• Transport cholesterol in the blood
• HDL, LDL, VLDL, Chylomicrons

Transport of Cholesterol

• LDL: transports cholesterol from the liver to peripheral tissues
• HDL: transports cholesterol from peripheral tissues to the liver

Steroid Hormones

• Adrenocorticoid hormones: regulate metabolism, immune response, and stress response.

Bile Salts

• Produced in the liver from cholesterol oxidation
• Important in solubilizing dietary fats

Prostaglandins, Thromboxane, Leukotrienes

• Lipid molecules derived from essential fatty acids
• Involved in inflammation, pain, fever, blood pressure, blood clotting, uterine smooth muscle tone, and allergic responses

Proteins

Functions

• Structural material
• Catalysis
• Movement
• Transport
• Hormones
• Protection
• Storage
• Regulation

Amino Acids

• 20 common amino acids
• Classified as nonpolar, polar neutral, acidic, or basic
• Except for glycine, all amino acids exist as two enantiomers
• Acidic: COOH
• Basic: Amino
• Neutral: Alcohol, Cysteine

Amino Acids as Zwitterions

• A zwitterion is a neutral molecule with both positive and negative charges.
• Amino acids are zwitterions (both solid state and in solutions)
• Amino acids are either positive or negative in an acidic or basic environment, but remain soluble either way

Protein Properties

• Isoelectric Point: the pH at which a molecule carries no net electrical charge.
• Amino acids can react with each other, forming peptide bonds and eventually proteins.

Primary Structure

• The sequence of amino acids.
• Covalent peptide bonds/links between amino acids.

Secondary Structure

• Regularly repeating arrangements (alpha-helices, beta-pleated sheets)
• Stabilized by hydrogen bonds between amino acids

Tertiary Structure

• 3D structure of a polypeptide chain
• Stabilized by bonds between R groups (Hydrophobic interactions, Hydrogen bonds, Ionic bonds, Disulfide bridges)

Quaternary Structure

• Multiple polypeptide chains linked together
• Example: hemoglobin (four polypeptide chains)

Non-Conjugated Proteins

• Proteins only consisting of peptides
• Examples: Insulin and Collagen

Hemoglobin

• Tetrameric protein (4 polypeptide chains)
• Oxygen transport in blood, cooperatively binding oxygen

Protein Denaturation

• A change in a protein's 3D structure, caused by heat or pH changes.
• Causes loss of function.

Enzymes

• Biological catalysts that speed up chemical reactions by lowering the activation energy.
• Substrate specificity (enzyme specifically fits to the substrate), a lock and key or induced fit model.

Enzyme Activity

• Measures enzyme efficiency in catalyzing the reaction.

Enzyme Substrate Concentration

• Increased substrate concentration leads to increased enzyme activity up to a point of saturation.

Temperature and pH

• Enzymes have optimal temperature and pH ranges
• Extreme conditions denature the enzyme.

Enzyme Inhibition

• Irreversible inhibitors: bind permanently to the active site; non-competitive inhibitors: bind to an allosteric site (and affect active site function; competitive inhibitors compete with substrate for the active site;
• maximum rate achieved at low substrate concentration (no inhibitor); maximum rate achieved at high concentrations (inhibitor) causes substrate displacement and equilibration.

Active Sites

• Site in the enzyme where the substrate binds;
• Pyruvate Kinase converts phosphoenolpyruvate and ADP into pyruvate and ATP; catalytic power is caused by His, Cys, Asp, Arg, and Glu.

Allosterism

• Allosteric regulation: occurs when a molecule binds to an allosteric site, altering enzyme activity (activator or inhibitor).

Protein Modification (e.g., Phosphorylation)

• Modification of the protein structure; either activates or deactivates the enzyme.

Isozymes

• Different forms of the same enzyme with varying protein sequences
• Function in different tissues/cellular compartments and can be regulated differently.

Enzyme Medical Uses and Clinical Applications

• Examples like Trypsin, Thrombin
• Details of uses and application.

Nucleic Acids

Bases

• Purines (Adenine, Guanine)
• Pyrimidines (Cytosine, Thymine, Uracil)

Sugars

• DNA: Deoxyribose; RNA: Ribose
• Forming the sugar-phosphate backbone

Nucleoside

• Combination of sugar and base (e.g., adenosine)

Phosphate

• Phosphate bond to nucleoside forms a nucleotide (e.g, RNA and DNA structure)

Primary, Secondary, Higher Order Structure

RNA Types

• mRNA: encodes protein sequence
• tRNA: carries amino acids to the ribosome
• rRNA: part of the ribosome

DNA Replication

• Semi-conservative process
• Helicase: unwinds the DNA helix
• DNA Polymerase: adds nucleotides to build new strands
• Ligase: joins Okazaki fragments

DNA Amplification (PCR)

• Denaturation, Annealing, and Elongation steps
• Critical for molecular diagnostics and other applications, uses heat-tolerant polymerase (Taq)

Telomeres

• Repeating nucleotide sequences at the ends of chromosomes
• Protect ends of chromosomes from degradation, important for maintaining genome stability.

Gene Expression and Protein Synthesis

• Central dogma (DNA -> RNA -> Protein)
• Transcription (DNA to mRNA)
• Translation (mRNA to protein)

Introns and Exons

• Introns are non-coding regions of DNA/RNA
• Exons are coding segments of DNA/RNA

Transcription Regulation

• Promoter (initial transcription); enhancer;
• elongation and termination (including capping of 5' end or polyadenylation of 3' end, intron removal/splicing)

Post-transcriptional Modifications

• Capping and tailing of mRNA (5' and 3' ends)
• Intron splicing (removal of non-coding sequences)
• Methylation

Translation

• mRNA serves as a template
• Initiation, elongation, translocation, and termination (using ribosomes)

Correspondence between 3 Bases (codons) and Amino Acids

Enzyme Inhibition

• Irreversible vs Reversible (competitive vs. non-competitive inhibitors)