BIOCHEM2280 - Biochemistry And Molecular Biology

CHEMISTRY BASIS OF LIFE Topic 1 Major Biological Polymer: Proteins Nucleic Acids Polysaccharides Four Major Biomolecules: Amino acids Carbohydrates Lipids Nucleotides Amino Acids Topic 2 Proteins are composed of amino acids based on genetic code DNA can encode 20 different acids to make protein Structure of Amino Acids: 20 amino acids in four classes Stereoisomers possible, D and L forms possible Proteins only contain L-amino acids amino acids have an alpha carbon that is attached to a carb

Chemistry Basis of Life Topic 1 Major Biological Polymer: Proteins Nucleic Acids Polysaccharides Four Major Biomolecules: Amino acids Carbohydrates Lipids Nucleotides

CHEMISTRY BASIS OF LIFE Topic 1 Major Biological Polymer: Proteins Nucleic Acids Polysaccharides Four Major Biomolecules: Amino acids Carbohydrates Lipids Nucleotides Amino Acids Topic 2 Proteins are composed of amino acids based on genetic code DNA can encode 20 different acids to make proteins Structure of Amino Acids: 20 amino acids in four classes Stereoisomers possible, D and L forms possible Proteins only contain L-amino acids amino acids have an alpha carbon that is attached to a carb

NUCLEIC ACIDS Unit C NUCLEIC STRUCTURE Topic 14 Nitrogenous Bases two types of bases 1. Purine adenine guanine 2. Pyrimidine cytosine thymine/uracil (differ by methyl) the ring structure of all nitrogenous bases are essentially flat flat surfaces of the bases are relatively hydrophobic edges have hydrogen bonds Nucleoside a molecule which nitrogenous base attached to a sugar the base is attached at the anomeric carbon two sugars used are ribose and deoxyribose Nucleotides add one or more pho

NUCLEIC ACIDS Unit C NUCLEIC STRUCTURE Topic 14 Nitrogenous Bases two types of bases least soluble part of nucleotide in water 1. Purine adenine guanine 2. Pyrimidine cytosine thymine/uracil (differ by methyl) the ring structure of all nitrogenous bases are essentially flat flat surfaces of the bases are relatively hydrophobic edges have hydrogen bonds Nucleoside a molecule which nitrogenous base attached to a sugar the base is attached at the anomeric carbon two sugars used are ribose and

NUCLEIC ACIDS Unit C NUCLEIC STRUCTURE Topic 14 Nitrogenous Bases two types of bases least soluble part of nucleotide in water 1. Purine adenine guanine 2. Pyrimidine cytosine thymine/uracil (differ by methyl) the ring structure of all nitrogenous bases are essentially flat flat surfaces of the bases are relatively hydrophobic edges have hydrogen bonds Nucleoside a molecule which nitrogenous base attached to a sugar the base is attached at the anomeric carbon two sugars used are ribose and

NUCLEIC ACIDS Unit C NUCLEIC STRUCTURE Topic 14 Nitrogenous Bases two types of bases 1. Purine adenine guanine 2. Pyrimidine cytosine thymine/uracil (differ by methyl) the ring structure of all nitrogenous bases are essentially flat flat surfaces of the bases are relatively hydrophobic edges have hydrogen bonds Nucleoside a molecule which nitrogenous base attached to a sugar the base is attached at the anomeric carbon two sugars used are ribose and deoxyribose Nucleotides add one or more pho

Amino Acids Topic 2 Proteins are composed of amino acids based on genetic code DNA can encode 20 different acids to make proteins Structure of Amino Acids: 20 amino acids in four classes Stereoisomers possible, D and L forms possible Proteins only contain L-amino acids amino acids have an alpha carbon that is attached to a carboxyl group and an amino group as well as a R group that is different for every amino acid, everything else is the same (except proline kind of) Major Properties of Si

NUCLEIC ACIDS Unit C NUCLEIC STRUCTURE Topic 14 Nitrogenous Bases two types of bases 1. Purine adenine guanine 2. Pyrimidine cytosine thymine/uracil (differ by methyl) the ring structure of all nitrogenous bases are essentially flat flat surfaces of the bases are relatively hydrophobic edges have hydrogen bonds Nucleoside a molecule which nitrogenous base attached to a sugar the base is attached at the anomeric carbon two sugars used are ribose and deoxyribose Nucleotides add one or more pho

NUCLEIC ACIDS Unit C NUCLEIC STRUCTURE Topic 14 Nitrogenous Bases two types of bases 1. Purine adenine guanine 2. Pyrimidine cytosine thymine/uracil (differ by methyl) the ring structure of all nitrogenous bases are essentially flat flat surfaces of the bases are relatively hydrophobic edges have hydrogen bonds Nucleoside a molecule which nitrogenous base attached to a sugar the base is attached at the anomeric carbon two sugars used are ribose and deoxyribose Nucleotides add one or more pho

NUCLEIC ACIDS Unit C NUCLEIC STRUCTURE Topic 14 Nitrogenous Bases two types of bases least soluble part of nucleotide in water 1. Purine adenine guanine 2. Pyrimidine cytosine thymine/uracil (differ by methyl) the ring structure of all nitrogenous bases are essentially flat flat surfaces of the bases are relatively hydrophobic edges have hydrogen bonds Nucleoside a molecule which nitrogenous base attached to a sugar the base is attached at the anomeric carbon two sugars used are ribose and

Protein Structure and Analysis Topic 3 Proteins are linear polymers of amino acids size 50 to greater than 30 000 amino acids Nomenclature Dipeptide: peptide chain with two amino acids Tripeptide: peptide chain composed of three amino acids Oligopeptide: peptide chain with 3-20 amino acids Polypeptide: many amino acids Protein: molecule composed of one or more polypeptide chain Peptide Bond In polypeptide each amino acid is a residue Always N-terminus first on left then C-terminus on right R

Protein Functions Topic 4 underlies almost everything that happens in cell including variants and PTM's (post-translational-modification) several hundred thousands Phosphorylation each amino acid with hydroxyl group (Ser, Thr, Tyr) can be phosphorylated by kinase enzymes creates side chains with two (negative) charges phosphorylation like off and on switch can turn off enzyme phosphatase (removes phos group) Ligand-Building Proteins reversible interactions many proteins contain sites to wh

Enzyme Catalysis Topic 5 Biological catalyst Perform nearly all chemical transformations in cell Accelerate but are unchanged by rxn Most enzymes are proteins (some RNA) Name often ends in -ase products of billions of years of evolution Substrate; molecule on which enzyme acts Specificity many enzymes recognize only one or few from hundreds thousands kinds of molecules in cell Fidelity Enzymes almost never make mistake Result in close to 100% yield Rapidity Enzyme can accelerate rxns

Lipids and Biological Membranes Topic 6 Lipids - one of the main classes of biomolecules very little solubility in water soluble in organic solvents can be enzyme cofactors or signalling molecules Classes of Lipids Fatty Acids hydrocarbon chains that end in -COOH usually linear and even number of carbons can vary in length 4-24 carbons saturated - no double bond monounsaturated - one double bond usually between 9-10 carbons almost always cis, forms bend/kink polyunsaturated - two or

Carbohydrate Structure Topic 7 important source of energy, cell-cell recognition coating to protect cells monosaccharides - basic unit of carbs Monosaccharides general formula (CH2O)n -> n is usually between 3-7 name carbon monomers by numbers of carbon all monomers have carbon=oxygen central carbon is chiral therefore has enantiomer can draw fischer projections to represent monomer D - Glyceraldehyde (most are D) OH on right L - Glyceraldehyde OH on left Aldoses - aldehyde Ketoses -

FUndamental Concepts of Metabolism Topic 8 living organisms built to maintain physical structure import and export passing genes to prodigy all of these tasks involve chemicals Gibbs Free Energy (G) G = amount of energy available to do work in chemical solution (some molecules in aqueous solution) G depends on: Chemical nature molecule Environmental conditions (Temperature, Pressure, Concentration) concentration increases, equals increase in G determines if forward/reverse rxn favoured ΔG

Glycogen metabolism Topic 9 polymer of glucose monomers found in livers and muscles Muscle: storage for cell goal - make ATP for muscle used by individual/muscle cells Liver: exists as energy reserve for entire body when blood glucose decreases, liver breaks down glycogen and sends - supply blood and organs with glucose Glycogen when G6P abundant some converted to G1P equilibrium removes phosphate carbon 6 ⟶ to carbon 1 G1P can be added to glycogen polymer - unfavourable need energy rxn c

Citric acid cycle Topic 10 pyruvate 3-carbon molecule that can be oxidized further ultimately to 3 CO2 molecules pyruvate made in cytosol pyruvate further oxidized in mitochondria some intermediates glycolysis and CAC are used in to synthesize amino acids and other essential molecules precursors for synthesis amino acids when degraded can be used as intermediates of CAC 1 g protein = 1g carbon ⟶ for ATP production The Mitochondria two membranes outer membrane relatively large pore that al

Oxidative phosphorylation Topic 11 electrons don't directly go from NADH/QH2 to O2 are passed from one electron carrier to another (ETC) Cofactors protein bound, non-protein chemical species some proteins require chemical 20 AA's don't have therefore need cofactors Electron Carriers 6 types of electron carriers in the ETC Nicotinamide electron carrier group of NADH and NADPH carries 2 electrons on ring bind transiently to proteins as co-substrates Flavins is alloxazine ring derived from vitami

lipid metabolism Topic 12 Release Acetyl-CoA from fatty acid storage breakdown triacylglycerols to make fatty acids main point: to release fatty acids from storage so that they can be broken down to acetyl-CoA release fatty acids from triacylglycerols is promoted by hormone ⟶ glucagon (indicates low blood glucose concentration) therefore body taps into fatty acid storage as less carbohydrates are available when blood glucose is high ⟶ insulin this inhibits breakdown of triacylglycerols when

Summary of Metabolic pathways Topic 13 Overview Energy Metabolism Fed State carbs ingested, will increase concentration glucose in blood will induce pancreas to release insulin tissues will take up glucose from blood via transporters and phosphorylate to glucose-6-phosphate, trapping glucose in cell G6P multiple uses insulin has effect up-regulating glycolysis so some G6P will convert pyruvate which further oxidized in CAC oxidative phosphorylation also active to produce ATP as ATP sup

Nucleic Acids Unit C Nucleic Structure Topic 14 Nitrogenous Bases two types of bases 1. Purine adenine guanine 2. Pyrimidine cytosine thymine/uracil (differ by methyl) the ring structure of all nitrogenous bases are essentially flat flat surfaces of the bases are relatively hydrophobic edges have hydrogen bonds Nucleoside a molecule which nitrogenous base attached to a sugar the base is attached at the anomeric carbon two sugars used are ribose and deoxyribose Nucleotides add one or more ph

DNA Replication Topic 15 DNA replication is very important DNA replication is semiconservatitive each double helix produced contains one strand from original double helix and a newly synthesized one each original strand template that's copied to make new complementary strand sequence one strand dictates sequence of others should be DNA Replication Four Steps Initiation Priming DNA Synthesis - proofreading Ligation Initiation in E. Coli bacteria like E Coli have small circular genomes E Coli ha

DNA Repair Topic 16 DNA Damage any unintended physical or chemical change in DNA information contained in sequence of DNA represents genetic instructions RNA continually being synthesized and degraded - transcription DNA in cells is permanent chromosomes are large and subject to damage sometimes changes DNA good often its damage effects DNA damage harmful to proper function reduced cell function cancer can even be caused this reasons cell strive preserve/protect DNA cells have evolved repair me

Molecular Basis of Cancer Topic 17 cancer can strike victims of all ages cancer more prevalent as pop ages attributed to the accumulation of errors in our cells genomes cancer is characterized by genetic and biochemical defects Cancer as a Genetic Disease susceptibility to cancer can be inherited retinoblastoma (eye cancer) xeroderma pigmentosa (skin cancer) some forms of breast cancer, prostate, ovarian, and intestinal this is why doctors take your family history Genetic Predisposition means

Prokaryotic (bacterial) Transcription Topic 18 bacteria and archea both prokaryotes transcription and translation are very different Transcription purpose of RNA first step in expression of any gene (highly regulated) RNA modified copy information found in DNA RNA production important 1st step in defining how much certain protein product made at a given time RNA can assume many functions that DNA cannot transfer RNAs ribosomal RNAs micro RNAs provides amplification of material available for

Eukaryotic Transcription Topic 19 much of bacterial and eukaryotic is same DNA that is replicated is not transcribed at the same time replication and transcription spatially separated Differences: Transcription of Eukaryotes and Bacteria In Proteins bacteria have one main RNA polymerase eukaryotes have 3, some have 5 eukaryotes don't need sigma factor but use transcription factors Rho not required in eukaryotes No Operons in Eukaryotes every gene in eukaryotes have own promoter Promoter Str

RNa Processing Topic 20 primary transcript kept at 5' end shortened polyadenylated at 3' and spliced to take out unneeded sections 5' Capping protects the 5' end of mRNA from degradation necessary for transport to the nucleus reverse methylated G nucleotide added to 5' end can't be easily cleaved by endonucleases so protects degradation 3' Capping tail of A nucleotides added these tails usually around 300 bases long can be longer or shorter special protein poly-A binding protein binds t

Translation Topic 21 during translation, genetic code deciphered as 3 RNA bases that code for one amino acid Genetic Code is the dictionary that allows us to translate four RNA bases into 21 amino acids genetic code spells out amino acids in 3-letter word codons RNA read in sections of three bases → each section is one amino acid every organism has 20 amino acids not every organism: 21 → selenocysteine (in humans) 22→ pyrrolysine How many Codons?4 x 4 x 4 = 64 codons 3 letter codes and 4 let

Recombinant dna tech Topic 22 these techs allow us to engineer living organism to have desirable properties or abilities techs moved us into era synthetic biology FoxP2 Gene → Guided Example patients struggle with complete sentences and tongue movements gene located on chromosome 7 want to clone gene to: determine sequence purify protein and investigate properties clone → copy of original E.coli commonly used for cloning Expressing FoxP2 in E.Coli determine which tissues express FoxP2 isol

Sequencing Genomes Topic 23 Steps in Genome Sequencing Create genomic DNA library Generate many independent sequencing reads Align independent reads into contiguous sequences (contigs) Fill gaps between contigs Annotate genome Example: Haemophilus Influenzae does not cause influenza it is a human pathogen gram (-), free living, self-replicating bacterium Genome Sequencing Strategies Genome Sequence Consecutively get sequence one section of genome (limit number of bases read) back then 500