Cell Biology L-1 PDF

BME Program (CHE 216) Dr. Amira Zaky Professor. Department of Biochemistry, Faculty of Science Alexandria University, Egypt. Tel: +20 1201796665 email: [email protected]...

BME Program (CHE 216) Dr. Amira Zaky Professor. Department of Biochemistry, Faculty of Science Alexandria University, Egypt. Tel: +20 1201796665 email: [email protected] 1  Biomedical engineering Biomedical engineering or medical engineering is the application of engineering principles and design concepts to medicine and biology for healthcare purposes. BME is also traditionally logical sciences to advance health care treatment, including diagnosis, monitoring, and therapy. Biomedical engineers focus on advances in technology and medicine to develop new devices and equipment for improving human health.  What is the role of biochemistry in ?biomedical engineering Biochemical techniques advance our understanding of the chemical structures and processes that underpin human health and disease, revealing the underlying transformations between them. The implications of uncovering the causes of pathologies on a cellular level are huge. ?What is Biomedical Engineering Artificial organs. Surgical robots. Advanced prosthetics. New pharmaceutical drugs. Kidney dialysis.  Here are the Best Biomedical Engineering Programs Johns Hopkins University, USA Georgia Institute of Technology. Massachusetts Institute of Technology. Stanford University. University of California, Berkeley. University of California--San Diego (Jacobs) Duke University (Pratt) University of Pennsylvania.  BME215 Biology 3 Cr. Hrs. = (2 LCT + 1 TUT + 2 LAB + 0 OTH) – SWL = 165 – ECTS = 6This course covers the following topics: macromolecules, biology of cells, metabolism, genetics, and evolution. BME213 Biochemistry 2 Cr. Hrs. = (2 LCT + 1 TUT + 1 LAB + 0 OTH) – SWL = 120 – ECTS = 4Prerequisite - - -Biochemical processes: Cells, Water, and Buffers/ Energy/ Structure and function/ Catalysis/ Flow of Genetic Information/ Metabolism I/ Metabolism II/Signaling/ Synthesis of Concepts in Biochemistry.  Contents Week Lecture Topic BME 1-2 Introduction to cell structure and functions of its basic components in pro- versus eukaryotes 3-4 Macromolecules: Overview on the genome structure and regulated steps of gene expression 5-6 Macromolecules: An overview of amino acid and proteins structures, functions and.metabolic reactions 7 Macromolecules: Carbohydrates structure, classification and functions and.metabolic homeostasis 8.Macromolecules: Lipids classification, metabolic and biological implications 9 Mid-Term 10 Genetic diversity and evolution concepts; insights on human genome project 11.COVID-19 challenges; Biological perspectives 12-13 Concepts of Basic Molecular Biology techniques (PCR, gel electrophoresis and ELISA) 14 Assignments discussion and Presentation by students 13 Application; Neurobiology 14 Assignments discussion and Presentation by students  Evaluation Method % Weight Mid-Term Exam 10 Final Exam 40 Oral Exam 10 Practical Exam 30 Home Work 10 Quizzes --- Other --- Total 100 Cells  Cell Theory All living things are made up of cells. Cells are the smallest working units of all living things. All cells come from preexisting cells through cell division.  Definition The cell is the structural and functional unit of all known living organisms. The word cell comes from the Latin cellula, meaning, a small room.  Types of cells There are a variety of ways in which cells can be classified: – a cell can be separated according to its tendency towards existing alone or in a group setting. A single cell (also known as unicellular) organism functions by itself without need of any other cells for survival. A multicellular organism, on the other hand, is made up of an entire community of cells that are all specialized, interdependent and interconnected in their requirements and functions. – based on genetic differences, two groups: the prokaryotes and the eukaryotes.  All cells at their essence have at least :three things in common Cell membrane. All cells have a phospholipid based cell membrane the cell membrane is selectively permeable. Cytoplasm. Cells are filled with a complex collection of substances in a water based solution (it has ribosomes). DNA. All cells contain DNA. In the simplest cells, the DNA is in one loop more loop like structures free in the cytoplasm. In some cells such as those making up our body the DNA is isolated from the cytoplasm in a special structure called a nucleus.  The Origin of Mitochondria Martin, W. & Mentel, M. (2010) The Origin of Mitochondria. Nature Education 3(9):58 Mitochondria arose through a fateful endosymbiosis more than 1.45 billion years ago. Many mitochondria make.ATP without the help of oxygen  Origin of eukaryotic cells The origin of cells has to do with the origin of life and is one of the most important steps in the theory of evolution. The birth of the cell marked the passage from prebiotic chemistry to biological life. The eukaryotic cell seems to have evolved from a symbiotic community of prokaryotic cells. One aspect of that evolutionary connection is particularly interesting.  One structure not shown in our prokaryotic cell is called a mesosome. Not all prokaryotic cells have these. The mesosome is an elaboration of the plasma membrane--a sort of rosette of ruffled membrane intruding into the cell EUKARYOTES Versus Prokaryotes  Sub-cellular components Cell membrane: A cell's defining boundary – The cytoplasm of a cell is surrounded by a plasma membrane. The plasma membrane in plants and prokaryotes is usually covered by a cell wall. – This membrane serves to separate and protect a cell from its surrounding environment and is made mostly from a double layer of lipids , phospholipid bilayer. – It may also be called a fluid mosaic membrane. – Embedded within this membrane is a variety of protein molecules that act as channels and pumps that move different molecules into and out of the cell Cell membrane: A cell's defining boundary  Cytoskeleton: A cell's scaffold – The cytoskeleton acts to organize and maintain the cell's shape; anchors organelles in place; helps during endocytosis (the uptake of external materials by a cell), and cytokinesis (the separation of daughter cells after cell division); and moves parts of the cell in processes of growth and mobility. – The eukaryotic cytoskeleton is composed of microfilaments, intermediate filaments and microtubules. There is a great number of proteins associated with them, each controlling a cell's structure by directing, bundling, and aligning filaments. – The prokaryotic cytoskeleton is involved in the maintenance of cell shape, polarity and cytokinesis.  Organelles (compartmentalization) – Cell nucleus (a cell's information center) The cell nucleus is the most prominent organelle found in a eukaryotic cell. It houses the cell's chromosomes, and is the place where almost all DNA replication and RNA synthesis occur. The nucleus is spherical in shape and separated from the cytoplasm by a double membrane called the nuclear envelope. nuclear envelope isolates and protects a cell's DNA from various molecules that could accidentally damage its structure or interfere with its processing. During processing, DNA is transcribed, or copied into a special RNA, called mRNA. This mRNA is then transported out of the nucleus, where it is translated into a specific protein molecule. In prokaryotes, DNA processing takes place in the cytoplasm. – Mitochondria and Chloroplasts (the power generators) Mitochondria are self-replicating organelles that occur in various numbers, shapes, and sizes in the cytoplasm of all eukaryotic cells. As mitochondria contain their own genome that is separate and distinct from the nuclear genome of a cell, they play a critical role in generating energy in the eukaryotic cell, they give the cell energy by the process of respiration, adding oxygen to food (typically pertaining to glucose and ATP) to release energy. Organelles that are modified chloroplasts are broadly called plastids, and are often involved in storage. Since they contain their own genome, they are thought to have once been separate organisms, which later formed a symbiotic relationship with the cells. Chloroplasts are the counter-part of the mitochondria. Instead of giving off CO2 and H2O Plants give off glucose, oxygen, 6 molecules of water (compared to 12 in respiration) this process is called photosynthesis. – Endoplasmic reticulum and Golgi apparatus (macromolecule managers) The endoplasmic reticulum (ER) is the transport network for molecules targeted for certain modifications and specific destinations, as compared to molecules that will float freely in the cytoplasm. The ER has two forms: the rough ER, which has ribosomes on its surface, and the smooth ER, which lacks them. – Ribosomes (the protein production centers in the cell) The ribosome is a large complex, composed of many molecules, in prokaryotes only exist floating freely in the cytosol, whereas in eukaryotes they can be found either free or bound to membranes.  Ribosome Ribosomes (from ribonucleic acid and "greek: soma (meaning body)") are complexes of RNA) are complexes of RNA and protein) are complexes of RNA and protein that are found in all cells. ProkaryoticProkaryotic ribosomes from archaeaProkaryotic ribosomes from archaea and bacteriaProkaryotic ribosomes from archaea and bacteria are smaller than most of the ribosomes from eukaryotesProkaryotic ribosomes from archaea and bacteria are smaller than most of the ribosomes from eukaryotes such as plantsProkaryotic ribosomes from archaea and bacteria are smaller than most of the ribosomes from eukaryotes such as plants and animalsProkaryotic ribosomes from archaea and bacteria are smaller than most of the ribosomes from eukaryotes such as plants and animals. However, the ribosomes in the mitochondrionProkaryotic ribosomes from archaea and bacteria are smaller than most of the ribosomes from eukaryotes such as plants and animals. However, the – Lysosomes and Peroxisomes (of the eukaryotic cell) The cell could not house such destructive enzymes if they were not contained in a membrane-bound system. These organelles are often called a "suicide bag" because of their ability to detonate and destroy the cell. – Centrosome (the cytoskeleton organiser) The centrosome produces the microtubules of a cell - a key component of the cytoskeleton. It directs the transport through the ER and the Golgi apparatus. Centrosomes are composed of two centrioles, which separate during cell division and help in the formation of the mitotic spindle. A single centrosome is present in the animal cells. They are also found in some fungi and algae cells. Major Polymer Biomolecules  Nucleosides and nucleotides – Nucleosides are molecules formed by attaching a nucleobase to a ribose ring. Examples of these include cytidine, uridine, adenosine, guanosine, thymidine and inosine. Nucleosides can be phosphorylated by specific kinases in the cell, producing nucleotides, which are the molecular building blocks of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).  Polypeptides and Proteins – Peptides are short polymers formed from the linking, in a defined order, of α-amino acids. The link between one amino acid residue and the next is known as an amide bond or a peptide bond. – Proteins are polypeptide molecules (or consist of multiple polypeptide subunits). The distinction is that peptides are short and polypeptides/proteins are long. – Amino acids are the building blocks of long polymer chains. With 2-10 amino acids such chains are called peptides, with 10-100 they are often called polypeptides, and longer chains are known as proteins. These protein structures have many structural and functional roles in organisms – The particular series of amino acids that form a protein is known as that protein's primary structureThe particular series of amino acids that form a protein is known as that protein's primary structure. Proteins have several, well-classified, elements of local structure and these are termed secondary structureThe particular series of amino acids that form a protein is known as that protein's primary structure. Proteins have several, well-classified, elements of local structure and these are termed secondary  Saccharides – Monosaccharides are carbohydrates in the form of simple sugars. Examples of monosaccharides are the hexoses glucose, fructose, and galactose and pentoses, ribose, and deoxyribose. – Disaccharides are formed from two monosaccharides joined together. Examples of disaccharides include sucrose, maltose, and lactose. Monosaccharides and disaccharides are sweet, water soluble, and crystalline. – Polysaccharides are polymerized monosaccharides, complex, unsweet carbohydrates. Examples are starch, cellulose, and glycogen. They are generally large and often have a complex, branched, connectivity. They are insoluble in water and do not form crystals. Shorter polysaccharides, with 2-15 monomers, are sometimes known as oligosaccharides.  Lipids – Lipids are chiefly fatty acid esters, and are the basic building blocks of biological membranes. Another biological role is energy storage (e.g., triglycerides). Most lipids consist of a polar or hydrophilic head (typically glycerol) and one to three nonpolar or hydrophobic fatty acid tails, and therefore they are amphiphilic. Fatty acids consist of unbranched chains of carbon atoms that are connected by single bonds alone (saturated fatty acids) or by both single and double bonds (unsaturated fatty acids). The chains are usually 14-24 carbon groups long, but it is always an even number. – For lipids present in biological membranes, the hydrophilic head is from one of three classes: – Glycolipids, whose heads contain an oligosaccharide with 1-15 saccharide residues. – Phospholipids, whose heads contain a positively charged group that is linked to the tail by a negatively charged phosphate group. – Sterols, whose heads contain a planar steroid ring, for example, cholesterol. – Other lipids include prostaglandins and leukotrienes which are both 20-carbon fatty acyl units synthesized from arachidonic acid. They are also known as fatty acids  Nucleic Acids (DNA and RNA) A nucleic acid is a macromolecule composed of chains of monomeric nucleotide. these molecules carry genetic information or form structures within cells. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are universal in living things, as they are found in all cells and viruses. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207041/) ?????Why we are different  …Genetic material of cells GENES – units of genetic material that CODES FOR A SPECIFIC TRAIT Called NUCLEIC ACIDS DNA is made up of repeating molecules called NUCLEOTIDES