Basic Concepts Biochemistry-1 PDF

basic concepts introduction Biochemistry–1 (1427-101) 1.1 What is Life 1.2 Biomolecules Dr. Ahmed Almehdi 1.3 Functional Groups 1.3 Bioch...

basic concepts introduction Biochemistry–1 (1427-101) 1.1 What is Life 1.2 Biomolecules Dr. Ahmed Almehdi 1.3 Functional Groups 1.3 Biochemical Reactions 1.3 Biochemical Energy Biochemistry–1 Biochemistry, the molecular basis of life – McKee , 7th Ed (2020) , Oxford University Press  1.1 What is Life  the overwhelming diversity of the living world makes it difficult to answer this simple question  life has been described in operational terms, such as movement, Biochemistry , Dr. Ahmed Almehdi reproduction, adaptation, and responsiveness to external stimuli  the experimental approaches of Biochemistry, has revealed that all organisms obey the same chemical and physical universal rules  biochemical reactions are catalyzed by enzymes 1) Life: is complex and dynamic:  all organisms are composed of the same set of chemical elements: carbon, nitrogen, oxygen, hydrogen, sulfur, and phosphorus  Biomolecules are carbon-based organic molecules synthesized by living organisms  Cont. …1.1 What is Life 2) Life: is organized:  living organisms are organized systems made of cells ranging from smallest atom to organs, to Biochemistry , Dr. Ahmed Almehdi largest organism  Biomolecules are linked to form polymers called macromolecules, such as nucleic acids (formed from nucleotides), proteins (formed from amino acids), and polysaccharides (formed from monosaccharides) 3) Life: is cellular:  cells, the basic units of living organisms, (surrounded by a membrane that controls transport), differ widely in structure and function  Cont. …1.1 What is Life 4) Life: is information-based:  information is expressed in the form of coded messages Biochemistry , Dr. Ahmed Almehdi  genetic information are stored in DNA genes, that codes for amino acids sequence that forms specific proteins with correct 3D structure  Proteins perform their function by interacting with other molecules such as receptors in membranes. an example is binding of insulin (a protein) with its receptors is a signal that initiates the uptake of glucose 3) Life: adapts and evolves:  some DNA mutations may contribute to an increased ability of the organism to survive and adapt to a new environment and reproduce and adopt to better capacity to exploit energy sources  1.2 Biomolecules  biomolecules: are organic (carbon-based) molecules synthesized by living organisms, classified as: proteins, carbohydrates, lipids, and nucleic acids Biochemistry , Dr. Ahmed Almehdi  there are hundreds of biochemical reactions (divided into biochemical pathways) catalyzed by enzymes that maintain life  living organisms are composed of organic and inorganic molecules consisting of 6 principal elements: carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorous (P), and sulfur (S) and some important trace elements (Na+, K+, Mg2+, and Ca2+)  the remarkable structural complexity and diversity of organic molecules are made possible by the capacity of carbon atoms to form 4 strong covalent bonds to other carbon atoms or to atoms of other elements  biochemical properties are determined by their functional groups  Cont. …1.2 Biomolecules Biochemistry , Dr. Ahmed Almehdi Figure 1.2 Hydrocarbon Structural Formulas  Functional Groups of Organic Biomolecules:  Most organic molecules are derived from hydrocarbons  Hydrocarbons are carbon- and hydrogen-containing compounds that are hydrophobic (water-insoluble)  Their chemical properties are determined by functional groups  Cont. …1.2 Biomolecules  cells contain four families of small molecules: amino acids, sugars, fatty acids, and nucleotides that are used in the synthesis of larger molecules, many of which are polymers Biochemistry , Dr. Ahmed Almehdi  amino acids form polypeptides and proteins  glucose (simple sugar) forms polysaccharides  fatty acids form lipids (not a polymer)  nucleotides form nucleic acids (DNA and RNA)  most biomolecules contain more than one functional group:  simple sugar have several hydroxyl groups and an aldehyde or ketone carbonyl  amino acids (monomers of proteins) have both an amino group and a carboxyl group  Cont. …1.2 Functional Groups Anything 0H Hydrophilic eat p → Biochemistry , Dr. Ahmed Almehdi → piggett → moleculewithcarboxyl group's it qq.iq – ggyqfd.any → angijitonated andmolecule with amino isabase g roup Hedean Institution → → → coffin → Disk iE →  Cont. …1.1 Biomolecules Biochemistry , Dr. Ahmed Almehdi  small organic molecules are the monomers for larger molecules (Biomolecules)  major small molecules are: amino acids, sugars, fatty acids, and nucleotides  Cont. …1.1 Biomolecules  Examples of amino Acids:  Hundreds of naturally occurring amino acids, but only twenty amino acids occur in proteins Biochemistry , Dr. Ahmed Almehdi  Classified as: , , or  amino acids according to amino group location  The most common type are -amino acids -amino acid -amino acid -amino acid  Cont. …1.1 Biomolecules  Sugars and Carbohydrates:  all have alcohol (–OH) and carbonyl (–C=O) functional groups  Two types of carbohydrates: aldoses and ketoses Biochemistry , Dr. Ahmed Almehdi  Range from monosaccharides to polysaccharides Figure 1.8 Some Biologically Important Monosaccharides  Cont. …1.1 Biomolecules  Fatty Acids:  There are two types of fatty acids: saturated and unsaturated  Very few fatty acids occur independently; most are components Biochemistry , Dr. Ahmed Almehdi of lipids (triacylglycerol) Figure 1.9 Fatty Acid Structure  Cont. …1.1 Biomolecules  Nucleotides and Nucleic Acids:  Nucleotides are composed of a five-carbon sugar, nitrogenous base, and one or more phosphate groups Biochemistry , Dr. Ahmed Almehdi  Two classes of bases: purine and pyrimidine  Nucleotides are monomers of DNA and RNA Figure 1.11 Nucleotide Structure  Cont. …1.1 Biomolecules  Nitrogen bases of Nucleotides : Biochemistry , Dr. Ahmed Almehdi Figure 1.12 The Nitrogenous Bases: Purines Figure 1.14 The Nitrogenous Bases: Pyrimidines  Cont. …1.1 Biomolecules  DNA  DNA (deoxyribonucleic acid) encodes the genetic information of an organism Biochemistry , Dr. Ahmed Almehdi  DNA structure: two antiparallel polynucleotide strands forming a right-handed double helix, held together by hydrogen bonds  An organism’s entire set of DNA sequences is called its genome  RNA  RNA is a single-stranded polynucleotide with ribose instead of deoxyribose  There are three types of RNA involved in protein synthesis: mRNA, rRNA and tRNA  Cont. …1.1 Biomolecules Biochemistry , Dr. Ahmed Almehdi Figure 1.13 DNA  1.3 Biochemical Reactions  living organisms have remarkable properties  living organisms are self-organizing, and self-maintaining (autopoiesis) Biochemistry , Dr. Ahmed Almehdi  life emerges from a self-regulating of thousands of biochemical reactions  the functional properties of thousands of enzymes make possible the process of metabolism  the main functions of metabolism are: 1) acquisition and utilization of energy 2) synthesis of biomolecules (proteins, carbohydrates, lipids, and nucleic acids) needed for cell structure and function 3) growth and development 4) removal of waste products  Cont. …1.3 Biochemical Reactions  There are several general types of Biochemical reactions occur in living organisms including: 1) Hydrolysis Reactions Biochemistry , Dr. Ahmed Almehdi (nucleophilic substitution ):  nucleophilic group (electron rich, A:) binds and replaces the leaving group (X:) A: + B–X  A–B + X: Figure 1.15 A Hydrolysis Reaction  Cont. …1.3 Biochemical Reactions 2) Elimination Reaction:  a double bond formation reaction when atoms in a molecule are Biochemistry , Dr. Ahmed Almehdi removed: Figure 1.17 An Elimination Reaction  Cont. …1.3 Biochemical Reactions 3) Addition reaction:  two molecules combine to form a single product Biochemistry , Dr. Ahmed Almehdi Figure 1.18 Addition Reaction 4) Isomerization reaction: Figure 1.19 Isomerization  intramolecular shifts Reaction or arrangement of atoms or groups  Cont. …1.3 Biochemical Reactions 5) oxidation-reduction reactions:  the electron donor is the reducing agent and the electron acceptor is the oxidizing agent Biochemistry , Dr. Ahmed Almehdi  when reducing agents donate electrons they become oxidized and when oxidizing agents accept electrons they become reduced Oxidation R–SH + HS–R ←→ R-S–S-R + H2 Reduction Ethyl Alcohol Acetic Acid  Cont. …1.3 Biochemical Energy  Energy  Energy is defined as the capacity to do work  Cells generate most of their energy with oxidation/reduction Biochemistry , Dr. Ahmed Almehdi (Redox) reactions  The energy captured when electrons are transferred from an oxidizable molecule to an electron-deficient molecule is used to synthesize ATP (energy molecule)  Acquiring energy from the environment happens in two ways:    Cont. …1.3 Biochemical Metabolism  Metabolism  Metabolic pathways come in two types: anabolic and catabolic Biochemistry , Dr. Ahmed Almehdi  Anabolic: large complex molecules synthesized from smaller precursors  Catabolic: large complex molecules degraded into smaller, simpler products  Energy transfer pathways capture energy and transform it into a usable form Figure 1.20 Biochemical Pathway  Cont. …1.3 Biochemical Reactions  metabolism are of two types: anabolism and catabolism  anabolism: large complex molecules synthesized from smaller precursor  catabolism: large complex molecules degraded into simpler products Biochemistry , Dr. Ahmed Almehdi  the two main energy molecules are: NADH and ATP (will be explained in Chapter-4 , Bioenergetics) NAD+ NADH Basic Concepts