Biochemistry Fundamentals

Four Classes of Biomolecules

• These include proteins, nucleic acids, carbohydrates, and lipids.
• Lipids are not polymers, whereas carbohydrates are polysaccharides/oligosaccharides.
• Proteins are linear polymers of L-amino acids joined by peptide bonds.
• Amino acids consist of an amino group, COOH, and a distinctive R chain.
• The alpha carbon is situated between the carboxyl and amino groups.
• Peptide bonds are created through condensation reactions, where water is removed between the COOH of one amino acid and the NH2 of the next.
• Peptidyltransferase facilitates this condensation reaction.

Protein Function

• Proteins are the most versatile biomolecules, acting as:
  • Signaling molecules like hormones and growth factors
  • Transporters of iron, amino acids, and glucose
  • Catalysts via enzymes
  • Aids in movement through actin, myosin, and tubulin
  • Structural components like collagen, elastin, keratin, and fibroin
  • Gene regulators through transcription factors

Nucleic Acids

• Information molecules of the cell
• DNA consists of deoxyribonucleotides, while RNA is composed of ribonucleotides.
• Nucleic acids are nucleotide polymers joined by phosphodiester bonds.
• Phosphodiester bonds are covalent bonds between nucleotides in DNA and RNA, catalyzed by DNA or RNA polymerase.
• Central dogma of molecular biology: Information flows from DNA to RNA and then to protein.
• Condensation reaction: water is eliminated between the OH of a nucleotide and the phosphate of the next.

Carbohydrates

• Linear or branched polymers of monosaccharides (sugars)
• Sugars primarily exist in cyclic form rather than open chain (acrylic).
• Ribose and glucose are common sugars.
• Alpha configuration occurs if the aldehyde and OH are in different directions, and beta if they are in the same direction.
• Thousands of different carbohydrates can link together in chains and form branches via glycosidic bonds (catalyzed by lactase or sucrose synthase).
• Carbohydrates function as:
  • Crucial fuel sources, especially glucose stored as glycogen in animals and starch in plants
  • Structural molecules like cellulose and chitin
  • Signaling molecules in cell-cell recognition, forming glycoproteins and glycolipids on cell membranes
  • Lubricants like hyaluronic acid in joints and mucus

Lipids

• Water-insoluble molecules highly soluble in organic solvents
• Serve mainly as fuel (free fatty acids) and as a storage form of fatty acids (triacylglycerols)
• Other molecules include:
  • Phospholipids: membrane lipids
  • Glycolipids: membrane components bound to carbohydrates
  • Steroids: polycyclic hydrocarbons, signaling molecules, and membrane components

Fatty Acids

• Main source of fuel
• Simplest form of a lipid, consisting of a long hydrocarbon chain and carboxyl group
  • Saturated fatty acids are single-bonded and found in meat/solids/long hydrocarbon chains
  • Unsaturated fatty acids contain double bonds and are common in natural fats/liquids.

Triacylglycerols

• Storage form of fatty acids
• Fats consist of glycerol and three fatty acids, created via three condensation reactions to form ester linkages between fatty acid carboxyl groups and hydroxyl groups in glycerol.
• This ester linkage produces an ester bond, also called esterification.

Membrane Lipids

• Phospholipids are amphipathic with hydrophilic parts that dissolve in water and hydrophobic hydrocarbon chains that do not.

Covalent Bonds

• Bonds where electrons are shared between participating atoms
• Examples of these bonds are:
  • Peptide bonds link amino acids (via peptidyltransferase)
  • Phosphodiester bonds hold polynucleotide chains together in RNA/DNA
  • Ester bonds are present in triglycerides
  • Glycosidic bonds link monosaccharides to make polysaccharide carbohydrates

Noncovalent Bonds

• Hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic bonds

Water

• A dipolar molecule with uneven electron distribution between hydrogen and oxygen
• The oxygen nucleus attracts electrons more strongly than hydrogen, resulting in unequal electron sharing and dipoles.
• Forms hydrogen bonds with other polar molecules.
• Universal solvent and very cohesive.
• Polarity and ability to form hydrogen bonds make water a solvent for charged or polar molecules.

Electrostatic Interactions

• Weak interactions between ions of opposite charges, also called ionic bonds or salt bridges.
• NaCl is an example.

Van der Waals Interactions

• Very weak interactions between molecules that are nonpolar and uncharged
• Involve short-range attractive interactions dependent on transient asymmetry in electrical charge due to close proximity of atoms
• An example is enzyme-substrate binding and antibody-antigen binding.

Hydrophobic Interactions

• Aggregation of non-polar molecules increases the randomness of water molecules.
• Hydrophobic effect: nonpolar molecules in aqueous solutions are driven together due to increase in entropy of water molecules.
• Second law of thermodynamics: universe's total entropy (system + surroundings) must increase in every spontaneous process.
• Hydrophobic effect powers membrane formation, resulting in lipids forming a bilayer with a hydrophilic exterior and hydrophobic interior.
• Protein folding is also powered by the hydrophobic effect.

Ionization of Water Molecules

• Water has a small but finite tendency to ionize to H+ and OH- ions.

Buffers

• Aqueous solutions that resist pH changes when acid or base is added
• Mixture of a weak acid (proton donor) and its conjugate base (proton acceptor), or vice versa
• Buffer capacity is best within ~1 pH unit of pKa Maintain cellular and body fluid pH

Important Weak Acids

• Ammonia buffer: pKa= 9.25
• Phosphate buffer: pKa= 6.86
• Acetate buffer: pKa= 4.76

Structural Features of Amino Acids

• Determined by their side chains and include protein folding, binding to ligands, and interaction with the environment
• Free amino acids have an alpha carbon between the carboxyl and amino groups
• A side chain makes each amino acid distinctive, determining each protein's properties
• Peptidyl transferase allows enzyme response for peptide bond formation

Peptide Bonds

• Exhibit partial double bond character
• Are rigid and planar in a trans configuration
• Uncharged but polar

Types of Amino Acids

• Amino acids grouped on chemical properties of R groups:
  • Hydrophobic AA: w/ nonpolar R groups
  • Polar AA: w/ neutral R groups but unevenly distributed charge
  • Positively charged AA: w/ R groups with a positive charge at physiological pH (7.4)
  • Negatively charged AA: w/ R groups with a negative charge at physiological pH

Hydrophobic Amino Acids

• Nonpolar; even electron distribution; do not gain/lose proteins or participate in hydrogen/ionic bonds, and remain inside protein molecules
• These include alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), methionine (Met), phenylalanine (Phe), tryptophan (Trp), proline (Pro), and glycine (Gly).
• Side chains made of only hydrogen and carbon
• Alanine and Glycine are ambivalent: meaning they can be inside or outside the protein molecule
• Hydrophobic amino acids cluster inside the protein

Hydrophobic Amino Acids & Hydrocarbon Side Chains

• Side chain bonded to the alpha carbon and the nitrogen atom limits rotation, and reduces structural flexibility of polypeptide regions
• Found in the protein chain's bends, forming collagen's fibrous structure

Location of Amino Acids in Proteins

• Nonpolar amino acids cluster inside soluble proteins.
• Nonpolar amino acids cluster also on membrane protein surfaces.
• Polar amino acids cluster on soluble protein surfaces.

Polar Amino Acids

• Have electronegative atom (oxygen) side chains
• Hydroxyl groups (-OH), NH2 participate in hydrogen bonds; phosphate groups can be added to OH via phosphorylation; sugar can be added to the amide in glycoproteins
• The thiol group (SH) oxidized to disulfide bond (S-S) at slightly basic pH

Amino Acids

• Glycine (Gly), serine (Ser), threonine (Thr), cysteine (Cys), tyrosine (Tyr), asparagine (Asn), and glutamine (Gln)

Positively Charged Amino Acids

• Hydrophilic (nitrogen): Lysine, Arginine, Histidine
• Histidine often found in enzyme sites

Negatively Charged Amino Acids

• Have acidic side chains
• Aspartate is the ionic form of aspartic acid; glutamate is the ionic form of glutamic acid
• The second carboxylic acid group on the side chain is deprotonated at neutral pH
• Asp and Glu side chains can donate protons or be important in enzyme catalysis

Sickle Cell Disease

• Causes cells to look like a C-shaped tool and leads to abnormal hemoglobin and wrong cell shape
• Caused by mutation of the beta globin gene (a valine replaces a glutamate residue)
• Valine is hydrophobic and tends to interact with other hydrophobic side chains to exclude water

Structures of Proteins

• Primary: amino acid residues, a sequence of a chain of amino acids
• Secondary: alpha helix, local folding of the polypeptide chain into helices or sheets
• Tertiary: three-D folding pattern of a protein due to a side chain interaction, polypeptide chain
• Quaternary: assembled subunits, protein consisting of more than one amino acid chain

Secondary Structure

• Alpha helix, hydrogen bond
• The main chain in the polypeptide forms the inner part of a right-handed helix
• Helix is stablized via intrachain hydrogen bonds between the carboxyl groups of the main chain that are 4 AAs apart

Amino Acids that Disrupt Alpha Helix in Secondary Structures

• Proline: often interrupts the alpha helices
• Rotation N-Alpha Carbon not possible & lacks hydrogen bond formation
• Large numbers of charged amino acids: Serine, aspartate, and asparagine
• Amino Acids with bulky side chains (tryptophan) or with branch side-chain (valine, isoleucine), aliphatic amino acids

Tertiary Structure of Globular Proteins

• Driven by hydrophobic interactions
• Covalent and noncovalent side chain interactions also contribute to the 3-D structure
• Hydrogen bonds between side chains and disulfide bridge

Quaternary Structure of Proteins

• Refers to associating individual polypeptide chain subunits in a geometrically and stoichiometrically specific manner (nonpolar side chains, hydrogen bonds, and ionic bonds)
• Hemoglobin consists of two subunits of one type and two subunits of another type

Globular, Fibrous, and Membrane Proteins

• Globular: soluble and compact, many are cytoplasmic, and some are secreted from cells; hydrophobic residues inside
• Fibrous: water insoluble, fiber-like, long strands or sheet repeating units
• Membrane: embedded in membranes and many have >1 alpha helix that spans a membrane

Protein Folding

• Follows specific folding pathways that leads from denatured to native state through formation of 2D structures

Protein Denaturation

• Transformation of a well-defined folded protein structure under physiological condition, to an unfolded state under un-physiological condition disrupts/weakens forces
• Affected by weak interactions in the protein such as hydrogen bonds
  • Characteristic melting temperature of a protein (Tm)

Denaturation by pH

• Acids and bases disrupt salt bridges held together by ionic charges/bonds
• Most proteins are denatured by acid or base because of electrostatic repulsion

Denaturation by Chemical Urea

• The denaturing agent urea forms H-bonds to NH and C=O in peptide bonds and blocks intramolecular H-bonding
• Interferes with hydrophobic interactions that normally stabilize the protein
• To reverse, dialyze away Urea to get refolding

Protein Misfolding

• Causes a general term for diseases (Amyloidosis)
  • Occurs because of a mutation in the protein or a defect in post-translational processing that leads to a nonfunctional insoluble protein

Protein Digestion

• Occurs when monomeric units are joined and the elements of H2O are eliminated from carbohydrates, and nucleic acids
• Begins in the stomach by HCl and enzyme pepsin
• Enzymes are secreted from the pancreas and into the small intestine- which is the major digestion site
• Final digestion of di/tri-peptides to amino acids occurs inside it
• The absorbed acids travel to the liver and regulate the distribution of amino acids to the rest of the body

Role Of HCl in Digestion

• Protein denaturation begins by gastric acids
  • disrupt salt bridges and prevents hydrogen bonding
• Pepsinogen is activated by both HCl and Pepsin
  • Acid denatures the proteins making them accesible to enzymatic cleavage
  • Pepsin hydolyzes peptide bonds to turn them into smaller fragments
• Dietary Protein is broken down into polypeptides and acids

Enzymes

• Proenzymes/Zymogens are activated to active enzymes by enteropeptidase proteases
• Enteropeptidase= a serine protease produced in the duodeum
• Protein Digestion happens when pepsin is activated in the stomach, pancreatic pronzmes in the small intestine, and peptides are broken down

Transport Amino Acids into Cells

• From the intestinal lumen to epithelial: Sodium Dependent Transport of Amino Acids
  • Sodium is pumped out on serosal
• From epithelial and into blood: the Amino Acid is transferred to a facilitated transporter along the concentration gradient
  • Transporter System: neutral amino acid, dibasic- deficiency causes diseases

Amino Aciduria

• Deficiency of Tryptophan
  • Genetic deficit is in the transporter genes, which affects absorption and causes serotonin melatonin and niacin

Cystinuria

• An error with the most common genetic transporter on the kidney; Cysteine will only resolve in the presence of urine
• The body cannot resolve the stones that form in the urinary tract

Digestion of Carbohydrates

• Digestion of Carbs starts in the mouth by salivary-alpha-amylase
  • it breaks down alpha 1,4 gycosidic bonds
  • The small intestine has alpha anylase that only breaks down 1,4 glycosidc bonds
• halted in an arcidide evnironment but resumed into enzymes which leads to dissacharides broken down

Lactose Intolerance

• Reduced levels from lactase due silencing of the lactose gene, is mostly affected by adults of african/asian descent

Digestion of Dietary Lipids

• Small intestine, with lingual lipase in the mouth
  • pancreatic enzymes is responsible

Lipid Digestion in Stomach

• enzymes are produced
  • these are acid stable and remove lipid chains; most active with the infants
  • emulsification occurs from chemical mixing an increases thr area

Emulsificiation of Lipid in a Small Intestine

• this occurs in the dueomeuem and increases area
• emulsification has two steps
  • Physical and chemical mixing
  • conjugated bile salts

Lipid Absorption

• Occurs when the bile salts break larger globules into smaller and hydrophilic
• this aids where the lipase occurs
• the digestion: Free Fatty Acids, monoaglcerol, cholesterol
• Michelles emulsify and solubiilize fatty acids

Assembly and Secreetion of Microns

• Small intestine has the absorbed cells that trnasport fat with cholesterol and proteins
  • this travels the system thorugh ducts and eventually to the tissues and delivers
• Golgi takes and processes cholestterol esters to lipid
• Key proteins like Apo are needed for all of this

Amino Acids

• Degredation is by oxidation, can have transamination
• Tissue Damage: Occurs when tissue is damaged because ALT (Alanine) enzymes leak which catalysts pyruvate
  • AST (Aspartate) catalyzing oxaloacetate.

Removals of Nitrogen

• Place: liver and kidney
• Enzyme: glutamate dehydrogenase: a process to remove an amino groiup but releases amonia
  • these are processed in liver and excreted to control nitrogen levels

Urea Cycle

• is how ammonium is converted to urea
  • Is the majority diposal derived to the amino acids and contains components: liveer and kidneys
• The body converts excess Amonia into urea to be excreted

TCA Cycle

• Takes place in the Mitochondria with two steps
  • These two combine to make carbonyl which goes out to cytosol

BUN and Nitrogen Test

• Test: measuring urine nitroge
  • measure in liver

Amino Acid Carbon Skeletons

• The amino aid broken skeleton can fall to two main pathways: TCA and can be glugenic

Transferase

• Is key as converting Histidine
• Can be tested with: The FIGLU test
• Phenylalanine to Tyrosine is key for proper function

Sam

• The molecule to donate proteins in chemicals called carbon metabolism

HomoCystene

• Pathways that maintain metalionine to protect gene and DNA.
• It is a harm is linked cardiovasuclar damage for the regulation

Synthesis of Cysteine

• A process in which vitamin B12 donates methyl-THF is used for Folate and Histadin
• Important carbon source

Nucleic Acids

• Are information
  • Nucleotide: a type of base wihth pentose
    • these include purines and uracil +guanina

Pathways of Synthesis

De Novo: the synthesis, base needs to be synthesized from materla

• Cell make two kinds of molecules Salvagem recycles these bases attaching them to the ribsos. useful building blocks.

Nuceotide Syntheses

• Adding carbon and nitrogen to prp-backbones with PP.

###Purine Synthesis

• Can be regulated in synthestase

Azathiptrine Drugs

• Inhibitors that help contropl Purine
• Salvages the purines and the molecules recycle

Lesch-Nyhan Syndrome

• Leads to an defencincy within HGPRT and acid

###Purine Nuceotides

• They paly with roles cells and de novas

Degredation

• Lead to to high leverl of uric acid and gout
• the regulation is critical to balance

###Gout Treament

• Preventions, colchine

###Sources of Purine

• Tissue
• Adenosine deficiency

De Nuove Synthesis

• Synthesis is where bicarbonate used and attached

Syntheses for Pylimandines

• These can savagel
• 5 Flouracil, helps prevent the tetrahydrolate

Structure and Forms

THF Derives

• One main carbon Carbon is the malate that generates the ATP yields. Then oxidates and can be uncoupled to prevent that high protien level of ATP

Test your knowledge of biochemistry with questions covering glucose and glycogen, fatty acids, and protein structures. Explore the functions of carbohydrates and the impact of amino acid mutations of hemoglobin. Investigate phospholipid structure and triacylglycerol formation.