Biochemistry Test 1 - All lectures for biochem test 1 with Dr. B PDF

Preview

Summary

All lectures for biochem test 1 with Dr. B...

Description











 







Carbohydrates o Sugars are composed of C,O, and H  Typically 3-7 carbons  Every carbon has an oxygen linked to it  Can be chain or ring Fatty acids is a long chain of carbons with Carboxylic acid at head o Double bond makes fatty acid unsaturated  Saturated= straight  Unsaturated= kinks o Glycerol sticks out to phosphate polar groups Amino Acids o Amino group (NH3+) Carboxyl group (COO-) and Side Chain o Peptide bond links Amino Acids after NCC-NCC-NCC Nucleic Acids o Make up nucleotides o Base, 5C sugar, and 1-3 phosphates o Typically lots of nitrogen in the base o G,A,T,C, U are 5 nucleotides Lipids: o Molecules that are typically hydrophobic because nonpolar covalent bonds linking the carbons and hydrogens aren’t attracted to the polar bonds of water  Phospholipids have hydrophobic tails and hydrophilic heads  Cholesterol is an example of a steroid where central core is four fused rings of carbon and hydrogen.  Most steroids have structure similar to this Enzymes don’t make unfavorable reactions happen, they just lower the Activation energy Covalent Bonds o Strong bonds that need enzymes to break—cant be broken by heat o Strength depends on size Noncovalent bonds o Can be broken by heat o Weak interactions between ions, molecules, and parts of molecules o All electrostatic by nature (hydrogen, van der waals, ionic) o Increasing the distance weakens the force of attraction Covalent vs Noncovalent bonds o Forces that hold atoms of nucleotides together are covalent. But the forces that hold the two chains of nucleotides together are noncovalent hydrogen bonds. This is key because they are strong enough to hold the chains together but weak enough to separate for DNA replication. Coloumb’s Law: o E=kq1q2 / Dr







Energy trends from coloumb’s law make sense in ionic vs hydrogen. Ionic charges are full charges while partial charges could arbitrarily be called 0.5 and would be less than 1 so it is weaker. Enthalpy vs Entropy o Free energy (/\G), always “sticks” with Enthalpy.  When both (-), Enthalpy driven so spont at low temps  When both (+), entropy driven so spont at high temps o Forming a weak interaction typically will be spontaneous and be enthalpy driven, so spontaneous at low temperatures. D vs L Configuration o Ketone or aldehyde must be on top in Fischer projection o Amino Acids  Every S A.A is L (SL)  Every R A.A is D (RD)  Only exception which is reverse is cysteine due to –SH  L-Cysteine has R chirality  Most Amino Acids are in L Configuration  If in Fischer projection then determine by where NH2 is

o Carbohydrates (Sugars)  For linear sugars, use the bottom –OH group on the straight chain  Use the chirality of bottom hydroxyl o If on the Left then use L o If on the Right then use D



Alpha vs Beta Linkages o Start labeling after the ether with the first carbon being “1”  Alpha has –OH group “anti” to CH2OH. Opposite Sides  Beta has –OH group “Syn” to CH2OH. Same Sides

Lecture: 9/14/17—Central Dogma Theory 





DNA RNA Protein o DNA to RNA is Transcription o RNA to Protein is Translation DNA o Major/ Minor Groove is the width between the phosphates o H-bonding is what keeps the bases bound together but Base Stacking is the stabilization force o Base Stacking energies are significant for DNA Structure  More energy than hydrogen bonds o DNA replication is Semi-conservative  DNA is pulled apart and the new strands are a hybrid of old/new DNA o DNA can come in many forms  A-DNA No major/minor grooves (all same size)  B-DNA Right-handed structure we normally see/ exists in nature  Z-DNA Twists the other way (left-handed) DNA Replication o Replication requires many proteins in a complex  Polymerase reads DNA, assembles new DNA/RNA on strand it is reading o Replication bubble and bidirectional replication





Active site is where chemistry happens  DNA polymerase binds waiting for nucleotide to match one needed at the active site o Read 3’  5’  3’ alcohol attacks the phosphate  alcohol is better Nucleophile o Carbon next to base is 1’ carbon and the carbon next to phosphodiester is 5’ carbon o Polymerase binds to backbone of DNA  Does Not bind to active site  If incoming nucleotide fits, weak interactions line up, catalysis occurs (Nuc added)  If not, bases won’t fit and nothing happens  Polymerase waits for nucleotide to fit, physically doesn’t add them together. o Processivity of Replication  Every time nucleotide is added polymerase slides forward  Sliding forward is due to “Brownian Motion”  Allows the polymerase to slide forward but can’t slide backwards due to nucleotide being added preventing it from sliding back  Video of lottery balls in machine with the rachet (visual)  Requires no specific energy (all random energy)  Can do 700 nucleotides a second Transcription o Transcription occurs over the Open Reading Frame  Only one strand is read over a short period of time o Convert RNA letters to protein  Coding + noncoding strand  Coding strand is strand that “matches” RNA sequence but not read.  Noncoding strand is read by RNA Polymerase and is template. Produces complement bases. o In RNA, TU o In Replication (DNA) there is an H on the 2’ carbon while in transcription, there is an –OH on the 2’ carbon.  However, extension process is the same by connecting via the 3’ carbon o Transcription Assembly and start sites  Promoters:  TATA Box: Rich in TATA which have weaker base stacking energies  Easier to manipulate strands o There are many proteins associated with transcription  Transcription factor  Most factors regulate polymerase binding and assembly



o TATA Binding Protein binds to backbone of DNA and looks for a section of backbone it can fit into and it deforms DNA to fit into that spot o Proteins recognize structure changes, not DNA bases Translation o mRNA processing o In prokaryotes, transcription and translation can be simultaneous o In Eukaryotes, mRNA processing includes adding a 5’ methyl-guanine cap and poly-A tail  Also introns are spliced out and exons are kept  Chemical mechanism of splicing requires 2’ hydroxyl (why only RNA)  Spliced out in form of a lariat (loop) o Need tRNA to convert to protein o Ribosome is a mixture of protein/RNA that reads mRNA, binds to RNA to read, and catalyzes to have energy for AA formation  Composed of small/ large subunit  Need both units for translation o Ribosome binds at 5’ end of RNA and when both subunits bind, it slides to the first AUG o Decoding: Match RNA to tRNA (requires GTP) o Transpeptidation: ? o Translocation: Ribosome slides over 3 nucleotides (requires GTP) o Code is Redundant but not ambiguous o Recognition of the tRNA by the ribosome  Both binding site of the tRNA and mRNA are composed pf nucleic acids so weak interactions are required to do translation o Active site of ribosome  If tRNA matches to mRNA then AA can fit and form into the chain o Termination of Translation  Genes have stop codons to ensure polypeptide chain (protein) is what you need to perform the cellular function...