Biochemistry Lec Midterms PDF

BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) CARBOHYDRATES ​ Major sources of energy and produced by photosynthesis in plants such as glucose are synthesized by plants from CO2H2O. ​ “Saccharide” is a Greek word for sugar or CHO. F...

BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) CARBOHYDRATES ​ Major sources of energy and produced by photosynthesis in plants such as glucose are synthesized by plants from CO2H2O. ​ “Saccharide” is a Greek word for sugar or CHO. FUNCTIONS: ​ Provides energy Presence of Chiral Center/s ​ GLYCOGEN - provides short term ​ Structural Isomers energy reserves. ​ Stereoisomers ​ Supply carbon for synthesis of other biochemical substances. MIRROR IMAGE ​ Parts of structures of DNA and RNA ​ Linked to lipids in cell membrane Superimposable Mirror Image - coincide ​ Linked to proteins in biological at all points recognition processes. Non-superimposable Mirror Image - ​ Spare the use of protein energy doesn’t coincide at all points. ​ Breakdown fatty acids and preventing ketosis CHIRAL CENTER ​ Provide flavor and sweetness ​ Source of dietary fiber ​ Atom in a molecule that has four different tetrahedrally bonded to it ​ Mirror images are not STRUCTURAL PROPERTIES superimposable Handedness ​ Left handed and Right Handed is determined by the configuration at the high numbered chiral carbon. BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) ISOMERISM ​ Compounds possessing identical molecular formulas but different structures. ​ GLUCOSE: single bond ​ FRUCTOSE: double bond TWO TYPES OF ISOMERISM 1.​ Structural Isomerism - same CLOCKWISE DIRECTION molecular formula but different from ​ Dextrorotatory (d) or (t) each other by having different structures. COUNTERCLOCKWISE DIRECTION Examples: Glucose and Fructose ​ Levorotatory (L) or (-) 2.​ Stereoisomerism - same molecular formula and same structure but differ in configuration. Its differ in arrangement of their atoms in space ​ Presence of chiral centers allows the formation of stereoisomerism. TYPES OF STEREOISOMERISM EPIMERISM ASSOCIATED WITH GLUCOSE ​ If two monosaccharides differ from each other in their configuration ★​ D and L Isomerism around a single specific carbon ★​ Optical (other than anomeric) atom. ★​ Epimerism ★​ A and B Anomerism Enantiomers - whose molecules are non-superimposable mirror images of each other. Diastereomers - whose molecules are not mirror images of each other. OPTICAL ISOMERISM ​ Optical activity is the capacity of a ANOMERISM substance to rotate the plane ​ Obtained from the change of position polarized light passing through it. of hydroxyl group attached to the BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) anomeric carbon e.g. a and B glucose ​ A carbonyl group (aldehyde or are 2 anomers. ketone) ​ Several hydroxyl groups ​ Colorless, crystalline solids ALDOSE ​ With an aldehyde group with many hydroxyl (-OH group) ​ Triose (3 carbon atoms) Tetrose ( 4 carbon atoms) Pentose (5 carbon atoms) and Hexose ( 6 carbon atoms) MUTAROTATION ​ Erythrose - tetrose ​ The change in the specific optical saccharide with the chemical rotation by the interconversion of a formula C4H8O4. and B forms of D glucose to an equilibrium mixture. KETOSE ​ Ketone group with many hydroxyl (-OH Group) ​ Triose (3 carbon atoms) Tetrose ( 4 carbon atoms) Pentose (5 carbon atoms) and Hexose ( 6 carbon atoms) ​ Fructose - a simple sugar, or monosaccharide, that's found in fruits, vegetables, and honey. CLASSIFICATION Based on molecular size D-GLUCOSE - found in fruits, corn syrup, 1.​ Monosaccharide - simplest and honey aldohexose with the formula carbohydrates C6H12O6 body sugar in the body. 2.​ Disaccharides - consists of 2 ​ Polymers of starch, glucose and monosaccharide glycogen 3.​ Oligosaccharides - contains of 3-10 monosaccharide 4.​ Polysaccharides - contains of many monosaccharide MONOSACCHARIDE ​ Consists of 3 to 6 carbon atoms BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) BLOOD GLUCOSE LEVEL - glucose has STRUCTURE OF a normal blood level of 70/90 mg/dl MONOSACCHARIDE GLUCOSE TOLERANCE TEST - test 1.​ Fischer Projection - the straight measures blood glucose for several hours chain structural formula. after ingesting glucose. ➔​ Hyperglycemia - Normal ➔​ Hypoglycemia - Abnormal D-FRUCTOSE ​ Ketohexose with the formula of C6H12O6 and it has the sweetest carbohydrate. It is also found in fruit juices and honey and converts glucose to the body. 2.​ Haworth Projection - Cyclic formula or ring structure. D-GALACTOSE ​ An aldohexose with the formula of C6H12O6 and not found free in nature. 3.​ X-Ray Diffraction Analysis - Boat ​ It is obtained from lactose, a and Chair Form. disaccharides and similar structure to glucose except for the -OH on C4. BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) DISACCHARIDES LACTOSE ​ Is a disaccharide of 6- D-galactose ​ Glycosides formed by the and a- or 6-D-glucose condensation of 2 simple sugars. ​ Contains a 6-1,4-glycosidic bond and ​ If the glycosidic linkage involves the is found in milk products. carbonyl groups of both sugars (as in sucrose) the resulting disaccharide is non-reducing. ​ If the glycosidic linkage involves the carbonyl group of only one of the 2 sugars (as in maltose and lactose) the resulting disaccharide is reducing. SUCROSE ​ also known as table sugar ​ obtained from sugar cane and sugar beets ​ Consists of a-D-glucose and b-D-fructose and has an a,b-1,2-glycosidic bond MALTOSE ​ also known as malt sugar ​ Composed of two D-glucose molecules ​ Obtained from the hydrolysis of starch ​ Linked by an a-1,4-gLycosidic bond formed from the u —OH on Cl of the first glucose and —OH on C4 of the second glucose ​ Used in cereals, candies, and RELATIVE SWEETNESS brewing and found in both the a- and B- forms. Fructose - sweetest even sweeter than sucrose ​ Honey-D-fructose and D-glucose Lactose - almost no sweetest and is sometimes added to food as a filler BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) POLYSACCHARIDES ​ formed by the condensation of n molecules of monosaccharides with the removal of n-1 molecules of water ​ Since condensation involves the carbonyl groups of the sugars, leaving only one free carbonyl group at the end of a big molecule, polysaccharides are non-reducing ​ polymers of D-glucose and Include amylose and amylopectin, starches made of a-D-glucose CLASSIFICATION ​ Include glycogen (animal starch in Based on reaction to oxidizing agents muscle), which is made of a-D-glucose. 1.​ Reducing Sugar - carbohydrate that ​ Include cellulose (plants and wood), gives a positive result with which is made of 6-D-glucose Benedict's and Tollen's test and it includes the monosaccharide, glucose, galactose, and fructose. 2.​ Non-reducing Sugar - negative with Benedict’s and Tollen’s Test. TYPES OF POLYSACCHARIDES BASED ON THEIR FUNCTION: OXIDATION OF D-GLUCOSE 1.​ Storage Polysaccharides - These polysaccharides store energy for later use. 2.​ Structural Polysaccharides - These provide structural support to cells and organisms. BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) CLASSIFICATION AMYLOSE Based on the repeating units ​ A polymer of a- D-glucose molecules 1.​ Homopolysaccharide - only one ​ Linked by u-1,4 glycosidic bonds type of monosaccharide monomer ​ A continuous (unbranched) chain unit is present. 2.​ Heteropolysaccharide - more than one (usually two) types of monosaccharide monomer units are present. AMYLOPECTIN CLASSIFICATION ​ Is a polymer of a-D- glucose Based on the degree of branching molecules ​ Is a branched-chain polysaccharide 1.​ Branched - polysaccharides formed ​ Has a-I,4-glycosidics bonds between from two major types of biochemical the glucose units polymers therefore forming ​ Has a-1,6 bonds to branches branches. 2.​ Unbranched - linear polymers GLYCOGEN ​ polysaccharide that stores STRUCTURE OF AMYLOSE AND a-D-glucose in muscle AMYLOPECTIN ​ similar to amylopectin, but is more highly branched CELLULOSE ​ polysaccharide of glucose units in unbranched chains ​ Has 6-1,4-glycosidic bonds ​ Cannot be digested by humans because humans cannot break down 6-1,4-glycosidic bonds. BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) ​ Human digestive enzymes easily Chemical Messenger - involved in cellular break alpha bonds in starch. communication ​ Human digestive enzymes cannot ​ Hormones like insulin are proteins break beta bonds in cellulose. that regulate processes such as metabolism and growth. PROTEINS ​ It is a peptide in which at least 40 Disease Defense - Antibodies amino acid residues are present. (immunoglobulins) ​ It contains Carbon, Hydrogen, ​ Are proteins that recognize and Oxygen, and Nitrogen neutralize foreign pathogens like ​ It sometimes contains Sulfur and bacteria and viruses. Phosphorous ​ The Greek word “Proteios” means of Enzymes - Many proteins are enzymes that first importance. catalyze biochemical reactions. ​ Speeding up processes like digestion, CHARACTERISTICS OF PROTEINS metabolism, and DNA replication. ​ Next to water, most abundant substances AMINO ACIDS ​ About 15% of a cell’s overall mass ​ Building blocks of proteins ​ C-Carbon, H-Hydrogen, O-Oxygen, ​ There are 700 different naturally N-Nitrogen (CHON) occurring amino acids but only 20 ​ Phosphorus and iron = essential are normally present in proteins. constituent of certain specialized ​ These 20 amino acids present in milk proteins are called the Standard ​ CASEIN - the main protein of milk, Amino Acids contain phosphorus an element important in the diet of infant and CHEMICAL STRUCTURE OF AMINO children ACIDS ​ HEMOGLOBIN - the oxygen ​ Amino acid is an organic compound transporting protein of blood, it that contains both an amino group contains iron. and a carboxyl group. ​ Attached to a a-carbon atom FUNCTIONS OF PROTEINS ​ Amino group acts like a base and tends to be positive Structural Component - provide structure ​ Carboxyl group acts like an acid and and support to cells and tissues. tends to be negative ​ Collagen in connective tissues ​ “R” group is variable and can range ​ Keratin in hair and nails from 1 to 20 atoms ​ Actin and Tubulin in the ​ Two amino acids can join to form a cytoskeleton dipeptide. BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) Polar Basic Amino 2 amino group Acids 1 carboxyl group (1 is part of side chain) NON-POLAR AMINO ACIDS ​ 1 amino acids, 1 carboxyl and nonpolar side chain ​ Hydrophobic when incorporated into a protein ​ Found in the interior of protein=limited contact with water ​ Tryptophan - borderline member=water can weakly interact 4 CLASSIFICATION OF AMINO through H bonding with NH ACIDS ring=polar neutral amino acids. ❖​ Based on side chain polarity ❖​ Based on number of peptide chain POLAR ACIDIC AMINO ACIDS ❖​ Based on chemical composition ​ 1 amino group, 2 carboxyl group, ❖​ Based on shape 2nd carboxyl are part of side chain ​ pH = side chain is negative charge, CLASSIFICATION OF AMINO ACIDS: carboxyl group lost its H atom. BASED ON SIDE CHAIN POLARITY POLAR NEUTRAL AMINO ACIDS Classification Description ​ 1 amino group, 1 carboxyl group, a side chain that is polar but neutral Non-Polar Amino 1 amino group ​ pH = neither acidic nor basic Acids 1 carboxyl group ​ 6 polar neutral amino acid 1 non polar side chain POLAR BASIC AMINO ACIDS ​ 2 amino acids, 1 carboxyl group, 2nd amino acid part of side chain Polar Neutral 1 amino group ​ pH = + charge Amino Acids 1 carboxyl group 1 polar neutral side chain CLASSIFICATION OF DIETARY PROTEIN Polar Acidic Amino 1 amino group Acids 2 carboxyl group Complete Dietary Protein (1 is part of side ​ Animal sources chain) BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) ​ CASEIN - milk,meat,fish and eggs ​ Amino acids have mirror images: ​ A protein that contains all the Right and Left based on the location essential amino acid which the body of the amino group. needs ​ Nature prefers the L-isomers of ​ May or may not contain all of the amino acids non-essential amino acid ​ Mixed pf plants provides essential THREE DIFFERENT AMINO ACIDS AA EXIST: INCOMPLETE DIETARY PROTEIN 1.​ Zwitterion -from german term ​ Plant Sources “double ion” ​ 3 AA = lysine (wheat rice. Oats, ​ It is a molecule that has both corn) methionine (beans and peas) positive and negative and tryptophan (corns and beans) changes. It is made up of two (or more) functional groups. ESSENTIAL AMINO ACIDS ​ One of its components has a positive charge and another ​ Essential Amino Acids - cannot be one with a negative charge. synthesized by the body, can be Because of this, the net acquired through food charge of a zwitterion is zero. ​ Non-Essential - amino acids can be 3. Positive Ion - an atom or molecule that synthesized by the body. has a positive charge because it has lost one ​ Ex. infants born prematurely cannot or more electrons. make sufficient Non-Essential amino acid. These 10 are needed Amino ACID-BASE PROPERTIES OF AMINO Acids until the baby matures, ACIDS ​ Human milk and milk formula = ​ Both acidic and basic group are sufficient amount of essential amino present in an a-amino acid acids. ​ White crystalline solids with high decomposition points. Most amino acids decompose before they melt. ​ If amino acid is in crystal form, it is not soluble with water due to a strong intermolecular force. CYSTEINE ​ The only standard amino acid that CHIRALITY OF AMINO ACIDS has a side chain that contain ​ Chirality refer to having a mirror sulfhydryl group (SH Group) image ​ Presence of mild oxidizing agent BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) ​ Dimerizes = reacts with another ​ Cysteine — Cysteinyl cysteine = Cystine Molecule ​ Glutamine — Glutaminyl ​ 2 Cysteine linked via Covalent ​ Asparagine - Asparaginyl Disulfide bond Rule 3 PEPTIDES -​ The amino acid naming sequence ​ Chain of covalent link amino acids begins at the N-terminal amino acid ​ Unbranched chain of amino acid residue ​ Classification according to the Example 1: number of amino acids present in the ​ Valine + Threonine + Cysteine chain ​ This will form a Tripeptide ​ Dipeptide - 2AA ​ The N terminal is Valine (Left side) ​ Tripeptide -3 AA ​ The C terminal is Cysteine (Right ​ Oligopeptide - 10 to 20 AA side) ​ Polypeptides = longer peptides and ​ Hence, Valine + Threonine + a long unbranched chain of AA Cysteine = Valinyl + Threonyl + Cysteine IUPAC RULES IN NAMING PEPTIDES ​ Final Name = Valinylthreonylcysteine Rule 1 ​ The C-terminal amino acid residue keeps its full amino acid name ISOMETRIC PEPTIDES ​ IUPAC Rules in naming small ​ Peptides containing same amino peptides acids but in different orders with ​ For Example: different molecules with different ​ Glycine + Alanine properties. ​ Glycine is the N-terminal amino ​ Ex. Ala-Gly = Gly-Ala acid -​ Ala-Ser-Cys = Ala —Cys-Ser ​ Alanine is the C-terminal amino -​ Ser-Ala-Cys acid -​ Ser-Cys-Ala Cys-Ala-Ser - ​ Hence, Glycine will become Glycyl Cys-Ser-Ala ​ While, Alanine gets to keep its name ​ Pentapeptide = contains 5 ​ Hence, Glycine + Alanine = differentAA = 120 isomers Glycylalanine BIOCHEMICALLY SMALL PEPTIDES Rule 2 -​ All the other amino acid residue Small Peptide Hormones names ending in -ine or -ic acid will ​ Oxytocin and Vasopressin are two be replaced with -yl, except: best known peptide hormones ​ Tryptophan - Tryptophyl BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) ​ Produced by the pituitary glands and ​ A complex protein consisting each hormone is a nonapeptide (9 of amino acids combined amino acid residues) with other substances. ​ Simple Protein + Prosthetic Small Peptides Neurotransmitter Group = Conjugated Protein Enkephalins - a pentapeptides neurotransmitter produced by brain that reduces pain -​ 2 best known a.) Met-enkephalins — Tyr-Gly-Gly-Phe-Met b.) Leu-enkephalins — Tyr-Gly-Gly-Phe-Leu Small Peptide Antioxidants ​ Tripeptide glutathione ( Glu-Cys-Gly) ​ Imponance as a regulation of STRUCTURE OF PROTEIN oxidation-reduction reactions Primary Protein Structure - sequence of a chain of amino acids. CLASSIFICATION OF PROTEIN: BASED ON NUMBER OF PEPTIDE CHAIN ​ Monomeric protein - only one peptide chain is present ​ Multimeric Protein - More than one peptide chain is present. Secondary Protein Structure - hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern. CLASSIFICATION OF PROTEIN: BASED ON CHEMICAL COMPOSITION ​ Simple Protein - Only amino acid residues are present. ​ Conjugated Protein - One or more non-amino acid entities present in its structure in addition to one or more ALPHA HELIX peptide chains. ​ The telephone cord shape of the alpha helix is held in place by BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) Hydrogen Bonds between every N-H group and the oxygen of a C=O group in the next turn of the helix, four amino acids down the chain. ​ The typical alpha helix is about 11 amino acids long. 4 TYPES OF STABILIZING BETA PLEATED SHEETS INTERACTION ​ The pleated sheet structure of the Beta Sheet is held together by the 1.​ Covalent Disulfide - strongest Hydrogen Bonds between the amide interactions from SH groups of 2 groups of linear polypeptide chains. Cysteine residues to form a covalent ​ The average number of amino acid disulfide bond. residues in a typical Beta Sheet is six 2.​ Electrostatic Interaction - also with an average of six strands called salt bridges bonding together. 3.​ Hydrogen Bond - can occur between AA with polar R group. 4.​ Hydrophobic Interaction - 2 nonpolar side chains that are close to each other. CLASSIFICATION OF PROTEIN: BASED ON SHAPE ​ Fibrous - have an elongated shape with one dimensions much longer than the others ​ Tertiary Protein Structure - ​ Globular - have peptide chains three-dimensional folding pattern of folded into spherical and globular a protein due to side chain shapes. interactions. ​ Quaternary Protein Structure - protein consisting of more than one amino acid chain. BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) CLASSIFICATION OF PROTEIN: PROTEIN DENATURATION BASED ON SHAPE ​ Involves the disruption of bonds in the secondary, tertiary, and quaternary structures. ​ Heat and organic compounds - break apart H + bonds and disrupt hydrophobic interactions. ​ Acids and Bases - Break H + bonds between polar R groups and disrupt ionic bonds ​ Heavy metal ions - React with S-S PROTEIN HYDROLYSIS (Sulfur-Sulfur) bonds to form solids ​ Splits peptide bonds to smaller ​ Agitation (Whipping or Shaking) - peptides and amino acids Stretches peptide chains until bonds ​ Occurs in the digestion of proteins break. ​ Occurs in cells when amino acids are needed to synthesize new proteins APPLICATIONS OF DENATURATION and repair tissues ​ Cooking eggs ​ In the lab, hydrolysis of a peptide ​ Wiping of Alcohol requires acid or base, water, and heat ​ Heat and used to Cauterize blood ​ In the body, enzymes catalyze the vessels hydrolysis of proteins ​ Sterilization of instruments in autoclave ​ Hair perming Example of Protein Hydrolysis PROTEIN HYDROLYSIS VS DENATURATION BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) NITROGEN BASES NUCLEIC ACIDS The nitrogen bases in DNA and RNA are; Nucleic acids are: ​ Pyrimidines (a monocyclic (1) base -​ Molecules that store information for with six-membered ring C, T, and U) cellular growth and reproduction. ​ Purines (a bicyclic (2 or more) -​ Capable of replication based with fused five and -​ Friedrich Miescher - Swiss six-membered rings) A and G. Physiologist who discovered nucleic acids in 1869 while studying the nuclei of white blood cells. 2 types of Nucleic Acids 1.​ DNA (Deoxyribonucleic Acid) -​ Found within the cell nucleus -​ Function: Storage and transfer of genetic information -​ Can be passed from existing cells to new cells during cell division PENTOSE SUGARS 2.​ RNA (Ribonucleic Acid) The pentose (five-carbon) sugar; -​ Occurs in all parts of a cell ​ If RNA is ribose -​ Functions: Synthesis of ​ If DNA is deoxyribose with no O proteins atom on carbon 2 -​ Carry out essential cellular ​ Has carbon atoms numbered with functions. primes to distinguish them from the atoms in nitrogen bases. ​ The nucleic acids DNA and RNA are unbranched polymers that consists of monomers called nucleotides that consists of a; ​ Pentose sugar ​ Nitrogen-containing base ​ Phosphate PHOSPHATE ​ Third component of nucleotide ​ Derived from phosphoric acid (H3PO4) ​ Loses two Hydrogen atoms BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) NUCLEOSIDES A Nucleosides; ​ Has a nitrogen base linked by a glycosidic bond to C1’ of a sugar (ribose or deoxyribose) ​ Is name by changing the nitrogen base ending to; -osine for purines and -idine for pyrimidines. NAMES OF NUCLEOSIDES AND NUCLEOTIDES FORMATION OF A NUCLEOTIDE ​ A nucleotide forms when the -OH on C5’ of a sugar bonds to phosphoric acid. PRIMARY STRUCTURE OF NUCLEIC ACIDS ​ Nucleic Acid ​ Are polymers, repeating units of nucleotides ​ Nucleotides linked through NUCLEOSIDES AND NUCLEOTIDES sugar-phosphate bonds WITH PURINES (SUFFIX-OSINE) ​ Alternating sugar and phosphate groups with base protruding RNA (RIBONUCLEIC ACID) ​ A nucleotide polymer in which each of the monomers contains ribose, a phosphate group, and one of the heterocyclic bases Adenine, Cytosine, Guanine or Uracil. ​ Backbone is Ribose sugar units and NUCLEOSIDES AND NUCLEOTIDES phosphate. WITH PYRIMIDINES (SUFFIX-ODINE BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) phosphate group on the 5’-carbon of the sugar of the next nucleotide. DNA (DEOXYRIBONUCLEIC ACID) STRUCTURE OF NUCLEIC ACIDS ​ A nucleotide polymer in which each A nucleic acid of the monomers contains ​ Has a free 5'-phosphate group at one deoxyribose, a phosphate group, and end and a free 3-OH group at the one of the heterocyclic bases other end. Adenine, Cytosine, Guanine or ​ Is read from the free 5’-end using the Thymine letters of the bases. ​ Backbone is phosphate and ​ This example reads -A-C-G-T-. deoxyribose sugar units. EXAMPLE OF RNA STRUCTURE PRIMARY STRUCTURE OF NUCLEIC The primary structure of RNA, ACIDS ​ Is a single strand of In the sequence in which nucleotides are nucleotides with bases linked together in a nucleic acid A,C,G, and U. ​ Nucleotides are joined by ​ Is linked by phosphodiester phosphodiester bonds. bonds between ribose and ​ The 3’-OH group of the sugar in one phosphate. nucleotide forms an ester bond to the BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) COMPLEMENTARY BASE PAIRS DNA contains complementary base pairs in which ​ Adenine is always linked by two hydrogen bonds with Thymine (A-T). ​ Guanine is always linked by three hydrogen with Cytosine (G-C). EXAMPLE OF DNA In DNA, ​ Nucleotides containing bases A,C,G and T are linked by ester bonds DOUBLE HELIX OF DNA between deoxyribose sugars and In the double helix of DNA phosphate groups. ​ Two standards of nucleotides form a double helix structure like a spiral stair case. ​ Hydrogen bonds link bases A-T and G-C. ​ The bases along one strand complement the bases along the other. DNA DOUBLE HELIX A double helix; ​ Is the structure of DNA. ​ Has two strands of nucleotides that wind together. ​ Is held in place by two hydrogen bonds that form between the base DNA REPLICATION pairs A-T. DNA molecules; ​ Is held in place by three hydrogen ​ Carriers of genetic information bonds that form between the base within a cell pairs G-C. ​ They are the molecules of heredity. BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) ​ Each time a cell divides, an exact nucleotides long) that provides the copy of the DNA of the parent cell is necessary 3’OH group for DNA needed for the new daughter cell. polymerase to start adding DNA ​ The process is called the DNA nucleotides. Replication. ​ DNA POLYMERASE - responsible for synthesizing new strands of DNA by adding nucleotides to an existing DNA template. ​ Is the Biochemical process by which DNA molecules produce exact duplicates of themselves. ​ OKAZAKI FRAGMENTS are short segments of DNA that are In DNA Replication synthesized on the lagging strand ​ 2 strands of the DNA double helix during DNA Replication. They are are pair of templates/patterns produced because DNA Polymerase ​ During replication strands separate can only synthesize DNA in the 5’ to and synthesis a new complementary 3’ direction, but the two strands of strand=daughter DNA molecules DNA are antiparallel (i.e they run with bases identical to those of in opposite directions.) This means parent double helix. that while one strand, called the ​ DNA HELICASE - unwinds the leading strand, is synthesized double strands like opening a zipper, continuously, the other strand, the breaking hydrogen bonds between lagging strand, is synthesized in a complementary bases and separating series of short segments. the two strands to create single ​ Ligase-join two DNA strands by stranded regions. forming a phosphodiester bond ​ REPLICATION FORK - a between the sugar-phosphate Y-shaped structure where the two backbone of adjacent nucleotides. strands of DNA separate. ​ PRIMASE - synthesizes a short RNA primer (typically about 10 BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) CHROMOSOMES ​ SMALL NUCLEAR RNA ​ Histones (interact with specific (snRNA) - facilitates the conversion proteins in the cell that form a of hnRNA to mRNA. structural unit that provide the most ​ MESSENGER RNA (mRNA) - stable arrangement for the long DNA carries genetic information from molecules. DNA to the ribosomes. (sites for ​ An individual DNA molecule bound protein synthesis). to a group of proteins. ​ TRANSFER RNA (tRNA) - brings ​ 46 chromosomes with 23 amino acids to the ribosome to make homologous pairs. the protein. ​ Homologous chromosomes are ​ RIBOSOMAL RNA (rRNA) - similar but not identical makes up ⅔ of ribosomes where ​ Identical twins=received DNA from protein synthesis takes place. their parents. PROTEIN SYNTHESIS ​ Skin, hair, enzymes, hormones, etc… ​ DNA establishes similarities between parents and offspring (hereditary characteristics) ​ 2 phases TRANSFER RNA (tRNA) Each tRNA ​ Has a triplet called an anticodon that complements a codon on mRNA. ​ Bonds to a specific amino acid at the acceptor stem. RNA ​ Transmits information from DNA to make proteins ​ Has several types ​ HETEROGENOUS NUCLEAR (hnRNA) - formed directly by DNA transcription PROTEIN SYNTHESIS BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) Protein synthesis involves; GENETIC CODE ​ TRANSCRIPTION - mRNA is The genetic code; formed from a gene on a DNA ​ Is a sequence of amino acids in a strand. mRNA that determines the amino ​ TRANSLATION - tRNA molecules acid order for the protein. bring amino acids to mRNA to build ​ Consists of sets of three bases protein. (triplet) along the mRNA called codons. ​ Has a different codon for all 20 amino acids needed to build a protein. ​ Contains certain codons that signal the “start” and “end” of a TRANSCRIPTION:SYNTHESIS OF polypeptide chain. mRNA During transcription; THE GENETIC CODE: mRNA Codons ​ A section of DNA containing the gene unwinds. ​ One strand of DNA bases is used as a template. ​ mRNA is synthesized using complementary base pairing with uracil (U) replacing thymine (T). ​ The newly formed mRNA moves out of the nucleus to ribosomes in the cytoplasm. CODONS AND AMINO ACIDS RNA POLYMERASE Determine the amino acids from the During transcription, following codons in a section of mRNA. ​ RNA POLYMERASE moves along -CCU-AGC-CGA-CUU the DNA template to synthesize the corresponding mRNA. According to the genetic code, the amino ​ The mRNA is released at the acids for these codons are termination point. CCU = Proline AGC = Serine GGA = Glycine CUU = Leucine This mRNA section codes for an amino acid sequence of -CCU-AGC-GGA-CUU -PRO-SER-GLY-LEU BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) NUCLEIC ACIDS TERMINATION In the termination step; ​ All the amino acids are linked ​ The ribosome reaches a “stop” codon: UGA,UAA, or UAG. ​ There is no tRNA with an anticodon for the “stop” codons ​ The polypeptide detaches from the ribosomes. INITIATION OF PROTEIN SYNTHESIS MUTATIONS For the initiation of protein synthesis A mutation can ​ A mRNA attaches to a ribosome ​ alter the nucleotide sequence in ​ The start codon (AUG) binds to a DNA. tRNA with methionine. ​ result from mutagens such as ​ The second codon attaches to a radiation and chemicals. tRNA with the next amino acids. ​ produce one or more incorrect ​ A peptide bond forms between the codons in mRNA. adjacent amino acids at the first and ​ produce a protein containing one or second codons. more incorrect amino acids. ​ produce defective proteins and TRANSLOCATION enzymes and cause genetic diseases. During translocation; ​ The first tRNA detaches from the EXAMPLES OF GENETIC DISEASES ribosome. ​ The ribosome shifts to the adjacent codon on the mRNA. ​ A new tRNA/amino acid attaches to the open binding site ​ A peptide bond forms and that tRNA detaches. ​ The ribosome shifts down the mRNA to read the next codon. EXAMPLES OF GENETIC DISEASES PEPTIDE FORMATION BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) NORMAL DNA SEQUENCE VIRUSES ​ The normal DNA sequence produces ​ are small particles of DNA or RNA a mRNA that provides instructions that require a host cell to replicate. for the correct series of amino acids ​ cause a viral infection when the in a protein. DNA or RNA enters a host cell. ​ are synthesized in the host cell from the viral RNA produced by viral DNA. MUTATION: SUBSTITUTION ​ A base in DNA changes a codon in the mRNA. ​ A different codon leads to the REVERSE TRANSCRIPTION placement of an incorrect amino acid In reverse transcription in the polypeptide. ​ a retrovirus, which contains viral RNA, but no viral DNA, enters a cell. ​ The viral RNA uses reverse transcriptase to produce a viral DNA strand. ​ The new DNA uses the nucleotides and enzymes in the host cell to synthesize new virus particles. ​ the viral DNA strand forms a FRAMESHIFT MUTATION complementary DNA strand. In frameshift mutation, ​ an extra base adds to or is deleted from the normal DNA sequence. ​ all the codons in mRNA and amino acids are incorrect from the base change. BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) HIV VIRUS AND AIDS prevents the synthesis of viral The HIV-1 VIRUS proteins. ​ is a retrovirus that infects T4 lymphocyte cells. ​ decreases the T4 level and the immune system fails to destroy harmful organisms. ​ causes pneumonia and skin cancer LIPIDS associated with AIDS. ​ Organic substances are relatively insoluble in water but soluble in organic solvents like chloroform ether benzene. TYPES OF LIPIDS 1.​ Fatty acids - basic building block of many lipids ​ Long hydrocarbon chains with a carboxyl group AIDS TREATMENT ​ Can be saturated (no double ​ One type of AIDS treatment prevents bonds between carbon atoms) reverse transcription of the viral ​ Can be unsaturated (one or DNA. more double bonds) ​ When altered nucleosides such as 2.​ Triglycerides (Fats and Oils) AZT and ddl are incorporated into ​ Formed by attaching three fatty acids viral DNA, the virus is unable to to a glycerol molecule replicate. ​ Molecules with 3 ester group ​ Energy storage molecules ​ TAGS are solid-fats 3.​ Phospholipids- Composed of two fatty acids, a glycerol backbone and a phosphate group ​ Major components of cell membrane, forming bilayers that act ​ Another type of AIDS treatment as a barrier to water-soluble involves protease inhibitors such as substances saquinavir, indinavir, and ritonavir. ​ HYDROPHILIC ​ Protease inhibitors modify the active (water-attracting) site of the protease enzyme, which ​ HYDROPHOBIC (water-repellent) BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) 4.​ Steroids - include molecules like Micelle - is a spherical structure that forms cholesterol, which is a vital by the aggregation of surfactant molecules. component of cell membranes. In water, the hydrophobic tails face inward ​ Four-ring structure and the hydrophilic heads face outward. ​ CHOLESTEROL: is important for maintaining membrane fluidity. ​ The lipid bilayer consists of two layers of phospholipids: Outer 5.​ Glycolipids - lipids with Layer (The hydrophilic), Inner carbohydrates group attached. Layer (The hydrophobic). ​ Play roles in cell recognition and communication and are found on the Functions surface of cells. 5.​ Absorption of vitamins (A, D, E , K) 6.​ Lipoproteins transporting lipids FUNCTIONS 1.​ Energy Storage Dehydration Reaction ​ Triglycerides store energy more -​ A dehydration reaction combines efficiently than carbohydrates two molecules into a single because they contain more molecule, with the loss of water. carbon-hydrogen bonds and thus yield more energy when broken 7.​ Fats serves as surfactants by down. reducing surface tension = lungs 2.​ Insulation and Protection - alveoli -​ Fatty tissue (adipose tissue) serves as 8.​ Improve taste and palatability = insulation, helping maintain body fat-soluble temperature and cushioning internal 9.​ Acts as electric insulators in the form organs. of Myelin Sheath = a fatty layer that 3.​ Signaling surrounds the axons of many -​ Some lipids such as steroid neurons. hormones and certain phospholipids, act as signaling Structural Property molecules regulating processes like -​ Very diverse growth, metabolism, and immune -​ Some (Pesters, Amides, Alcohols) responses. (Acyclic, Cyclic, Polycyclic) 4.​ Structural Support- Structural -​ All insoluble in water Support- proteins in cell membranes provide structural Fatty Acids- naturally occurring the support for lipids. monocarboxylic acid BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) ​ A type of organic acid that contains 1.​ CIS Configuration only one carboxyl group (-OOH) in 2.​ TRANS Configuration its structure. ​ Always contains an even number of Nonlinear chains - do not allow nucleolus Carbon atoms to pack closely ​ Have a carbon chain that -​ Few interactions between chains -​ Low melting points CLASSIFICATION OF FATTY ACIDS -​ Liquids at room temperature 1.​ Even chain fatty acid - a fatty acid Ex, Olive oil and canola fish that has an even number of carbon atoms. SUMMARY OF PROPERTIES 2.​ Odd chain fatty acid - fatty acids with an odd number of carbon atoms Property Saturated Unsaturated Length 1.​ Short chain fatty acid - 4 to 6 Structure No double One double carbons bonds bonds (beut (straight chains) 2.​ Medium - 8 to 10 carbons chains) 3.​ Long chain fatty acid - 12 to 26 carbons Physical Solid at Liquid at State room room Saturated Fatty Acids - single bond temperature temperature Monounsaturated Fatty Acid - double Melting High Low bonds point melting melting Polyunsaturated Fatty Acids - two or more point point double bonds Reactivity Less More reactive reactive, Properties of Saturated Fatty Acids prone to -​ Contains only single C-C bonds oxidation -​ Closely packed -​ Strong attractions between chains Health Can raise Can lower and high melting points effects LDL cholesterol -​ Solids at room temperature Ex: butter, land, coconut oil TRIACYLGLYCEROL (TAGS) Unsaturated Fatty Acids -​ Energy storage lipids -​ Contains one or more double C-C -​ Found in Adipocytes (Adipose Cells) bonds -​ Adipocytes are specialized for -​ Double bonds contains kink in the storing large quantities of acid triglycerides as a reserve of energy Fatty Chains BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) -​ Formed by esterification of glycerol COO-) between the glycerol and and 3 fatty acids fatty acid. -​ Much more efficient at storing 2.​ Mixed Triacylglycerol - triester energy than glycogen formed from the esterification of glycerol with more than 1 kind of fatty acid CLASSIFICATION based on its form 1.​ FATS - naturally occurring mixtures of triacylglycerol in which many different triacylglycerol molecules are present which are solid or semi- solid at room temperature (250C). -​ Butter, Lard, Coconut Oil (partially, due to high saturated fat CLASSIFICATION content). Based on Fatty acid molecules -​ Animal Fats: Most animal fats, such 1.​ Simple Triacylglycerol - triester as beef fat or pork fat, are formed from esterification of composed of solid triglycerides. glycerol with 3 identical fatty acids. -​ In esterification, a hydroxyl group 2.​ OILS - naturally occuring mixtures (-0H) from glycerol reacts with the of triacylglycerol in which many carboxyl group (-COOH) of a fatty different triacylglycerol molecules acid. This reaction eliminates a are present which are liquid at room molecule of water (H20) and forms temperature (250C) an ester bond (- BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) -​ Olive oil, Canola oil, Sunflower oil, three-carbon alcohol) with three fatty acids. Soybean oil. Each fatty acid forms an ester bond with one -​ Vegetable Oils: Most plant oils are of the hydroxyl groups (-0H) on the glycerol liquid at room temperature due to molecule, releasing water in the process. their unsaturated fatty acid content. FATS AND OILS 2.​ SAPONIFICATION - a chemical reaction that produces soap by combining fat and a chemical salt to create glycerol and soap. GOOD FAT VERSUS BAD FAT 3.​ HYDROGENATION - the chemical reaction in which a molecular hydrogen atom is added to OMEGA 3 VERSUS OMEGA 6 the organic compound for reduction or saturation in the presence of catalysts such as nickel, platinum, and palladium. CHEMICAL REACTIONS 1.​ Esterification / Dehydration Synthesis - is the chemical process by which triglycerides (also called triacylglycerols) are formed. This process involves the reaction of a glycerol molecule (a BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) 4.​ OXIDATION - chemical reaction -​ Ni or Pt are catalysts that occurs when a substance comes -​ C=C bonds - C-C bonds into contact with oxygen or another oxidizing substance -​ Converts cis double bonds to trans double bonds -​ Trans fatty acids have ill effects on blood chemistry similar to those of HYDROLYSIS Saturated Fatty Acids ​ Triacylglycerol is split by water and acid or enzyme catalyst) ​ Produce glycerol and 3 fatty acids ​ Reverse of Esterification OXIDATION -​ C-C double bonds present in SAPONIFICATION Unsaturated FA are subject to ​ Triacylglycerol undergoes hydrolysis oxidation with Oxygen (from air) with a strong base and is split into -​ Results to short chain aldehydes glycerol and salts of fatty acids -​ Further oxidation will form short ​ The salts of fatty acids are "soaps" chain carboxylic acids MEMBRANE LIPIDS -​ Lipids that are structural components HYDROGENATION of cell membrane. -​ Unsaturated compounds react with H2 BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) PHOSPHOLIPIDS -​ Lipids that stabilize and disperse -​ most abundant type of membrane water-insoluble material in aqueous lipid solution. -​ contains 1 or more fatty acids, a platform molecule, and a phosphate group with an alcohol MESSENGER LIPIDS -​ Regulatory lipids that act in the tissue where they are synthesized or at other locations after transport via the bloodstream SPHINGOGLYCOLIPIDS -​ Contains a fatty acid and a carbohydrates component attached to a sphingosine. SEX HORMONES Estrogen - female sex hormones; synthesized in the ovaries and adrenal cortex Androgens - male sex hormones; synthesized in the testis and adrenal cortex CHOLESTEROL Progestins - pregnancy hormones; -​ C27 steroid molecule synthesized in the ovaries and placenta. -​ Component of cell membranes and precursor for other steroid based ADRENOCORTICOID HORMONES lipids Mineralocorticoids - control the balance of Na+ and K+ ions in cells and body fluids Glucocorticoids - control glucose metabolism and counteract inflammation EICOSANOIDS Prostaglandin - involved in many regulatory functions in the body Thromboxane - promote the formation of EMULSIFICATION LIPIDS blood clots by promoting platelet aggregation BIOCHEMISTRY LEC (MIDTERMS) (Magbanua) Leukotriene - found in leukocytes and are associated with various inflammatory and allergic responses. BIOLOGICAL WAXES -​ Water insoluble, water repellant lipids with protective coating and lubricating functions