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Biochem-midterm - A biochemistry reviewer
BIOCHEMISTRY (CHM3)
Our Lady of Fatima University
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LESSON 1:
LIPIDS
4 MAJOR CLASSES OF BIOORGANIC
SUBSTANCES
- Carbohydrates
- Lipids
- Protein
- Nucleic Acid
Lipids - known as fats provide a major way of storing chemical energy and carbon atoms in the body.
- A lipid is an organic compound found in living organisms that is insoluble (or only sparingly soluble) in water but soluble in nonpolar organic solvents.
BASIC COMPONENTS OF CELL MEMBRANE
- Phospholipids
- Glycolipids
- Cholesterol
5 CATEGORIES ON THE BASIS OF LIPID FUNCTION
- Energy - Storage Lipids (Triacylglycerols)
- Membrane Lipids (Phospholipids, Sphingogllycolipids, Cholesterol)
- Emulsification Lipids (Bile Acids)
- Messenger Lipids (Steroid Hormones and Eicosanoids)
- Protective- Coating Lipids (Biological Waxes)
Fatty Acids - is a naturally occurring monocarboxylic acid.
TYPES OF FATTY ACIDS
LONG CHAIN FATTY ACIDS - C12 TO C26.
MEDIUM CHAIN FATTY ACIDS - C8 TO C10.
SHORT CHAIN FATTY ACIDS - C4 TO C6.
SATURATED FATTY ACIDS
- Carbon-carbon bonds are SINGLE BONDS. MONOUNSATURATED FATTY ACIDS
- One carbon-carbon double bond is present.
- Double bond is nearly always cis.
POLYUNSATURATED FATTY ACIDS - Two or more carbon-carbon double bonds are present. - Up to 6 double bonds are found in biochemically important PUFAs.
PHYSICAL PROPERTIES OF FATTY
ACIDS
Water solubility for fatty acids is a direct function of carbon chain length; solubility decreases as carbon chain length increases.
Short-chain fatty acids have a slight solubility in water.
Long-chain fatty acids are essentially insoluble in water.
Melting points for fatty acids are strongly influenced by both carbon chain length and degree of unsaturation (number of double bonds present). As carbon chain length increases, melting point increases.
ENERGY STORAGE IN LIPIDS: TRIACYLGLYCEROLS
Lipids known as triacylglycerols also function within the body as energy-storage materials.
Adipose tissue containing these cells is found in various parts of the body: under the skin, in the abdominal cavity, in the mammary glands, and around various organs.
Triacylglycerols are much more efficient at storing energy than glycogen because large quantities of them can be packed into a very small volume.
Fatty acids are the carboxylic acids involved in triacylglycerol formation.
TRIACYLGLYCEROL/TRIGLYCERIDE - a triacylglycerol/ triglyceride is a lipid formed by esterification of three fatty acids to a glycerol molecule.
- An acyl group,—OH group is removed from the carboxyl carbon atom.
FATS - are naturally occurring complex mixtures of triacylglycerol molecules in which many different kinds of triacylglycerol molecules are present.
A fat is a triacylglycerol mixture that is a solid or a semi-solid at room temperature (25 ̊C).
Generally, fats are obtained from animal sources.
OILS - Oils are also naturally occurring complex mixtures of triacylglycerol molecules in which there are many different kinds of triacylglycerol molecules present.
An oil is a triacylglycerol mixture that is a liquid at room temperature (25 ̊C).
Generally, oils are obtained from plant sources.
Fats are composed largely of triacylglycerols in which saturated fatty
acids predominate, although some unsaturated fatty acids are present.
Oils contain triacylglycerols with larger amounts of mono- and polyunsaturated fatty acids than those in fats.
- Pure fats and pure oils are colorless, odorless, and tasteless.
Current dietary fat recommendations are that people limit their total fat intake to 30% of total calories—with up to 15% coming from monounsaturated fat, up to 10% from polyunsaturated fat, and less than 10% from saturated fats.
BAD FATS
- Saturated fats.
GOOD FATS - Monounsaturated fats.
POLYUNSATURATED FATS - Can be both bad and good fats.
Studies indicate that saturated fat can increase heart disease risk.
Monounsaturated fat can decrease both heart disease and breast cancer risk,
Polyunsaturated fat can reduce heart disease risk but promote the risk of certain types of cancers.
OMEGA FATTY ACIDS
OMEGA 3 - Are essential fats that you must get from your diet. - They have important benefits for your heart, brain, and metabolism.
OMEGA 6 - Are essential fats that provide energy for the body. However, people should eat more omega 3 than omega 6.
OMEGA 9 - Are nonessential fats that the body can produce some
three ester linkages in triacylglycerols.
SPHINGOPHOSPHOLIPIDS - Sphingosine based. - have structures based on the 18-carbon monounsaturated aminodialcohol sphingosine. - is a lipid that contains one fatty acid and one phosphate group attached to a sphingosine molecule and an alcohol attached to the phosphate group
MEMBRANE LIPIDS: SPHINGOGLYCOLIPIDS - A sphingoglycolipid is a lipid that contains both a fatty acid and a carbohydrate component attached to a sphingosine molecule.
MEMBRANE LIPIDS: CHOLESTEROL
is a specific compound rather than a family of compounds like the phospholipids and sphingoglycolipids.
Cholesterol is a steroid.
Cholesterol is a C27 steroid molecule that is a component of cell membranes and a precursor for other steroid-based lipids.
The -ol ending in the name cholesterol conveys the information that an alcohol functional group is present in this molecule; it is located on carbon 3 of the steroid nucleus.
STEROID - is a lipid whose structure is based on a fused ring system that involves three 6- membered rings and one 5-membered ring.
CELL MEMBRANE - is a lipid-based structure that separates a cell’s aqueous-based interior from the aqueous environment surrounding the cell.
LIPID BILAYER - is a two-layer-thick structure of phospholipids and glycolipids in which the nonpolar tails of the lipids
are in the middle of the structure and the polar heads are on the outside surfaces of the structure. TRANSPORT ACROSS CELL MEMBRANE
PASSIVE TRANSPORT - is the transport process in which a substance moves across a cell membrane by diffusion from a region of higher concentration to a region of lower concentration without the expenditure of any cellular energy.
FACILITATED TRANSPORT - is the transport process in which a substance moves across a cell membrane, with the aid of membrane proteins, from a region of higher concentration to a region of lower concentration without the expenditure of cellular energy.
ACTIVE TRANSPORT - is the transport process in which a substance moves across a cell membrane, with the aid of membrane proteins, against a concentration gradient with the expenditure of cellular energy.
EMULSIFICATION LIPIDS: BILE ACIDS
EMULSIFIER - is a substance that can disperse and stabilize water-insoluble substances as colloidal particles in an aqueous solution.
BILE ACID - is a cholesterol derivative that functions as a lipid emulsifying agent in the aqueous environment of the digestive tract.
Bile acids differ structurally from cholesterol in three respects:
- They are tri- or dihydroxy cholesterol derivatives.
- The carbon 17 side chain of cholesterol has been oxidized to a carboxylic acid.
- The oxidized acid side chain is bonded to an amino acid (either glycine or taurine) through an amide linkage.
MESSENGER LIPIDS: STEROID
HORMONE
HORMONE
is a biochemical substance, produced by a ductless gland, that has a messenger function.
Hormones serve as a means of communication between various tissues.
STEROID HORMONE - is a hormone that is a cholesterol derivative.
2 MAJOR CLASSES OF STEROID HORMONE
SEX HORMONES - which control reproduction and secondary sex characteristics.
3 MAJOR GROUPS
- Estrogens—the female sex hormones
are synthesized in the ovaries and adrenal cortex and are responsible for the development of female secondary sex characteristics at the onset of puberty and for regulation of the menstrual cycle.
They also stimulate the development of the mammary glands during pregnancy and induce estrus (heat) in animals
- Androgens—the male sex hormones
are synthesized in the testes and adrenal cortex and promote the development of secondary male characteristics.
They also promote muscle growth.
- Progestins—the pregnancy hormones
are synthesized in the ovaries and the placenta and prepare the lining of the uterus for implantation of the fertilized ovum.
They also suppress ovulation
ADRENOCORTICOID HORMONE
which regulate numerous biochemical processes in the body.
Produced by the adrenal glands, small organs located on top of each kidney
2 TYPES OF ADRENOCORTICOID
HORMONES
MINERALOCORTICOIDS
- control the balance of Na+ and K- ions in cells and body fluids.
GLUCOCORTICOIDS - control glucose metabolism and counteract inflammation.
MESSENGER LIPIDS: EICOSANOIDS
EICOSANOID
- is an oxygenated C20 fatty acid derivative that functions as a messenger lipid.
The physiological effects of eicosanoids include mediation of:
- The inflammatory response, a normal response to tissue damage
- The production of pain and fever
- The regulation of blood pressure
- The induction of blood clotting
- The control of reproductive functions, such as induction of labor
- The regulation of the sleep/wake cycle
PROSTAGLANDIN - is a messenger lipid that is a C20- fatty-acid derivative that contains a cyclopentane ring and oxygen-containing functional groups.
ASPIRIN - reduces inflammation and fever because it inactivates the enzyme needed for prostaglandin synthesis.
THROMBOXANE - is a messenger lipid that is a C20-fatty-acid derivative that
a-AMINO ACID - amino acids found in proteins.
A standard amino acid is one of the 20 a-amino acids normally found in proteins. 4 CATEGORIES OF AMINO ACIDS
- Nonpolar Amino Acids
amino acid that contains one amino group, one carboxyl group, and a nonpolar side chain.
They are generally found in the interior of proteins, where there is limited contact with water.
9 NONPOLAR AMINO ACID
- Glycine (Gly, G)
- Alanine (Ala, A)
- Valine (Val, V)
- Leucine (Leu, L)
- Isoleucine (Ile, I)
- Proline (Pro, P)
- Phenylalanine (Phe, F)
- Methionine (Met, M)
- Tryptophan (Trp, W)
- is a borderline member of this group because water can weakly interact through hydrogen bonding with the NH ring location on tryptophan’s side-chain ring structure.
- Polar Neutral Amino Acids
is an amino acid that contains one amino group, one carboxyl group, and a side chain that is polar but neutral.
In solution at physiological pH, the side chain of a polar neutral amino acid is neither acidic nor basic.
6 POLAR NEUTRAL AMINO ACID
Serine (Ser, S)
Cysteine (Cys, C)
Threonine (Thr, T)
Asparagine (Asn, N)
Glutamine (Gln, G)
Tyrosine (Tyr, Y)
Polar Acidic Amino Acids
is an amino acid that contains one amino group and two carboxyl groups, the second carboxyl group being part of the side chain.
the side chain of a polar acidic amino acid bears a negative charge;
2 POLAR ACIDIC AMINO ACID
Aspartic Acid (Asp, D)
Glutamic Acid (Glu, E)
Polar Basic Amino Acids
is an amino acid that contains two amino groups and one carboxyl group, the second amino group being part of the side chain.
The side chain of a polar basic amino acid bears a positive charge; the nitrogen atom of the amino group has accepted a proton.
3 POLAR BASIC AMINO ACID
- Lysine (Lys, K)
- Arginine (Arg, R)
- Histidine (His, H)
ACID BASE PROPERTIES OF AMINO
ACIDS
- amino acids are white crystalline solids with relatively high decomposition points. (Most amino acids decompose before they melt.)
ZWITTERION - is a molecule that has a positive charge on one atom and a negative charge on another atom, but which has no net charge.
CYSTEINE: A CHEMICALLY UNIQUE AMINO ACID
is the only standard amino acid that has a side chain that contains a sulfhydryl group.
In cystine, the two cysteine residues are linked via a covalent disulfide bond.
pH VALUES
+1 = if the bases are 0- +0 = if the base is 7 which is neutral -1 = if the bases are 8-
PEPTIDES - is an unbranched chain of amino acids, each joined to the next by a peptide bond.
DIPEPTIDE - A compound containing two amino acids.
TRIPEPTIDE - three amino acids joined together in a chain.
OLIGOPEPTIDE - refer to peptides with 10 to 20 amino acid residues.
POLYPEPTIDE - is used to refer to longer peptides - is a long unbranched chain of amino acids, each joined to the next by a peptide bond.
PEPTIDE BOND - The bonds that link amino acids together in a peptide chain. - is a covalent bond between the carboxyl group of one amino acid
and the amino group of another amino acid.
AMINO ACID RESIDUE
- is the portion of an amino acid structure that remains, after the release of H2O.
PEPTIDE NOMENCLATURE
▪ IUPAC rules for naming small peptides are as follows:
Rule 1: The C-terminal amino acid residue (located at the far right of the structure) keeps its full amino acid name.
Rule 2: All of the other amino acid residues have names that end in -yl. The -yl suffix replaces the -ine or -ic acid ending of the amino acid name, except for tryptophan (tryptophyl), cysteine (cysteinyl), glutamine (glutaminyl), and asparagine (asparaginyl).
Rule 3: The amino acid naming sequence begins at the N-terminal amino acid residue.
EXAMPLE: Glu-Ser-Ala
- Glutamyl - Seryl - Alanine (Glutamylserylalanine)
ISOMERIC PEPTIDES - Peptides that contain the same amino acids but in different order are different molecules (constitutional isomers) with different properties.
BIOCHEMICALLY IMPORTANT PEPTIDES
Small Peptide Hormones - The two best-known peptide hormones, both produced by the pituitary gland, are oxytocin and vasopressin.
Small Peptide Neurotransmitters - Enkephalins are pentapeptide neurotransmitters produced by the brain itself that bind at receptor sites in the brain to reduce pain.
2 BEST KNOWN ENKEPHALINS
- Met Enkephalin
- Leu - enkephalin
the interactions between amino acid side chains (R groups) that are widely separated from each other within a peptide chain.
PROTEIN CLASSIFICATION BASED ON SHAPE
FIBROUS PROTEIN - is a protein whose molecules have an elongated shape with one dimension much longer than the others.
- Fibrous proteins tend to have simple, regular, linear structures.
GLOBULAR PROTEIN - is a protein whose molecules have peptide chains that are folded into spherical or globular shapes.
- globular proteins are water-soluble substances
MEMBRANE PROTEIN - is a protein that is found associated with a membrane system of a cell.
- with most of the hydrophobic amino acid side chains oriented outward
PROTEIN CLASSIFICATION BASED ON
FUNCTION
CATALYTIC PROTEINS
- Proteins with the role of biochemical catalyst are called enzymes. Enzymes participate in almost all of the metabolic reactions that occur in cells.
DEFENSE PROTEINS - immunoglobulins are central to the functioning of the body’s immune system.
- They bind to foreign substances, such as bacteria and viruses, to help
combat invasion of the body by foreign particles
TRANSPORT PROTEINS - These proteins bind to particular small biomolecules and transport them to other locations in the body and then release the small molecules as needed at the destination location.
MESSENGER PROTEINS - These proteins transmit signals to coordinate biochemical processes between different cells, tissues, and organs.
CONTRACTILE PROTEINS - These proteins are necessary for all forms of movement. Muscles are composed of filament-like contractile proteins that, in response to nerve stimuli.
STRUCTURAL PROTEIN - proteins confer stiffness and rigidity to otherwise fluid like biochemical systems.
COLLAGEN - is a component of cartilage and a keratin gives mechanical strength as well as protective covering to hair, fingernails, feathers, hooves, and some animal shells.
TRANSMEMBRANE PROTEINS - These proteins, which span a cell membrane, help control the movement of small molecules and ions through the cell membrane.
STORAGE PROTEIN -. These proteins bind (and store) small molecules for future use.
FERRITIN - an iron-storage protein, which saves the iron for use in the biosynthesis of new hemoglobin molecules.
MYOGLOBIN - is an oxygen storage protein present in muscle.
REGULATORY PROTEIN
- These proteins are often found “embedded” in the exterior surface of cell membranes.
NUTRIENT PROTEINS
- These proteins are particularly important in the early stages of life, from embryo to infant.
PROTEIN DENATURATION - is the partial or complete disorganization of a protein’s characteristic three dimensional shape as a result of disruption of its secondary, tertiary, and quaternary structural interactions.
LESSON 3:
NUCLEIC ACID
The Swiss physiologist Friedrich Miescher (1844–1895) discovered nucleic acids in 1869 while studying the nuclei of white blood cells.
1865 - Mendel - Documents patterns of heredity in pea plants.
1869 - Miescher - First identifies DNA (nuclein)
1902 - Sutton & Boveri - Propose chromosome theory of heredity.
1915 - Morgan - And his fly room colleagues confirm the chromosome theory of heredity.
1927 - Muller - Shows that X-rays induce mutations.
1928 - Griffith - Transformation experiments transform non-pathogenic bacteria strains to pathogenic.
1930 - Hammerling - Shows that hereditary information is contained in the nuclei of eukaryotic cells.
1931 - McClintock - Demonstrates genetic recombination in corn.
1941 - Beadle & Tatum - Describe the one gene one enzyme hypothesis.
1944 - Avery McLeod & McCarty - Shows that DNA is the transforming principle responsible for heredity.
1950 - Chargaff - Discovers that A=T and C=G.
1952 - Hershey & Chase - Use radioactive labeling to prove that DNA is responsible for heredity.
1953 - Watson & Crick - Propose the double helix structure of DNA.
1961 - Jacob & Monod - Propose the existence of mRNA.
1990s - Genome - Sequencing project begins.
TYPES OF NUCLEIC ACID
- DNA (Deoxyribonucleic Acid)
Its primary function is the storage and transfer of genetic information.
In addition, DNA is passed from existing cells to new cells during cell division.
- RNA (Ribonucleic Acid)
- occurs in all parts of a cell. It functions primarily in synthesis of proteins, the molecules that carry out essential cellular functions.
NUCLEOTIDES - is a three-subunit molecule in which a pentose sugar is bonded to both a phosphate group and a nitrogen containing heterocyclic base.
PENTOSE SUGAR - The sugar unit of a nucleotide is either the pentose ribose or the pentose 2’-deoxyribose
- is RNA that facilitates the conversion of heterogeneous nuclear RNA to messenger RNA. It contains from 100 to 200 nucleotides.
RIBOSOMAL RNA (rRNA) - is RNA that combines with specific proteins to form ribosomes, the physical sites for protein synthesis. Ribosomes have molecular masses on the order of 3 million amu. The rRNA present in ribosomes has no informational function.
TRANSFER RNA (tRNA) - is RNA that delivers amino acids to the sites for protein synthesis. Transfer RNAs are the smallest of the RNAs, possessing only 75– nucleotide units.
POST TRANSCRIPTION PROCESSING: FORMATION OF mRNA
EXON - Is a gene segment that conveys genetic information. - Are DNA segments that help express a genetic message.
INTRON - Is a gene segment that does not convey genetic information. - Are DNA segments that interrupts a genetic passage.
SPLICING - Is the process of removing introns from an hnRNA molecule and joining the remaining exams together to form an mRNA molecule.
TRANSCRIPTOME - Is all of the mRNA molecules that can be generated from the genetic material in a genome.
CODON - Is a three nucleotide sequence in an mRNA molecule that codes for a specific amino acid.
GENETIC CODE - Is the assignment of the 64 mRNA codons to specific amino acids.
mRNA codon to SEQUENCE of Amino Acid translation.
5’ GCC - AUG - GUA - AAA - UGC - GAC - CCA 3’
Ala Met Val Lys Cys Asp Pro
Splicing Process
hnRNA 3’UAA-GCA-ACA-AAA-GGG- UCA-CGG 5’ (tanggalin yung wala sa UC)
mRNA 3’ UAA-ACA-AAA-CGG 5’
Structure of mRNA obtained from DNA template strand
mRNA 3’ ACG - AGC - CCU - CUU 5’
DNA 5’ UUC - UCC - CGA - GCA 3’ Phe Ser Arg Ala
ANTICODON
- Is a three nucleotide sequence on a tRNA molecule that is complementary to a codon on an mRNA molecule.
Codon = DNA Anticodon = RNA
TRANSLATION - Is the process by which mRNA codons are deciphered and a particular protein molecule is synthesized.
RIBOSOME - Is an rRNA protein complex that serves as the site for the translation phase of protein synthesis.
VIRUS
- Is a small particle that contains DNA or RNA surrounded by a coat of protein and that cannot reproduce without the aid of a host cell.
RESTRICTION ENZYME - is an enzyme that recognizes specific base sequences in DNA and cleaves the DNA in a predictable manner at these sequences. The discovery of restriction enzymes made genetic engineering possible.
TRANSFORMATION - is the process of incorporating recombinant DNA into a host cell.
CLONES - are cells with identical DNA that have descended from a single cell.
LESSON 4-5 :
ENZYMES
AND VITAMINS
ENZYMES
govern all chemical reactions in living organisms.
An enzyme is an organic compound that acts as a catalyst for a biochemical reaction.
VITAMINS - which are necessary components of a healthful diet, play important roles in cellular metabolism.
GENERAL CHARACTERISTICS OF
ENZYMES
As catalysts, enzymes are not consumed during the reaction but merely help the reaction occur more rapidly.
The word enzyme comes from the Greek words en, which means “in,” and zyme, which means “yeast.”
Enzymes undergo all the reactions of proteins, including denaturation.
Even vigorous shaking of an enzyme solution can destroy enzyme activity.
Enzymes differ from non biochemical (laboratory) catalysts not only in size, being much larger, but also in that their activity is usually regulated by other substances present in the cell in which they are found.
In some cases, if a certain chemical is needed in the cell, the enzyme responsible for its production is activated by other cellular components. When a sufficient quantity has been produced, the enzyme is then deactivated.
ENZYME STRUCTURE
SIMPLE ENZYMES - is an enzyme composed only of protein (amino acid chains).
CONJUGATED ENZYME - is an enzyme that has a non protein part in addition to a protein part. By itself, neither the protein part nor the nonprotein portion of a conjugated enzyme has catalytic properties.
APOENZYME - is the protein part of a conjugated enzyme
HOLOENZYME - is the biochemically active conjugated enzyme produced from an apoenzyme and a cofactor.
COENZYME - is a small organic molecule that serves as a cofactor in a conjugated enzyme.
NOMENCLATURE OF ENZYMES 1. The suffix -ase identifies a substance as an enzyme. Thus urease, sucrase, and lipase are all enzyme designations. The suffix -in is still found in the names of some of the first enzymes studied, many of which are digestive enzymes. Such names include trypsin, chymotrypsin, and pepsin.
ANTIBIOTICS THAT INHIBIT ENZYME
ACTIVITY
ANTIBIOTIC
An antibiotic is a substance that kills bacteria or inhibits their growth.
Antibiotics usually inhibit specific enzymes essential to the life processes of bacteria.
2 FAMILIES OF ANTIBIOTICS
- Sulfa Drugs (Sulfanilamide)
- The 1932 discovery of the antibacterial activity of the compound sulfanilamide by the German bacteriologist Gerhard Domagk (1895–1964).
- Penicillin
one of the most widely used antibiotics, was accidentally discovered by Alexander Fleming in 1928 while he was working with cultures of an infectious staphylococcus bacterium.
Penicillin inhibits transpeptidase, an enzyme that catalyzes the formation of peptide cross links between polysaccharide strands in bacterial cell walls
- Cipro (ciprofloxacin hydrochloride)
is an effective agent against bacterial infections in many different parts of the body. It is effective against skin and bone infections as well as against infections involving the urinary, gastrointestinal, and respiratory systems.
is believed to attack the enzyme DNA gyrase, which controls how DNA in a bacterial chromosome coils into its tertiary structure.
MEDICAL USES OF ENZYMES
- Enzymes can be used to diagnose certain diseases.
- Enzymes can also be used in the treatment of diseases.
- Enzymes are in clinical laboratory chemical analysis.
GENERAL CHARACTERISTICS OF
VITAMINS
A vitamin is an organic compound, essential in small amounts for the proper functioning of the human body, that must be obtained from dietary sources because the body cannot synthesize it.
Vitamins differ from the major classes of foods (carbohydrates, lipids, and proteins) in the amount required; for vitamins it is microgram or milligram quantities per day compared with 50– 200 grams per day for the major food categories.
A well-balanced diet usually meets all the body’s vitamin requirements. However, supplemental vitamins are often required for women during pregnancy and for people recovering from certain illnesses
Biochem-midterm - A biochemistry reviewer
Course: BIOCHEMISTRY (CHM3)
University: Our Lady of Fatima University
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