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Unit 1 Outline

by: TCU2461

Unit 1 Outline BIOL 30603

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These are the notes over materials such as cell structure, basic chemistry, energy, catalysis and biosynthesis, proteins
Molecular, Cellular, and Developmental Biology
Dr. Akkaraju, Dr. Misamore, Dr. Chumley, Dr. McGillvray
Class Notes
cellular biology, Cell, Protein function, Basicchemistry




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This 10 page Class Notes was uploaded by TCU2461 on Saturday April 30, 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 62 views. For similar materials see Molecular, Cellular, and Developmental Biology in Biology at Texas Christian University.


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Date Created: 04/30/16
Monday, February 8, 2016 Cell/Molecular/Developmental Biology CELL STRUCTURE ▯ -In nucleus there are two types of DNA: • Euchromatin: the DNA being used • Heterochromatin: DNA stored away -Endoplasmic reticulum is in charge of the movement and production of proteins. -The golgi apparatus is responsible for protein modification and transport. -Microscopy: • Light microscopy • Fluorescence microscopy • Confocal microscopy • Transmission electron microscopy • Scanning electron microscopy -Cytoskeleton • Actin Myosin • • Microtubles -Model Organisms • E.Coli • Saccharomyces Cerevisae/Schizosaccaromyces pombe (A unicellular eukaryote) • Arabidopsis thaliana (Model organism for plant development) • Drosophila melanogaster (Fruit fly) • Caenorhabditis elegans (A eukaryotic worm, apoptosis was learned from this) • Mus musculus (House mouse) • Danio rerio (Zebra fish) • Homo sapiens ▯ ▯ CHEMISTRY ▯ - Covalent bonds (share electrons) - Non-covalent bonds • Ionic bonds • Hydrogen bonds • Van der Waals bonds - Ionic substances such as NaCl dissolve because water molecules are attracted to positive sodium or negative chlorine. - Polar substances dissolve because molecules form hydrogen bonds with surrounding water molecules.
 1 - HYDROPHILIC compounds dissolve readily in water. - HYDROPHOBIC compounds are usually insoluble in water. - Proteins have both hydrophobic and hydrophilic regions which allows them to spontaneously fold into their unique shapes. - SUGARS: • Monosaccharides: - Aldoses (Figure 1) • 3-carbon (Trioses) — Glyceraldehyde • 5-carbon (Pentoses) — Ribose 6-carbon (Hexoses) — Glucose • - Ketones (Figure 2) • 3-carbon — Dihydroxyacetone • 5-carbon — Ribulose • 6-carbon — Fructose - Ring formation • Aldehyde or ketone group of sugar tends to react with hydroxyl group of the same molecule closing the ring. • Know how to number the carbons. - Isomers • Glucose, galactose, and mannose
 are isomers of each other. • These three isomers are used to tell
 the cell where to send proteins since they are used as tags. The order of these there sugars on a protein tell the cell where it needs to go. • The hydroxyl group can change from the α and β forms. α-glycosidic and β-glycosidic bonds are formed based on type of sugars that are attached and the orientation of the hydroxyl group. - Sugar derivatives • The hydroxyl groups of simple monosaccharaides can be replaced by other groups: - KNOW THE FOLLOWING STRUCTURES (Figure 4) - Glucuronic acid - Glucosamine - N-acetylglucoseamine • Disaccharides - Carbon that carries aldehyde or ketone can react with another hydroxyl group to form disaccharaide. This is a condensation reaction (loss of water). - Maltose (glucose + glucose) - Lactose (galactose + glucose) - Sucrose (glucose +fructose) • Oligosaccharides and Polysaccharides - An oligosaccharide is a small number of repeating units, about less than 100. - A polysaccharide are long chains well over 100! ▯ 2 - Lipids • Fatty acids - Saturated: Contains NO double bonds and will solidify as you lower the temperature. • - Unsaturated: • Contain ONE or more double bonds giving the carbon chain a kink. This allows it to remain a fluid as you lower the temperature because it doesn’t pack quite as tightly. - VLCFA (very long chain fatty acids) are stored within the peroxisome so they do not kill the cell (?). Within the peroxisome, the fatty acids are broken down. In some disorders, the fatty acids are not transferred to the peroxisome and cannot break down the fatty acid. - “Lorenzo’s Oil” - Triacylglcerols (Triglycerides) • Fatty acids are stored in cells as an energy reserve by placing them onto a glycerol through an ESTER LINKAGE. • Lipid aggregates - Fatty acids that have a hydrophilic head and a hydrophobic tail. In water, these can form a circle called a MICELLE or a surface film. - PHOSPHOLIPIDS and GLYCOLIPIDS form LIPID BILAYERS which is the bases for cell membranes. Phospholipids • - It is important that one of the fatty acids is unsaturated. If all the FA were saturated, then the phospholipid bilayer all the FAs would stack next to each other and solidify at low temperatures. Because one fatty acid is unsaturated, it gives the cell fluidity. - Know the general structure of a phospholipid! (Figure 5) - The phospholipid bilayer is the most energetically favorable configuration. - Steroids • They have a common multiple-ring structure Steroids are used for signaling and also keeps cell to be not so rigid. You can think of • cholesterol as LCFA that has folded up on itself, so they are kind of similar. Cholesterol is derivitized to form other steroids such as testosterone. - Amino Acids • The general formula for an amino acid contains an amino group, carboxyl group, and an R group (that determines the different amino acids) all connected to a central, chiral carbon. (Figure 6) • Amino acids are grouped according to their side chains: - Acidic • When there is a negative charge (due to loss of H) • Aspartic acid, glutamic acid - Basic • When there is a positive charge • Lysine, arginine, histidine - Uncharged Polar 3 - Nonpolar • Presence of -OH, Oxygen, or nitrogen. • Peptide bonds - Amino acids are typically joined by an amide linkage called a PEPTIDE BOND. There are two ends to amino acids, the C-TERMINUS and the N-TERMINUS. The 
 -OH on the C-terminus and the -H on the N-terminus join and water leaves (condensation). - Proteins are long polymers of amino acids. Peptides are shorter, usually <50 amino acids longer. Depending on nature of amino acid will determine how the protein folds. For examples, if • you have high number of non-polar amino acids, it will tend to be hydrophobic. Proteins will fold in such a way to hide hydrophobic part of polypeptide. • Protein folding involves a negative change in free energy. • The alpha-carbon is chiral so optical isomerism is present. ALL AMINO ACIDS IN THE BODY ARE LEVO AMINO ACIDS! - Nucleotides • A nucleotide consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups. - The base is attached to carbon #1 and the phosphate is attached to carbon #5. - The base-sugar linkage is an N-GLYCOSIDIC BOND. • Pyrimidines: - Thymine - Cytosine - Uracil • Purines: - Adenine - Guanine • The pentose sugar — two types are used: (Figure 7) - β-D-ribose (used in ribonucleic acid; RNA) - β-D-2-deoxyribose (used in deoxyribonucleic acid; DNA) - Phosphates • The phosphates are joined to the C5 HYDROXYL of the ribose or deoxyribose sugar (5’ carbon). • Nucleotides can be phosphorylated by adding up to three phosphate groups to them. They are linked by phosphodiester bonds. These are high energy linkages! The phosphates make nucleotide negatively charged. • - BASE + SUGAR = NUCLEOSIDE - BASE + SUGAR + PHOSPHATE = NUCLEOTIDE - Nucleotides (particularly ATP) are very versatile because: it can be used in the cell to carry energy and drive unfavorable retains forward. • • it can be linked to other molecules and acts as cofactor for enzymes to function. • in cyclic form (particularly cyclic AMP and cyclic GMP) can serve as important signaling molecules in the cell. 4 - Weak noncovalent bonds • Van der Waals attractions, electrostatic attractions, and hydrogen bonds. • As you increase the number of weak interactions, the linkage between two proteins becomes stronger and its’s harder to separate the proteins. An example of this phenomenon is DNA. The bases come together through H-bonds. • Because there are so many nucleates coming together and thousands of H-bonds, it takes a lot of energy to separate nucleotide strands. • Proteins that come together can have a high or low affinity for each other which is based on these non covalent bonds. If two proteins come together but do not have enough of these bonds, they will not stick and have a LOW AFFINITY for each other. - Rate of dissociation: • If two molecules have a low affinity for each other, then the ROD will be high because they will want to come off each other more than wanting to bond with each other. If two things have a high affinity for each other, the ROD will be low. - Two Hydrophobic molecules will want to come towards each other, because the amount of surface exposed to the water goes down. ▯ ▯ ENERGY, CATALYSIS AND BIOSYNTHESIS ▯ - Reactions are broken down into smaller steps to make them more energy efficient. The amount of energy input required for each step goes down. - Catabolic pathways: • Breaking things down/increasing entropy - Anabolic pathways: • Building things into large molecules/decreasing entropy - Light energy can be transferred to “energy currency” (activated carriers) which gives energy to other systems to build molecules as in photosynthesis. - Photosynthesis: • CO 2 H 2 ----> O +2Sugars - Cellular respiration: • O2+ Sugars ----> CO 2 H O2 5 - Reaction must overcome an activation energy barrier, enzyme-catalyzed reactions have a Molecules with▯ average energy lower the Ea. In the presence of an enzyme, the amount of energy required for reaction decreases and number of molecules converted goes up. - Nature tends toward an INCREASE in entropy, which corresponds to DECREASE in free energy. - FREE ENERGY measures the energy of a molecule which can bemused to do useful work. Know how to calculate Δ∆G for a given equation (products - reactants). You can use this to • predict reactions. - Δ∆G < 0 indicates a SPONTANEOUS reaction. Δ∆G > 0 indicates a NON-SPONTANEOUS reaction. • Note: a spontaneous reaction does not necessarily mean a fast reaction! • As disorder increases, Δ∆G becomes more and more negative. - Unfavored reactions proceed by being coupled with an ACTIVATED CARRIER. Coupled reactions force unfavorable reactions to move forward. - Phosphates attached to nucleosides contain a lot of energy that is often used in coupling reactions. - When poking at substrate concentration vs. rate of reaction when analyzing enzyme activity, you typically want to look at 1/2MAXand then find the KMvalue which is the affinity constant. If there is a higM K value, then you know that there low affinity between substrates and enzyme since it takes so long for the reaction to occur.MIf K is small, then the slope of the reaction is steep indicating a fast reaction and high affinity. - Coupled Reactions • The energy from an energetically favorable reaction is captured and used to make an energetically unfavorable reaction favorable. • The phosphate bonds on a nucleoside triphosphate has high energy because of the proximity of the high electronegative elements. 6 • NAD and NADP (nicotinamide adenine dinucleotide phosphate) are both energy carriers! (Pg. 4 on lec. 3) - In it’s reduced form, NADPH has ability to transfer energy to something else. - You can also have NAD which doesn't have phosphate attached. NAD and NADP are both energy carriers. - NAD and NADP are a COMBINATION OF TWO NUCLEOTIDES and a PROTON gets added to the NICOTINAMIDE ring on NAD and NADP to reduce it. This energy can be transferred to an unfavorable reaction to make it happen. - Biosynthesis • Biosynthesis is typically due to a condensation reaction. • Polysaccharides: - Two -OH groups join, and through a loss of water and the energy from nucleoside triphosphate, two sugars can be joined. • Nucleic Acids: - The -OH groups on the 3’ C on the sugar and the phosphate group of another nucleotide can join by condensation. • Proteins: - The -OH from the C-temrinus of the amino acid joins with a hydrogen from the N- terminus of another nucleotide to form water and join the nucleotides together. • ATP --- >AMP + 2P i - The 2Pican be further broken down for more energy! ▯ ▯ ▯ PROTEIN SHAPE AND STRUCTURE ▯ - Levels of protein folding • Primary structure: - The initial order of amino acids. • Secondary structure: - The innate property of the protein based on amino acid composition to fold into ALPHA HELICES or BETA-PLEATED SHEETS. The formation of these structures is due to bond angles and hydrogen bonding. - Alpha helices and beta-pleated sheets are an energetically favorably conformation. • Tertiary structure: - Noncovalent interactions • Electrostatic interactions • Hydrogen bonds • Van der Waals interactions • Disulfide bridges • Hydrophobic/hydrophilic regions 7 - Proteins fold naturally and there are many shapes it can assume, however only one shape allows it to function. Therefore, other proteins can assist a protein to fold into its most energetically favorable conformation. - The GroEL and GroES proteins act as a box and cap. The box will pull at folded protein unfolding it and allowing it to refold over and over. Eventually, the folded protein will assume the most stable conformation and the box can no longer pull it apart. - Mutations can give rise to abnormally folded proteins, an example being the PRION PROTEIN. Prions bind to correctly folded proteins and convert them to an incorrectly folded form. This can form deposits in the cell and neurodegenerative diseases such as ALZHEIMER’S, PARKINSON’S, and MAD COW. - Some unstructured regions allow for flexibility within a protein. - Coiled coils is a helix wrapped around another helix. Due to some hydrophobic amino acids that might shot up in a regular manner, it can wrap around another section of hydrophobic region on another helix. - Other formations of proteins are dimers, helix, rings, tubes, etc. - Disulfide bonds link together two -SH groups from cysteine side chains that are adjacent in the folded protein. Disulfide bonds do not change a protein’s conformation, but instead acts as an “atomic staple” to reinforce the protein’s most favored conformation. - These bridges are formed from the oxidation of -SH groups. Reduction breaks the disulfide bridge. • Reduction can be done by using the common reducing agent BETA-MERCAPTYL ETHANOL. These can reduce disulfide linkage, break open the protein into a more linear configuration. - Point mutations can change binding sites and make it have a lower affinity for the substrate. Substrates can create a conformational change and actually activate an enzyme by opening up other active sites and allow if it to bind to other substrates. Cyclic AMP and other cofactors can do this. • Binding of any molecule to protein is VERY specific and based on temporary hydrogen bonding. - LYSOZYME is an antibacterial protein because it binds to sugars on the surface of bacteria and cleave them. • Found in tears, egg-whites, saliva. • Glutamic acid and Aspartic acid cause a bond strain in glycosidic bond of the sugar to be cleaved. - Enzymes can alter substrates in different ways: • Forcing molecules together allowing them to grab each others electrons • Binding substrates to enzymes and rearranging the charge leaving a partial positive or partial negative charge making reaction go faster • Strain molecules into a transition state (as seen with lysozyme) ▯ - Feedback inhibition is a NEGATIVE REGULATION as it keeps an enzyme from producing more product. Regulation can also be POSITIVE as the product in the metabolic pathway stimulates activity of the enzyme. ▯ 8 - The tails of histones are subject to covalent modifications such as methylation, acetylation, or phosphorylation. ▯ - DNA Replication • DNA Polymerase adds nucleotides on the leading strand as it runs from 3’--- >5’ (building the new strand from 5’--- >3’). • The enzyme primase places RNA primers which is needed to start replication. • On the lagging strand, a nuclease degrades RNA primer that is placed, repair polymerase then replaces that stretch with DNA. DNA Ligase finally joins the 5’-phosphate end of one DNA fragment to the adjacent 3’-hydroxyl end of the next. DNA Helicases and single-strand DNA-binding proteins unzip the DNA as the polymerase • goes along to replicate. The helices sits at the very front of replication machine using the energy of ATP hydrolysis to propel itself forward and pry apart the double helix. The single-strand DNA-binding proteins bind to the single-stranded DNA and prevent the bases from being bound and keeping them elongated to act as an efficient template. • The unzipping of DNA can cause twisting and tension further down the DNA strand. A build up of tension can greatly impede the replication process. DNA Topoisomerases relieve this tension by nicking one side of the DNA strand allowing the DNA to twist along its single bond. • Another protein, a sliding clamp, keeps the DNA polymerase on the DNA strand to keep it replicating. If it were on it’s own it would only replicate short strands and fall off. • A clamp loader hydrolyzes an ATP each time it locks a sliding clamp around a newly formed DNA double helix. - DNA Repair • The genetic disease xeroderma pigmentosum is when a person lacks the ability to repair damage done by UV light. - DNA Damage • Depurination is the loss of the nitrogenous base. Note that it does not break the phosphodiester bond, so it resembles missing teeth. • Deamination is the loss of the amino group on the base which produces the base uracil. • UV radiation can cause the formation of dimers between two adjacent nucleotides. For example, you can have a thymine-thymine dimer or even a cytosine-thymine dimer! The failure to repair thymine dimers is what causes xeroderma pigmentosum. ▯ ▯ - DNA to RNA to Protein Type of RNA Function Messenger RNAs (mRNAs) Code for proteins Ribosomal RNAs (rRNAs) From the core of the ribosome’s structure and catalyze protein synthesis microRNAs (miRNAs) Regulate gene expression 9 Type of RNA Function Transfer RNAs (tRNAs) Serve as adaptors between mRNA and amino acids during protein synthesis Other noncoding RNAs Used in RNA splicing, gene regulation, telomeres maintenance, and may other processes. ▯ Types of Polymerase Genes Transribed RNA Polymerase I Most rRNA genes RNA Polymerase II All protein-coding genes, miRNA genes, plus genes for other noncoding RNAs (such as those in splicesomes) RNA Polymerase III tRNA genes, 5S rRNA gene, genes for many other small RNAs ▯ - RNA to Protein Aminoacyl-tRNA synthetases covalently couple each amino acid to its appropriate set of • tRNA molecules. ▯ Antibiotic Specific Effect Tetracycline Blocks binding of aminoacyl-tRNA to A site of ribosome Streptomycin Prevents the transition from initiation complex to chain elongation; also causes miscoding Chloramphenicol Blocks the translocation reaction of ribosomes Cycloheximide Blocks the translocation reaction on ribosomes Rifamycin Blocks initiation of transcription by binding to RNA polymerase ▯ ▯ ▯ NAME ROLES IN TRANSITION INITIATION TFIID Recognizes TATA box TFIIF Stabilizes RNA polymerase interaction with TBP and TFIIB; helps attract TFIIE and TFIIH TFIIE Attracts and regulates TFIIH TFIIH Unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase CTD; releases RNA polymerase from the promotor▯ (A kinase that phosphorylates RNA polymerase) 10


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