Biochemistry Lecture - Lesson 1, August 2024 PDF

BIOCHEMISTRY LECTURE jan christian de leon|BSN - 1ST YEAR Lesson 1| august 28, 2024 POLAR BIOCHEMISTRY...

BIOCHEMISTRY LECTURE jan christian de leon|BSN - 1ST YEAR Lesson 1| august 28, 2024 POLAR BIOCHEMISTRY Hydrophilic head- attracts water study of chemical substances and vital processes occurring in living organisms Hydrophobic tail (non polar tail) - repels water study of chemistry behind biological MOVEMENT ACROSS PLASMA MEMBRANE processes and the synthesis of biologically A few molecules move freely active molecules. - Water, Carbon dioxide, Ammonia, Oxygen Carrier proteins transport some molecules Significance and Importance of biochemistry in nursing - Proteins embedded in lipid bilayer review of the application of biochemistry in - Fluid mosaic model – describes fluid nature of a nursing needs to mention many therapeutic lipid bilayer with proteins agents whose existence was first CYTOPLASM demonstrated in lab experiments (e.g hormone insulin , all the vitamins and All organelles reside in the cytoplasm. many other products of therapeutic components of cytoplasm significance.) Interconnected filaments & fibers If an infant is always vomiting after giving milk, Fluid = cytosol she or he probably has galactose intolerance. storage substances If an infant is born with jaundice, her or his liver MITOCHONDRIA ( THE POWERHOUSE OF THE CELL ) is not fully functional. Complete the breakdown of glucose, when the color of an infant's urine turns dark, producing ATP (Adenosine Triphosphate) probably he/she suffers from an amino acid (ATP = energy) metabolic disorder. Involved in cellular respiration GOLGI COMPLEX cell The protein packaging and transport center of the cell. the basic unit of life Has incoming and outgoing vesicles. Principles of Cell Theory RIBOSOMES Smallest living unit of structure and function of Synthesizes proteins. all organisms is the cell Present in the cytoplasm. All living things are made of cells Present with Rough ER. All cells arise from pre-existing cells No membrane present. Made of RNA and protein cell types SMOOTH ENDOPLASMIC RETICULUM PROKARYOTIC CELL ( UNICELLULAR ) Transports materials throughout the cell. Digests lipids. First cell type on earth Produces proteins. Cell type of Bacteria and Archaea Involved in producing phospholipids. Archaea - single cell organism No membrane bound nucleus ROUGH ENDOPLASMIC RETICULUM Pseudo means “false or fake” Covered with ribosomes. Nucleoid = region of DNA concentration Produces proteins. Can not live without host Site of the synthesis of lysosomal enzymes and Organelles not bound by membranes proteins for extracellular use Example : Viruses Russell bodies of the plasma cells EUKARYOTIC CELL ( MULTICELLULAR ) LYSOSOME Nucleus bound by membrane Breaks down materials for digestion. Include fungi, protists, plant, and animal cells Contains special enzymes for digestion in the Possess many organelles cell. Example : protozoan, humans Hydrolytic Enzymes digest the tissue NUCLEUS cell organelles The control center of the cell. PLASMA MEMBRANE ( CELL MEMBRANE ) It contains the DNA code for the cell coiled into Contains cell contents chromosomes. Double layer of phospholipids & proteins Protection from leakage biomolecules phospholipids = most abundant Just like cells are building blocks of tissues Glycoprotein = antigens (A,B, AB,O) likewise molecules are building blocks of cells. Animal and plant cells contain approximately A. ACTIVE TRANSPORT (NEEDS ATP) 10, 000 kinds of molecules (bio-molecules) movement of molecules from high to low Water constitutes 50-95% of cells content by concentration weight. B. PASSIVE TRANSPORT (NO ATP NEEDED) Ions like Na+, K+ and Ca+ may account for another 1% movement of molecules from low to high Almost all other kinds of bio-molecules are concentration organic (C, H, N, O, P, S) 1.OSMOSIS Infinite variety of molecules contain C. 2. DIFFUSION Most bio-molecules considered to be derived from hydrocarbons. PHOSPOLIPIDS The chemical properties of organic bio- Interacts with water molecules are determined by their functional groups. Most bio-molecules have more than one.  BIOCHEMISTRY LECTURE jan christian de leon|BSN - 1ST YEAR Lesson 1| august 28, 2024 ANABOLISM Major Classes of small Bio-molecules energy requiring biosynthetic pathways AMINO ACIDS CATABOLISM Building blocks of proteins. degradation of fuel molecules and the Contains amino group and production of energy for cellular function carboxyl group function groups PRIMARY FUNCTIONS OF METABOLISM : (behavioral properties) R Group (side chains) determines a. Acquisition & utilization of energy the chemical properties of each b. Synthesis of molecules needed for cell amino acid. structure and functioning (i.e. proteins, nucleic Also determines how the protein acids, lipids, & CHO folds and its biological function. c. Removal of waste products Individual amino acids in protein connected by peptide bonds. Frequent reaction encountered in biochemical processes Functions as transport proteins, NUCLEOPHILIC SUBSTITUTION structural proteins, enzymes, One atom of group substituted for another antibodies, cell receptors. ELIMINATION REACTIONS SUGARS Double bond is formed when atoms in a molecule is Carbohydrates are the most abundant organic removed molecule found in nature. ADDITION REACTIONS Initially synthesized in plants from a complex Two molecules combine to form a single product. series of reactions involving photosynthesis. HYDRATION REACTIONS Basic unit is monosaccharides. Water added to alkene > alcohol (common addition rxn) Monosaccharides can form larger molecules e.g. glycogen, plant starch or cellulose. ISOMERIZATION REACTIONS Glycogen - stored form of glucose Involve intramolecular shift of atoms or groups Forms with same chemical composition but in different structure OXIDATION-REDUCTION ( REDOX ) REACTIONS Occur when there is a transfer of electrons (e-) from a donor to an electron acceptor HYDROLYSIS REACTIONS Cleavage of double bond by water. energy for cells Living cells are inherently unstable. Constant flow of energy prevents them from becoming disorganized. FUNCTIONS Cells obtains energy mainly by the oxidation of bio- Store energy in the form of starch (photosynthesis in plants) or glycogen (in molecules (e- transferred from 1 molecule to another animals and humans). and in doing so they lose energy) 1. Starch - plant How do complex structure of cells maintain high internal order? 2. Glycogen - human and animals SYNTHESIS OF BIO-MOLECULES Provide energy through metabolism pathways and cycles. TRANSPORT ACROSS MEMBRANES Cell membranes regulate the passage of ions and FATTY ACIDS molecules from one compartment to another. Are monocarboxylic acid contains even CELL MOVEMENT number C atoms Two types: saturated (C-C sb) and Organized movement- most obvious characteristics of unsaturated (C-C db) living cells. The intricate and coordinated activities Fatty acids are components of several lipid required to sustain life require the movement of cell molecules. components. E,g. of lipids are triacylglycerol, steroids WASTE REMOVAL (cholesterol, sex hormones), fat soluble Animal cells convert food molecules into CO2, H20 & FUNCTIONS NH3. If these are not disposed properly they can be Storage of energy in the form of fat toxic. Membrane structures Insulation (thermal blanket) Synthesis of hormones SHORTCUTS Cell Types - PE biochemical reactions Cell Organelles - PPCMG, RSRLN All reactions are catalyzed by enzymes Major Classes of small Bio-molecules METABOLISM - ASF (F=SU) Primary functions of metabolism total sum of the chemical reaction happening - ASR in a living organism (highly coordinated and Frequent reaction encountered in biochemical processes purposeful activity) - NEAIOH How do complex structure of cells maintain high internal order? - STCW  BIOCHEMISTRY LECTURE jan christian de leon|BSN - 1ST YEAR Lesson 2| september 5, 2024 4 PHASES OF MITOSIS (PMAT) the cell 1.) Prophase CELL WALL Mitosis begins (cell begins to divide) Rigid and strong wall Centrioles (or poles) appear and begin to move to Protects and maintains the shape opposite end of the cell of the cell Spindle fibers form between the poles Nuclear envelope disappears very important for CHLOROPLAST (PLANT CELL ONLY) chromosomes to expose Contains chlorophyll Makes plants green 2.) Metaphase Uses light energy to make ATP and sugars Chromatids (or pairs of chromosomes) attach to the Photosynthesis takes place here spindle fibers CENTRAL VACUOLE (PLANT CELL ONLY) All chromosomes lined up at the equator 1. Each chromatid faces opposite pole Most plant cells have large one 2. Spindle fibers attach to centromere of chromosomes Filled with fluid 3. Centromeres of chromosomes line up in the middle Force between the cell that pushes the plasma forming equatorial plate. membrane against the cell wall STAGES OF CELL CYCLE Equitorial plate =lining of chromatids to center Series of events that takes place in a cell leading to Centromere = separates the chromatid’s upper and its division and duplication (replication) lower arm PROKARYOTES 3.) Anaphase Eg. Bacteria do not undergo interphase and mitotic Chromatids (or pairs of chromosomes) separate and but undergoes binary fission begin to move at opposite ends of the cell EUKARYOTIC CELLS’ 2 BRIEF PERIOD 1. Chromosomes break at centromeres, and sister 1.) Interphase chromatids move to opposite ends of the cell Not a part but a preparation for mitosis Cell accumulates nutrients needed for mitosis, 4.) Telophase duplicating its DNA before moving on to mitotic Two new nuclei form proper Chromosomes appear as chromatin (threads rather than rods) a.) G1 phase/Growth Phase Mitosis ends End of the previous M phase until the beginning of 1. The chromosomes are cordoned off into distinct new DNA synthesis nuclei in the emerging daughter cells G stands for “gap” Cleavage furrow = indentation of the cell's surface CYTOKINESIS b.) S Phase DNA is replicated, and chromosomes form sister Occurs after mitosis chromatids (left and right chromatids r identical) Cell membrane moves inward to create daughter cells - each with its own nucleus with identical chromosomes MEIOSIS A process that decreases the chromosome number so that each daughter nucleus receives only one chromosome from each homologous pair. Think of it as a double mitotic division with only a single S phase. The amount of DNA in the cell has effectively Special cell division that converts diploid body cells doubled, though the ploidy of the cell remains the into haploid gametes. (only occurs in specialized same cells) PLOIDY= num. of complete cells of chromosome in Produce 4 haploid non identical cells a cell (23 pairs) Takes 2 cell divisions, M1 and M2, with no DNA synthesis between c.) G2 Phase Eg. (ex cells gametes sperm and egg cell) Mitochondria divide, precursors of spindle fibers Same phases to mitosis but phases happens 2 times are synthesized 2.) Mitosis (Mitotic/M phase) Process by which a eukaryotic cell separates chromosomes in its cell nucleus into 2 identical sets in two nuclei Relatively brief M phase consist of nuclear division called karyokinesis Other types of cells excluding sex cells  BIOCHEMISTRY LECTURE jan christian de leon|BSN - 1ST YEAR Lesson 2| september 5, 2024 FIRST MEIOTIC DIVISION (M1)/PMAT 1 III. ANAPHASE 2 I. PROPHASE 1 Centromeres divide, chromosomes are now monads which get pulled to opposite poles Very long, with a number of sub-stages Ang kaibahan nito sa anaphase 1, sister Main event in prophase of M1 is crossing over, chromosomes ang hiniltak pero dito isa nalang pero also called recombination meron parin silang recombination tingnan mo yung In crossing over, homologous chromosomes paa pair up, and exchange segments by breaking and rejoining at identical locations. Reason why products are not identical IV. TELOPHASE 2 Cytoplasm divided into 2 cells Meron cleavage furrow ulet Centrioles will move on opposite end of chromosome Nuclear envelope will condensate II. METAPHASE 1 Pairs of homologous chromosomes line up together III. ANAPHASE 1 The spindle pulls the two homologous poles to opposite poles. However, buong chromosomes ang V. INTERKINESIS 2 mahihiltak at hindi ang kalahating side lang Para magtotally mahati yang dalawang yan IV. TELOPHASE 1 Total of 4 cells from the original cell. Each contains Magkakaroon na ulit ng cleavage furrow one haploid set of monad chromosomes Since specialized cells ang nag uundergo ng meiosis V. INTERKINESIS 1 si sperm cell since haploid sila ang laman nalang is Mahahati yung cleavage furrow maghihiwalay na so 23 chromosomes hindi pa pairs oke mamaya pa yon dalawa na ang product tapos uulit ka pa ulit mula tapos sa egg cell naman 23 chromosomes din same prophase lang di parin pairs yan Parang siyang cytokinesis if compare sa mitosis Pag nagmeet yang dalawang yan and mafertile mag aadd yang mga chromosome nila edi magkakaron ng SECOND MEIOTIC DIVISION (M2)/ PMAT 2 46 PAIRS of chromosomes Meiosis 2 is just like mitosis I. PHROPASE 2 In prophase 2, the chromosomes condense and spindle forms II. METAPHASE 2 Dyad chromosomes line up singly on the middle  BIOCHEMISTRY LECTURE jan christian de leon|BSN - 1ST YEAR Lesson | september 19, 2024 WATER’S HIGH SPECIFIC HEAT Water: The medium of life Water resists changing its temperature because of its THE MOLECULE THAT SUPPORTS ALL OF LIFE high specific heat Water is the biological medium on Earth The specific heat of a substance is the amount of heat All living organisms require water more than any that must be absorbed or lost for 1 gram of that other substance substance to change its temperature by 1°C Most cells are surrounded by water, and cells A calorie (cal) is the amount of heat required to raise themselves are about 70–95% water the temperature of 1 g of water by 1°C, so water’s The abundance of water is the main reason the specific heat is 1 cal/g °C Earth is habitable Water’s high specific heat can be traced to hydrogen bonding POLAR COVALENT BONDS IN WATER MOLECULES – Heat is absorbed when hydrogen bonds break RESULT IN HYDROGEN BONDING – Heat is released when hydrogen bonds form The water molecule is a polar molecule: the The high specific heat of water minimizes opposite ends have opposite charges temperature fluctuations to within limits that permit Polarity allows water molecules to form life hydrogen bonds with each other EVAPORATIVE COOLING Evaporation is transformation of a substance from liquid to gas Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas – For water, 540 cal/gram As a liquid evaporates, its remaining surface cools, a process called evaporative cooling Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water FLOATING OF ICE ON LIQUID WATER Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense FOUR EMERGENT PROPERTIES OF WATER Water reaches its greatest density at 4°C CONTRIBUTE TO EARTH’S SUITABILITY FOR LIFE If ice sank, all bodies of water would eventually freeze Four of water’s properties that facilitate an solid, making life impossible on Earth environment for life are – Cohesive behavior WATER: THE SOLVENT OF LIFE – Ability to moderate temperature A solution is a liquid that is a homogeneous mixture of – Expansion upon freezing substances – Versatility as a solvent A solvent is the dissolving agent of a solution The solute is the substance that is dissolved COHESION OF WATER MOLECULES An aqueous solution is one in which water is the Collectively, hydrogen bonds hold water solvent molecules together, a phenomenon called Water is a versatile solvent due to its polarity, which cohesion allows it to form hydrogen bonds easily Cohesion helps the transport of water against When an ionic compound is dissolved in water, each gravity in plants ion is surrounded by a sphere of water molecules Adhesion is an attraction between different called a hydration shell substances, for example, between water and Water can also dissolve compounds made of nonionic plant cell walls polar molecules Adhesion also helps with the transport of water Even large polar molecules such as proteins can in plants to counter gravity dissolve in water if they have ionic and polar regions Surface tension is a measure of how hard it is to break the surface of a liquid HYDROPHILIC AND HYDROPHOBIC SUBSTANCES Surface tension is related to cohesion A hydrophilic substance is one that has an affinity for The ability of water molecules to form hydrogen water bonds with each other results in the high A hydrophobic substance is one that does not have surface tension of water an affinity for water Oil molecules are hydrophobic because they have MODERATION OF TEMPERATURE BY WATER relatively nonpolar bonds Water absorbs heat from warmer air and releases stored heat to cooler air SOLUTE CONCENTRATION IN AQUEOUS SOLUTIONS Water can absorb or release a large amount of Most biochemical reactions occur in water heat with only a slight change in its own Chemical reactions depend on collisions of molecules temperature and therefore on the concentration of solutes in an Water has a high heat of fusion compared to aqueous solution other substances, 80 cal/gram – This is the amount of heat that has to be Molecular mass is the sum of all masses of all atoms in added or removed to make ice melt or water freeze a molecule HEAT AND TEMPERATURE Numbers of molecules are usually measured in moles, Kinetic energy is the energy of motion where 1 mole (mol) = 6.02 x 1023 molecules Heat is a measure of the total amount of kinetic Avogadro’s number and the unit dalton were defined energy due to molecular motion such that 6.02 x 1023 daltons = 1 g Temperature measures the intensity of heat due Molarity (M) is the number of moles of solute per liter to the average kinetic energy of molecules of solution  BIOCHEMISTRY LECTURE jan christian de leon|BSN - 1ST YEAR Lesson | september 19, 2024 ACIDIC AND BASIC CONDITIONS AFFECT LIVING BUFFERS ORGANISMS The internal pH of most living cells must remain A hydrogen atom in a hydrogen bond between two close to pH 7 water molecules can shift from one to the other Buffers are substances that minimize changes in – The hydrogen atom leaves its electron behind concentrations of H+ and OH– in a solution and is transferred as a proton, or hydrogen ion (H+) Most buffers consist of an acid-base pair that – The molecule with the extra proton is now a reversibly combines with H+ hydronium ion (H3O+), though it is often represented as H+ – The molecule that lost the proton is now a hydroxide ion (OH–) Though statistically rare, the dissociation of water molecules has a great effect on organisms Changes in concentrations of H+ and OH–can drastically affect the chemistry of a cell Concentrations of H+ and OH–are equal in pure water Adding certain solutes, called acids and bases, modifies the concentrations of H+ and OH– Biologists use something called the pH scale to describe whether a solution is acidic or basic (the opposite of acidic) ACID AND BASES An acid is any substance that increases the H+ concentration of a solution A base is any substance that reduces the H+ concentration of a solution THE PH SCALE Acidic solutions have pH values less than 7 Basic solutions have pH values greater than 7 Most biological fluids have pH values in the range of 6 to 8