Biochemistry Notes PDF

1. Proteins perform a wide range of functions = proteins are the main bui...

1. Proteins perform a wide range of functions = proteins are the main building blocks from which cells assemble shape and - provide cell with structure also execute nearly all myriad function - of the complete picture proteins a cell = Proteome - cells have the not all contain same proteome allowing - for specialization functions : - Speed up chemical reactions proteins enzymatic - - defense defensive - protein - antibodies - storage -storage protein -storage of amino acid - transport transport - protein -transport of substance - cellular communication movement - - structural support each three-dimensional shape protein has - unique a -wide range of protein function depends on their Diversity (shape + sizes) L. Amino Acids A a building block of protein -.. - proteins are made from 20 a a.. in unbranched polymers - all amino acids have the same basic structure of acid 3 R -side chain identity amino I Is defined by the R-group H2N- C-COOH it]Scarboxyl ↓ amino groa group & carbon - amino acids are optical somers chiral X carbon atom i s asymmetric -> two m i r ro r - image ↳L they behave differently and D - only La a make proteins -.. - 20 amino acids : Non-polar , hydrophobic : fear water, n o n polar 4- 1. glycine (Gly or G) 2 Alanine. (Ala or A) 3 Valine. (Valor 1) Leucine (Ler CH3 or 1) H32 > - Hsn-coo HsNccool C Hand-coo -Y * z H H H N-c-coo H , H 1)Methionine I 5. Isoleucine (Ile or (Met or 4) Phenylalanine (phe or F) CHs i aromatic I T F 5 &H2 Hz H CH2 CH2 HzN-C-co Hin-C-coo Hand-coo H H 8. Tryptophan (TrporW) 9. Proline (Pro or P E HzC 11 -PA CH2 HsNcoo HzN-C-co H aromatic  polar side chains : hydrophilic (has "OH" or double bonded 0 I 10 Serine (Ser or S) "Threonine (Thrort) 12 Cysteine (cys - we a k or hydrophobic C) 13 Tyrosine (Tyr or E - weak hydrophilic aromatic OH weakly polar - He ofCH As SH Hand-co 1 -H HoNcoo + HIN-c-Coo H H #No H 14 Asparagine (Asn or N) Glutamine (ain or Q) NHz c 0 Polar acids HYDROPHILIC NH = amino : I I CH2 A 9 -.. dechain CH2 CH2 1 + 1 + aspartic acid Asp D - charged H N-c-coo H N-c-coo , , Glu E glutamic acid - charged H H R + Arginine Arg charged electrically charged side chains : hydrophilic lysine Lys K + charged It + Histidine His charged acidic negatively charged : Asparagine Asn N uncharged 17 Is aspartic acid (Asp or D) Glutamic acid (G orE) Glutamine Gin Q uncharged 0 0 0 0 - S = Serine Ser uncharged i I Threonine Thr T CH2 uncharged 1 Y + H N-c-coo Tyrosine Tyr uncharged , H N-c-coo , H H basic : positively charged Non-Polar amino acids: HYDROPHOBIC 19 20 18 Lysine (Lys K) Arginine (Arg or NH2 or R Histidine (His or H) aA -. chain Hst c = NH2t Alanine Ala A nonpolar Tr I Gly i G NH Glycine nonpolar i Valine Val v nonpolar CHz Leucine Leu nonpolar CH2 1 1 1 + + + H N-c-coo Isoleucine Ile I nonpolar H N-c-coo H N-c-coo , , , H H H Proline Pro P nonpolar Phenylalanine PheF nonpolar Methionine MetM nonpolar Tryptophan TrpW nonpolar * Cystine CysC nonpolar  I Amino acids can act as both acids and bases acid-any hydrogen containing substance that is capable of donating protons (Ht) base-molecule o r on able to accept (Ht) protons from an and -function and carboxyl group conizable R-group of a. a as we a k acd base - amino some. or , when acid i s R-group dissolved water, it exist solution as amino lacking Ionizable in - an is in dipolar ion or "zwitterion" > - can act as an acid or base Camphoteric Amino acid bonding molecule made protein is of of acd - up a long chain amino ↳ bonds by covalent peptide proteins polypeptides - = ↓ their amino acid chains chain polypeptide - = - condensation reaction - a 9.. which are in chains a re called residues the chemical of acids side chains roles amino play role determining - a in the 3D structure be of hydrophobic effects hydrophilic residues are found surface - > - on > - hydrophobic residues a re found in the interior ↳ need to avoid wa t e r all start · methionine polypeptides with ↳ START CODON acid refers to as PRIMARY STRUCTURE sequence · amino of a protein  3D structure of Proteins and their functions - 3D structures determine their functions. 4 levels 3 of Protein Structure 3D - each protein has a specific shape and structure Sometimes - 2 proteins (e g antibody and.. virus) can have complementary shapes structure protein is important in va r i o u s ways - > - BCR - Abl > - to of cells etc. can block pathways prevent unhealthy production 4 types of noncovalent interactions -electrostatic interactions - va n der Waals bond hydrogen - -hydrophobic interac tions ↳ water dipole forces hydrophobic a a.. to -Non-polar be on the inside H20 interacts' with , hydrophilic region -polar these bonds involve a to m s in the polyptetide backbone as well as atoms in the amino acid chain - proteins can in principle fold in enormous number of ways -as these a re non-covalent bonds It t a ke s c ova l e n t bonds to many non - hold two of regions polypeptide chain together stability of shape is influenced by the combined strength of large number of non - covalent bonds 4) levels of Protein structure -primary , secondary , tertiary quaternary , when protein consists of t wo m o re polypeptide chains - or primary acid - amino sequence - the final shape is specified by A A.. Sequence  Secondary polypeptides takes on a certain orientation on space - of -result hydrogen bonding > - between C=O of a a and N-H of another one a g in polypeptide backbone.... coiling of the chain results (2) alpha helix (spiral) , - in folding of the chain results (B) beta pleated sheet - a in 4 a 9. interacts -every.. bond hydrogen bondings between atoms of the peptide holds the shape - of a stabilized specific conformations struc tures by -regions in a.. sequences or between of the backbone hydrogen bonds atoms polypeptide B sheets - antiparallel - - parallel B sheets - both common in proteins C-terminus of a r row points towards polypeptide chain - elements of secondary structure pack togetherI n t o stable , independent - foldings - form globular domains 1 multiple globular domains -> protein - ↳ linked by unstructured polypeptide Tertiary final 3D - shape determines molecules the the type of protein can interac t with - - hydrophilic outside hydrophobic > - inside bonding between R-groups - > - covalent > - electrostatic hydrophobic > - > - va n der Walls hydrogen bonding - - disulfide bridges > - two cystine residues in polypeptide chan stabilizes tertiary structure  & Quaternary proteins have some m o re than polypeptide = one structure tertiary with and secondary > - each ow n primary , disulfide bridges and bonds - non covalent -different chains interact with each other S Misfolded proteins cause disease may they can inter fere with the functions of normal proteins - - mutations in proteins coding sequences of the gene structures disease eve n slight change cause - primary in can > - 4. regulations of proteins activity of regulation proteins ↓ protein production (gene regulations. 2 protein degradation. 3 protein localization/transport in subcellular compartments 4) direct and rapid inhibition/activation of at the proteins level of polypeptide chain itself 1 protein production. cell primary defines the amount of protein - in. 2 protein degradation. 3 proteins localization/transport in specific subcellular compartments protein transported into organelles - fate of any protein molecule synthesized in the cytosol depends Its on a. a. Sequence - which can contain "sorting signal" that to directs protein organelle required 4 proteins (e enzymes). the of activity.. g a re often regulated by other molecules (reversible interactions) - Inhibition - transient interactions covalent modifications - structural conformation , regulate - location, interaction repertoire  Lecture 3 14 10. Human Genome 1 :. DNA - Genome transcription W RNA s transcriptome translation N Protein > proteome Proteome - complete set of proteins encoded by the genome of a specific cell or organism at a specific time or under specific set of conditions 3% human only proteome - - proteome varies widely between different cell types in an organism cells -humans typically contain several thousand proteins detected proteins can be and identified by specific molecular interactions - , in most cases using antibodies or ligands for no procedure cloning or amplifying proteins -  Genome (DNA) Proteome (proteins) static (no change with time) dynamic (highly variables with - - can be amplified time ; many proteomes for - - little sample complexity one genomes (4 base pairs, very similar, - cannot be amplified same order of conc ). - high sample complexity (wide -good solubility of variety physical and chemical properties ; come. Can differ various solubility - - proteomes can be analyzed for different purposes : datar a n to : comparing help > elucidate fundamental aspects of biology/physiology - our permit of that also be helpful greater understanding d i s e as e processes may > - in diagnosing and treating disease them? why we study humans - proteins are active biological agents in DNA sequences don't show how proteins function how biological processes occur - or post-transcriptional and post-transitional modifications that affect proteins undergo - their function in health & disease affect 3D structures protein functions health & disease - in drug discovery - - diagnostic/prognostic markers. methodologies 2 chromatography - - centrifuge - SDS-PAGE Immunology - - Western blotting - Fluorescent tagging -mass spectrometry - Biomarkers  Lecture 4 : 14 10. 1. The structure of DNA - life depends on the ability of cells to store , retrieve and translate the genetics instructions required to m a ke and maintain a living organish DNA - genes > - chromosomes > - genomes - our DNA is a "constructional and operational manual" info to "build" and "run" human > - stores body info passed from cell daughter genetic on to its cell - and > - generation to generation Flow of info genetic : DNA -RNA > - protein Finding the Structure of DNA Rosalind of DNA Franklin X-ray diffraction pattern - - Crick , Watson , Wilkins ↳ nucleic acid Structure Acid DNA-Deoxyribose - - two complementary chains of nucleotides - each strand composed of 4 types of nucleotide subunits. - Ademine - Guanine Cytosine - thymine - -two strands held together hydrogen bonds between bases by nucleotides a re composed of nitrogen- - containing base and SC sugar  RNA VS DNA A A G G bases C C W T IDeoxyribose 5C sugar T ↓ ribose - nucleotides a re joined together by phosphodiester bonds between 5' and 3' carbon atoms -chain has a directionality built from 5'- 3' always = - written S' + 3 AATCT - two strands run antiparallel to each other held G = C A T together by hydrogen bonds - = , ↓ 3 bonds 2 bonds A with T C G always with - always , - a purine with a pyrimidine strands double helix-10 5 twist base pairs - i n to. per turn twisting favorable conformation also creates a energetically - important an d -complementary of bases in both copying - DN A repairing A, B 2 , conformations - A ,B 2 all conformation of DNA double helix , A &B right hand - - Z left handed  Copying of the DNA - each strand acts as a template for the new one when double stranded DNA complete there daughter -> is is t wo copying 2. genes are DNA sequence that makes RNA and Proteins to encode information that must copied and transmitted. genes be - - DNA sequence generates a "Linear message" - information is encoded in the order , or sequence of the nucleotides along each DNA strand > - A C ,T G - can be used to spell out biological messages , , - organisms differ from one another because their DNA molecules have different nucleotide sequences of DNA that contains the -gene : a segment instructions for a particular protein making or RNA molecule RNA molecules to m a ke proteins - RNA final - sometimes is product ↳ structural , catalytic , gene regulatory of two each only one the DWA strands actually encodes the > - in gene , info to make RNA contain introns and exons genes > - > - # of each human chromosome genes on varies > - chromosome 1 : 2706 > - Y chromosome : 104. 3 Gene the structure of Typical Human and associated -typical human gene is with regulatory non translated DNA sequence -transcription factors ↳ bind to DNA regulatory sequences (enhancers & promoters) ↳ define of site transcription initiation > - aswell time and of transcription as quantity. 1 DNA Packaged is in Chromosomes Week 4 information - be considered genetic can at several levels - from DNA , to genes , to chromosomes , to genomes eukaryotic cell packaged multiple - is in chromosomes - 23 chromosomes each of linear associated consisting a single enormously long DNA molecule with proteins - , , a typical duplicated m i to t i c chromosome is highly compact - - DNA is replicated during interphase ↳ contains DNA molecule each chromosome two identical daughter - each called a chromatin they separate - once : chromosomes duplication and of chromosomes segregation occur - through an ordered cell cycle chromosomes Interphase occupy - their ow n distinct territories within the nucleus so ch rom os om e s do not become tangled - - each c h ro m o s o m e a re attached to particular sites on nuclear envelope - human cell about 2 m e te r of DNA 2. nucleosomes from chromatin which forms chromosomes which bind to DNA h ave t wo proteins classes - an d bNA Chromatic complex with both proteins nuclear is : - - nonhistone chromosomal proteins histones - ↳ responsible for the first and most fundamental level of c h ro m a t i n packing > - NUCLEOSOME ↳ each n u cle os om e - 8 histone - double stranded DNA (147 paired long)  - linker DNA between nucleosome can vary - nucleosomes condenses DNA and provides the first level of DNA packing of c h ro m o s o m e s that regions contain - genes that a re being expressed (more extended) : Euchromatin those contain silent a re m o re condensed : Heterochromatin genes = - detailed structure of interphase chromosomes can differ from cell to cell determines which are expressed - genes - chromosome at multiple packing o c c u rs levels. 3 all human chromosomes constitute human genome - total number of ~ 2 1 , 000 genes : of depends number genes on the species - -gene density also va r i e s - In addition to protein-coding genes (21 , 000) > - t h e re a re 8 4 75 , that code for RNA CARNA , rRNA , shRNA , miRNA) Week 4. Intro 1 to Enzymes biological catalyst - each step of metabolic pathwaysI s catalyzed by a specific enzyme - -metabolism is composed of many coupled , interconnecting reac tions performed (catatyzed) by ENZYMES also mediate the transformation of for m of into another energy - one quarter of genes human encodes in genome enzymes - and specificity catalytic powers - -take place particular site the called ac tive sites at a on enzyme  few RNA enzymes a re proteins or a re - - Inter molecular forces enzyme brings s u b st r a te s together In an optimal orie n t at ion - > - then m a ke s or b re a ks Chemical bonds. 1 and high affinity bind enzymes usually a substrate with specificity active sites are physical pockets In enzyme where substrate binds and catalytic reactions take place - an. 2 to the active site structural substrate binding induces changes in the enzyme interactions the substrate and the these large of enzyme we a k In - result in changes a number and facilitate the struc tural changes needed to form product Is highly regulated cells. 3 enzyme activity in bioavailability - - amount of enzyme present in cells as a result of regulated gene expression and protein turnover catalytic efficiency - - quantitative m e a s u re of activity enzyme controlled of - can be by the binding regulatory molecules 2 Enzymes. are powerful and highly specific chemical catalysts fac tor of enzymes catalyze re a c t i o n s by as much as a million or m o re - a - enzymes alter the rate of re a c t i o n (AB) without changing the ratio of s u b st rate s and products at equilibrium decrease to reach the time it t a ke s equilibrium - - Inc. rates in both direc tions in both direc tions the same amount how does it wo r k of COFACTORS catalytic activity depends on the presence small molecules - : execute chemical performed acids -cofactors to reac tions that cannot be by the 20 a re able amino apoenzyme + cofactors holoenzyme - = ↳ w i t h out cofactors cofactors metals or coenzymes - :. 3 how does adding an enzyme catalyst inc rate of reaction Chemical transition States transition Conversion of substrates to product involves high st a te - a energy st ate unstable high energy is level which must be reached in o rd e r to convert substrate -> product -energy  DG = difference energy between reac tants and products for need to operate t wo themodynamic properties : enzymes you -free difference (DG) energy -defines wether the reaction will take place spontaneosly energy required to initiate the conversion of reac tants i n to products (auF) -rate of reac tion lower AGF Enzymes DG : 1 -reaction If DG will t a ke place spontaneosly. = - exergonic/exothermic - 2 at equilibrium system -. - DG = 0 3. If DG cannot t a ke