Cell Notes 1/11-1/15 (Lectures 1-3)
Cell Notes 1/11-1/15 (Lectures 1-3) BIOL 30603
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This 6 page Class Notes was uploaded by Mallory Notetaker on Thursday January 28, 2016. The Class Notes belongs to BIOL 30603 at Texas Christian University taught by Dr. Akkaraju, Dr. Misamore, Dr. Chumley, Dr. McGillvray in Spring 2016. Since its upload, it has received 64 views. For similar materials see Molecular, Cellular, and Developmental Biology in Biology at Texas Christian University.
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Date Created: 01/28/16
1/11/16 What you know so far…. virus is non-living outside a cell, needs a cell to live -viruses are compact packages of DNA or RNA encased in protein Ancestral cell is 3.5-3.8 billion years ago -prokaryotes most closely resemble ancestral cell (no nucleus) the cell is the functional unit of all free-living organisms Prokaryotes can use inorganic materials (sulfer, CO2) to generate energy instead of only depending on oxygen. Prokaryotes are the most diverse group of organisms on the planet (more variety of species) -eukaryotes have a symbiotic relationship with prokaryotes to help us survive What is the consistency of the cytosol of the cell? -gel-like, snot -cytosol is the liquid part of the cytoplasm (area between nucleus and cellular membrane) -If things have to move they have to be transported across the membrane -organelles are ﬁxed in space Nucleus has DNA, and it is distributed unevenly (nonuniform), some packed tightly some packed loosely -euchromatin: loosely packed -heterochromatin: tightly packed, permanently silenced -after replication the DNA condenses (so it is not chromatin) in the metaphase Endoplasmic Reticulum- helps in the transportation of proteins and in the processing of proteins, proteins get modiﬁed here Golgi Apparatus- protein motiﬁcation and protein transport Plasma membrane- holds the cell together Plant- cell wall (helps resist osmotic change) What are the different types of organelles? Mitochondria function: generators of chemical energy for the cell, produce ATP, cell respiration nature of their membranes: they have two membranes, came from bacteria that were engulfed by a eukaryotic cell (created a symbiotic relationship between eukaryote and bacteria) Chloroplasts function: photosynthesis membranes: two membranes, also have internal stacks of membranes containing chlorophyll Endoplasmic Reticulum function: make materials that get exported, synthesis, modify, and transport proteins membranes: contain ribosomes (rough ER) that convert RNA into proteins, continuous with the membranes of the nucleus Golgi Apparatus function: modiﬁes and packages molecules made in ER membranes: stacks of ﬂattened membrane enclosed sacs Lysosomes function: break down food Peroxisomes function: breaks down fatty acids, etc and turns them into hydrogen peroxide then further breaks down that toxin The cytoskeleton: made up of… -microﬁlaments: made up of actin and myosin, thin threads that spread across cell to give it shape -Microtubules: larger than microﬁlaments, hollow tubes, help transport things across cell, important during cell division (pulls apart chromosomes during metaphase) and the separation of DNA Model Organisms: these things we discover in these organisms we can apply them in humans Saccharomyces cerevisiae: Yeast: has the same genes that work in eukaryotes Arabidopsis thaliana- helps study plants Drosophila melanogaster- ﬂies Caenorhabditis elegans: sea elegans: helps unravel the development of eukaryotes -nematode, helped us understand apoptosis (a form of programmed cell death by which surplus cells are disposed of in all animals) -important in cancer research Mus Musculus- zebra mussels, good for studying vertebrates 1/13/16 Questions: protein-protein interactions are not covalent bonds covalent bonds are permanent and it takes energy to break it the resolving power of a microscope is limited by the wavelength of radiation used -the ability to see detail in the cell Electron microscope can see DNA and ribosome Organelle has both an outer and an inner membrane -mitochondrion -endosymbiosis: one little membrane organelle got swallowed by another Mitochondria -has own genome -able to duplicate -divide on a different time line from the rest of the cell -it cannot live outside the cell and the cell cannot live without the mitochondria so mitochondria and the cell are endosymbionts Bonds Strength: Covalent- takes energy to break, strong Noncovalent: ionic hydrogen bonds vanderwaals -Electrostatic bonds help proteins bind Water structure -cohesive nature of water gives its unusual properties -high surface tension -high speciﬁc heat -high heat of vaporization -it dissolves other polar molecules because it is polar -hydrophilic will dissolve in water, hydrophobic is opposite -ionic and polar molecules are hydrophilic, they dissolve -the hydrophobic (nonpolar) parts of proteins stay on the inside and are sheltered from the aqueous environment of the cell Sugars -Aldose: sugar with an aldehyde on it -Ketose: contains ketone group -know that a three carbon sugar is a triose, and know pentoses and hexoses -Glucose is a hexose aldose -know the monosaccharides chart really well, even the speciﬁc names Sugars can form ring structures, they switch back and forth from their straight chain to ring -know the numbering of the carbons on the ring formation slide -enzymes will look for certain orientations of functional groups on their substrates (sugars) -example: glucose is different from galactose -mannose is a sugar that used to tag proteins in the cell, called glycosylation -the order in which the sugars are added to the proteins, tells where to send the protein and this is speciﬁc because of their distinct properties -glycosidic bond is when sugars are linked together -glycosidic bond created by condensation, taking out water -as soon as they are linked, the beta and alpha form of the hydroxyl group is frozen -3 linked together, trisaccharide -chitin are sugars linked together and is very hard to break down -you can add other groups in place of hydroxyl groups on sugars -know and be able to name the substituted sugars -Oligosaccharides: a small number of repeating units -Polysaccharides: lots of repeating units -can be branched Lipids Long carbon chains, carboxyl group at one end and hydrocarbon tails off them Hydrophobic because non polar Fatty acid bonds have energy in them, the cell break them and use them to form ATP -fatty acids can also be bad for the cell so they are stored in the peroxisome and broken down there Very long chain fatty acids = VLCFA Double bond in the chain creates a kink= unsaturated unsaturated = good saturated (butter) = bad for you - because of the kinks of unsaturated fatty acids, they are more ﬂuid and don’t stick to your arteries as well as fatty acids do -triglyceride: 3 fatty acids stuck on glycerol by ester linkages -when you go into the clinic they look at your levels of triglycerides (can be bad) Membranes are made up by lipids -phospholipids and glycolipids form self-sealing bilayers -Naturally occurring fatty acids interacted with water and formed the ﬁrst bilayer trapped inside of it DNA making ﬁrst life Phospholipids -3 carbon backbone and add a phosphate -one side is polar(phosphate) and the other is non polar (fatty acids) -one fatty acid is saturated and one is unsaturated (important) -The unsaturated fatty acids in the membrane make it more ﬂuid and less rigid Steroids -long chain fatty acids folded back in on itself -storage of energy -need cholesterol in cell membranes to keep ﬂuidity -testosterone- male sex hormone Amino Acids -Stucture: 4 things attached to an alpha C -amino group -carboxyl group -hydrogen -side chain (R) (20 side chains) -they are grouped according to whether their side chains are -basic -acidic -uncharged polar -nonpolar Basic: sucks up hydrogen (amine group), reducing acidity acidic: gives hydrogen into the system -anytime you see a charge on a molecule, it is polar Peptide Bonds -can form peptide bonds by linking the carboxyl group to the amino group of another -all peptide bonds in our body are the L form not D -Protein contain exclusively L-amino acids -peptide bonds are formed by condensation and are ﬂexible because single bonds Nucleotides Pyrimidine- base in a hexagon shape Thymine Cytosine Uracil Purine - base in a almost naphthalene shape Adenine Guanine -they are phosphorylated and can attach up to 3 phosphates on them -phosphates add on the 5’ of the sugar -phosphates are connected by phosphodiester bonds -Base adds on the 1’ of the sugar -2 types of sugars (pentoses) are used in nucleotides -Beta-D-ribose -in RNA -Beta-D-2-deoxyribose -in DNA 1/15/16 The nature of the amino acids determines how the protein will fold phosphates are bonded by phosphodiester bonds shorter chains of the nucleotides are oligotides base is attached to carbon number one and phosphate is on carbon number 5 a covalent bond between two atoms is formed as a result of the sharing of electrons Cells need ribose to build nucleotides Weak non covalent chemical bonds -two proteins come together and have a high afﬁnity to each other -things in the cell are constantly moving and can randomly ﬁnd a substrate and act on it Vander walls attractions -at short distances, any two atoms show a weak bonding interaction due to their ﬂuctuating electrical charges Hydrogen Bonding: -when an H is between two electron-rich atoms (oxygen) -strongest when the 3 atoms are in a line - is important in holding proteins together and forming shape electrostatic attractions: between two charged atoms -water breaks up electrostatic interactions, dissolving the compound If two things have a high afﬁnity for each other the rate of dissociation will be low hydrophobic interactions -two drops of oil in water, they want to come together to reduce the amount of surface area that is touching the water -no charge but come together Reactions in the cell are broken down into smaller steps because it is easier to move something uphill one step at a time Catabolic pathway: break down; release energy through oxidative pathways anabolic pathways: build up The second law of thermodynamics: universal tendency of things to become disordered -The disorder in the universe can only increase -increasing overall entropy of the universe Reactions that tend to increase order will require energy, the universe naturally slides to non order energetically unfavorable reactions can occur only if it is coupled to a second energetically favorable reaction -negative delta G coming from the synthesis of ATP is coupled with the positive delta G of the synthesis of sugar on test will give a reaction and give the free energy of the components and you need to come to a conclusion about whether it will happen G products - G reactants = delta G
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