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Biochemistry Midterm 2 Review.docx

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Department
Biochemistry
Course
Biochemistry 2280A
Professor
Christopher Brandl
Semester
Fall

Description
Biochemistry Midterm Review Topic 7: Lipids and Biological Membranes Biological Membranes  Biological membranes are composed of lipids, proteins and carbohydrates; they play an important role in dividing eukaryotic cells into different compartments  Biological membranes have many important functions, including the following: 1. Separate contents of a cell or organelle from the surrounding environment 2. Control import and export of molecules (e.g. nutrients, waste, ions) into and out of the cell or organelle, using proteins that span the organelle 3. Contain sensors of receptors that allow the cell to respond to external stimuli including communications from other cells 4. They are involved in cell movement Lipids  A biological molecule which has little or no solubility in water (hydrophobic) – but are soluble in organic solvents  Function predominantly as structural components of biological membranes, but also function as energy storage molecules, enzyme cofactors, signalling molecules, and pigments (for colour absorption) Types of Lipids 1. Fatty Acids (amphipathic)  Used for energy storage and structure  Fatty acids are hydrocarbon chains ending with a carboxyl group  Contain an even number of carbons (4–36 in length, 12– 20 for humans)  Can be either saturated (no double bonds) or unsaturated (containing double bonds)  Polyunsaturated fatty acids contain more than one double bond (monounsaturated only contain one) – the first double bond is usually between C9 and C10 (counting from the –COOH end of the molecule)  Unsaturated fats are almost always cis (forming a kink in the chain) and any additional double bonds are usually at every third carbon  Nomenclature: C(# of Carbons):(# of double bonds) (c/t),(c/t)-∆ position of dbl bonds (e.g. C18:2 cis,cis-∆ 9,1)  Alternate Nomenclature: C(# of Carbons):(# of double bonds)(# of double bonded carbon closest to methyl end in brackets) (e.g. C18:2 (n-6))  Older Nomenclature: the terminal carbon is called the omega carbon and you’ll see the abbreviation in the form of C18:2(ω-6)  Effect of fatty acid saturation on blood cholesterol: o LDL: low density lipoprotein—carries cholesterol to tissues o HDL: high density lipoprotein—scavenges cholesterol from tissues o Saturated fats will raise both of these types of lipoproteins o Cis-unsaturated fats will lower LDL and increase HDL lipoproteins o Trans-unsaturated fats ill raise LDL and lower HDL—this is bad as cholesterol accumulates in tissues (can lead to cardiovascular disease) 2. Triacylglycerols (hydrophobic)  Three carbon molecule with 3 hydroxyl groups attached to each carbon  Triacylglycerols are obtained by attaching a fatty acid to each hydroxyl via ester linkage  Most molecules contain two or more different types of fatty acids  Triacylglycerol is used to store fatty acids as energy reservoirs in adipocytes (fat cells) 3. Glycerophospholipids (amphipathic)  Contain both hydrophobic (fatty acid) and hydrophilic (phosphate) regions  Found in membranes  Same as Triacylglycerols, but one fatty acid chain is removed and replaced with a phosphate group  Phosphate group is often conjugated to a polar Terminal OH alcohol, serine or choline 4. Sphingolipids  Are based on sphingosine  If a fatty acid is attached to the nitrogen of, sphingosine via amide linkage the molecule is a ceramide  The terminal hydroxyl group can be modified with phoshoethanolamine or phosphocholine to make sphingomyelins, or glycosphingolipids 5. Steroid – hormones  Based on a system of four fused rings: three with 6 carbons and one with 5 carbons (5 carbon ring is almost planar), this is a Cyclopentanoperhydrophenanthrene ring system  Steroids that have a hydroxyl group at C3 are called sterols 6. Other lipids  Other lipids have structures that do not fit into other classes  Retinol (Vitamin A) is a polyisoprenoid (i.e. long polymer of isoprene) that our bodies convert into retinal, which is a photoreceptor in the rod cells of the retina (Retinol is very hydrophobic) Lipid Bilayers  Glycerophospholipids, sphingolipids and the steroid cholesterol are all amphiphatic – this makes them well-suited to be the basic structural components of biological membranes  In water, glycerophospholipids assemble into bilayers such that hydrophobic groups do not contact the polar solvent (water)  The hydrophilic ―head‖ groups are on the outside of the bilayer and the hydrophilic ―tail‖ groups form the interior of the bilayer  Amphipathic lipids are bonded together by glycerols to form the bilayer  Lipid bilayers are ~5nm thick  Lipid bilayer sheets are flexible, allowing them to be seal up in a spherical vesicle or liposome; thus, preventing their hydrophobic edges from contacting water  Individual lipid molecules can move and diffuse within the plane of the bilayer  The rate of diffusion is determined by a bilayer’s fluidity, there are a few factors which determine the fluidity at a constant temperature: 1. The proportion of unsaturated fatty aycl chains within the glycerophospholipds and spingolipids – Cis double bonds imede tight packing of the fatty acyl chains, increasing fluidity 2. The length of fatty acyl chains present in the glycerophospholipids and sphingolipids – Shorter chains mean more mobility and fluidity 3. The amount of cholesterol in the bilayey – increasing the amount of cholesterol in the membrane reduces the fluidity of the bilayer (cholesterol fills gaps created by unsaturated fatty acyl chains). BUT, at low temperatures cholesterol increases the fluidity of the bilayer by interfering with orderly packing of other lipids.  Biological lipid bilayers are assymetrical (i.e. the lipid composition of one half or surface of the bilayer is different than the composition of the other half) – inner half and outer half may have different types of lipids, giving rise to differing properties  Lipids attached to carbohydrates are called glycolipids and are not normally found on the cytosolic face of the membrane  Cholesterol is evenly distributed to both halves  Assymetry is regulated by phospholipid translocases that are either ATP-dependent (flippases or floppases) or by ATP-independent (scramblases)  Spontaneous flip flop from one side of the bilayer to the other seldom occurs Topic 8: Membrane Proteins  Proteins make up roughly 50% of the mass of a typical biological membrane  Fluid Mosaic Model: Proteins are free to diffuse laterally within the bilayer, unless their movements are restricted by cellular components Functions of Membrane Proteins  Transporters: Move ions and polar molecules which do not readily transport across bilayer to different compartments of the cell or in/out of the cell  Anchors: Pride structural stability to the membrane and help to control the shape of the cell/ its position relative to other cells  Receptors: Sense chemical signals on the outside of the cell and carry the message to the inside of the cell – recognize a very specific molecular signal  Enzymes: Catalyze chemical reactions that are associated with the membrane – many receptors also have enzymatic activities (e.g. insulin receptor relays signal by adding phosphate groups to certain proteins of the cell) Types of Membrane Proteins 1. Transmembrane Proteins (integral membrane):  Associate with both sides of the membrane  Have both hydrophobic (lie in the interior by the hydrophobic tails of lipids) ad hydrophilic (exterior of bilayer exposed to aqueous solution)  The orientation of the protein with respect to the membrane are fixed (same side always faces the cytosol)  Usually exhibit α-helical structure which maximizes the hydrogen bonding between polar backbone groups, minimizing reactions between the backbone and hydrophobic interior of the membrane  Most membrane-spanning α-helices are composed of at least 20 consecutive hydrophobic amino acid residues – making more favourable interactions with the interior of the bilayer  The α-helix does not readily leave the bilayer, because to do so would expose its hydrophobic side chains to water  In some transmembrane proteins, there is multiple α-helices with hydrophobic side chains facing the bilayer and have polar residues facing the other helices giving rise to an aqueous channel  In a few transmembrane proteins, β-strands come together to form a barrel-like shape – the outside of the barrel is hydrophobic and the inside forms aqueous center with polar side chains 2. Monolayer-associated (integral membrane):  Proteins that contact the hydrophobic interior of a protein but only associate with one side of the protein – accomplished by amphipathic helix 3. Lipid-linked (integral membrane):  One or more lipid molecules are covalently attached to the end of the protein or to particular side-chains (usually cysteine)  Lipids are embedded in the membrane but the protein backbone and side chains themselves are not necessarily exposed to the bilayer’s hydrophobicity 4. Protein-attached (peripheral):  Proteins are anchored into the bilayer—they are attached to proteins that are transmembrane, monolayer-associated or lipid-linked  Integral membrane proteins are more difficult to study than peripheral membrane proteins because they are difficult to purify without disrupting the bilayer – detergents must be used to cover hydrophobic regions during purification Topic 9: Carbohydrates  Carbohydrates (or sugars) are one of the main 4 classes of biomolecules Monosaccharides  Monosaccharides have the simple formula (CH O) 2hene n=3–7  Often represented in the form of Fischer projections, which depict stereochemistry— horizontal bonds come out towards viewer, vertical bonds go back behind the plane of the paper  Enantiomers bend plane-polarized light in different directions (D-right, L-left)  When –OH is on right-hand side it is D and when –OH is on left-hand side it is L  If the carbonyl group is at the end of the molecule it is called a ketose, if it is not at the end of the molecule it is called an aldose  Each carbon in a monosaccharide is numbered from the end closest to the carbonyl group Hexoses  A six carbon chain with 4 chiral centers  At the highest numbered chiral carbon, most monosaccharides have the –OH on the right side – rendering most biological sugars to be in the form of their D enantiomer Cyclization  Most pentoses and hexoses are predominantly found in their ring structures (i.e. equilibrium favours the cyclical form in solutions  To form the ring, a hydroxyl group reacts with the carbon of the carbonyl group; this atom is called the anomeric carbon  Monosaccharides are said to be either α or β configuration based on the stereochemistry of the anomeric carbon  The configuration can determined by comparing the position of the hydroxyl formed at the anomeric carbon relative to the highest numbered carbon (the monosaccharide is in its β- configuration when they are on the same side  When a ring forms it adopts α or β configuration randomly  A monosaccharide that exists in its five-membered ring is called a furanose and one that exists in a six membered ring is called a pyranose * -OH on the left of the Fischer projection end up on top Disaccharides  Two monosaccharides can join together in a condensation reaction to form a disaccharides  This reaction occurs where water is released where carbon 1 of β-galactose is joined to carbon 4 of glucose to form a O- glycosidic bond (this is a β(1→4) linkage) – other monosaccharides can be added to form oligosaccharides or polysaccharides  After this linkage has been made, the anomeric carbon is fixed and it cannot interconvert (stuck in β configuration)  Anomeric carbon on glucose can still interconvert as it is the reducing end (it is the reducing end) – this means that lactose, or galactose-β(1→4)-glucose, occurs in two different forms Polysaccharides  Polysaccharide chains can be branched, depending on which hydroxyl groups react  An example of a polysaccharide is glycogen, which is the main storage of sugar molecule in animals, where starch is the energy storage molecule for plants  Glycogen contains chains of 12–14 glucose monomers joined by an α(1→4) linkage – the first chain is covalently attached to the protein glycogenin  Starch contains two components: amylose and amylopectin  Amylopectin (70–80% of starch) contains α(1→4)-polyglucose with few monomers involved in α(1→4) linkages  Amylose (20–30%) contains α(1→4)-polyglucose with very few branch points (very long glucose chains)  Both starch and glucose are easily digested by humans through enzymatic activity Dietary Fibre  Consists of carbohydrates and related polymers that are not digested in the small intestine but may be broken down by bacteria in the large intestine (e.g. Cellulose, Chitin and Pectin)  Cellulose involves a β(1→4)-polyglucose linkages—humans do not have the enzymes to break down beta linkages (i.e. they are not useful for energy purposes) Oligosaccharides as Cell-Coating  Sugars are covalently attached to lipids (glycolipids) and membrane proteins (glycoproteins) in order to provide both protection and lubrication for the cell membrane  Cell needs physical protection from being punctured and is quite lubricated for the purpose of sliding through narrow cappilaries  Lubrication is accomplished because of carbohydrates being well-hydrated (containing a lot of OH groups and water)  Sugars are often used for cell-cell recognition—Lectins are proteins that recognize oligosaccharides on the of cell membranes Summary of Carbohydrates  Sources of energy (polysaccharides are energy storage molecules, mnsaccharides are oxidized to form ATP)  Used for structural purposes (e.g. cellulose)  Part of nucleotides  Linked to lipids or proteins on the surfaces of cells to protect the cells, make them slippery and for recognition purposes Topic 10: Biological Forms of Energy and Reducing Power Gibb’s Free Energy  Reactants ↔ Products  Gibb’s free energy (∆G) is a thermodynamic measure which indicates whether a reaction is nergetcally favourable (spontaneous) or energetically unfavourable  The ∆G for a reaction depends on inherent characteristics of the reaction and the molecules involved  If ∆G=0, the reaction is said to be at equilibrium (occurring both forwards and backwards at the same rate)  If ∆G>0, Reactants are favoured and the reaction occurs non-spontaneously (i.e. requires energy input)  If ∆G<0, Products are favoured and the reaction proceeds spontaneously  Reactions proceed until equilibrium is reached (Le Chatelier’s Principle)  ∆Gº is the ∆G of the reaction under ―standard conditions‖ – provides information about the nature of the molecules involved in the reaction  Note: Enzymes cannot change the ∆G of the reaction, they can only lower the activation energy (i.e. speed up the rate of reaction) Energy Coupling  In order to make an energetically unfavourable reaction proceed, it must be chemically ―coupled‖ with an energetically favourable reaction  This may not always yield an efficient result (e.g. coupling formation of glutamine with cellular respiration: ∆G=-686kcal/mol) – the most efficient coupled reactions have a slightly negative ∆G so energy isn’t dissipated as heat Stepwise Oxidation  Process of combusting glucose on its own is one that requires stepwise oxidation  Slow, controlled release of energy in order to conserve as much as possible for doing work in the body  Cells store energy from food in carrier molecules – allowing for it to be spent a little at a time The Hydrolysis of Adenosine Triphosphate  Adenosine triphosphate exists as the main energy carrier in living systems  The hydrolysis (catabolic) of ATP is an energetically favourable – it involves phosphate being hydrolyzed to yield ADP and inorganic phosphate  The phosphate groups, starting with the group closest to the ribose, are referred to as the alpha (α), beta (β) and gamma (γ) phosphates  The forward reaction is favourable because the release of Pidecreases charge repulsion, the release of P is stabilized by resonance, products are more highly solvated and the I ATP/ADP ratio is usually high (Le Chatelier’s Principle)  ATP is said to have high-energy phosphoanhydride bonds (Note: Even though the breaking of the bond yields a negative ∆G, it has nothing to do with the bond itself; but with the potential energy present in ATP) Formation of Glutamine:  The formation of glutamine is an energetically unfavourable reaction; however it can be coupled with ATP hydrolysis to make the forward reaction proceed spontaneously  ATP accomplishes this by making glutamine more reactive (unstable) in order to react with ammonia  This coupling is enzyme-catalyzed Maximum Energy Usage of ATP  If more energy is required, two phosphate groups (β and ϒ) may be removed to yield AMP and an even greater release of energy  This may be used to make a stubborn reaction occur more readily  ATP is not the only energy carrier used by the body, other phosphate carrying molecules may be (e.g. the conversion of phosphocreatine to creatine may be coupled to the non- spontaneous process of ATP synthesis)  NOTE: Kinetics cannot be determined by the thermodynamics of a reaction  ATP is stable in aqueous solutions Redox Reactions  Involves the transfer of electrons, where one molecule is reduced (i.e. gains electrons) and the other is oxidized (loses electrons)—these two reactions always occur simultaneously  The oxidation stat of carbon increases with the number of electronegative bonded to it Electron Carriers NADH and NADPH  The nicotinamide group of electron carriers NADH (involved in ATP production) and NADPH(involved in biosynthesis) are involved in bodily reactions  A lone pair of nitrogens is carried on the nitrogen in the ring in the reduced form  The electrons are addd onto another molcule when it is oxidizd Reduction of Acetaldehyde to Ethanol  When acetaldehyde is reduced to ethanol, NADH also becomes oxidized to NAD in the process Topic 11: Metabolism and Enzyme Regulation: Basic Concepts Metabolism  Metabolism is the sum of all reactions that happen in a cell  Metabolism includes both catabolism (breakdown) and anabolism (biosynthesis) Metabolic Pathways  Metabolic Pathways are coordinated series of reactions, catalyzed by enzymes and designed to make specific proteins  Generally, catabolic pathways provide energy and reducing power to the cell, while anabolic pathways consume energy and reducing power  Metabolic pathways contain reactions that are coupled together to form a new product  Flux is the rate of conversion from initial reactants to the final product of a metabolic pathway  This conversion is efficient when the net ∆G for the entire reaction is negative  Generally, a metabolic pathway is consists of mostly reactions at equilibrium (∆G≈0), but some reactions with great spontaneity (∆G<<0) and are considered irreversible—adding products has little-or-no effect on the equilibrium of the reaction  At ∆G≈0, the reaction is considered near equilibrium and changes in concentration heavily influence the extent of the reaction (Le Chatelier’s Principle)—Enzymes here catalyze both the forward and reverse reactions at approximately equal rates  Irreversible reactions are the targets of regulation in metabolic pathways, as reactions at equilibrium will have approximately the same concentration of reactants as products Methods of Regulating the Rate of Reaction 1. Concentration of enzyme may be altered by either inhibiting or activating it’s expression during transcription, translation or degradation  This makes more enzyme available for substrate to bind to 2. Concentration of substrate or product to alter the equilibrium of the reaction to either increase or decrease the amount of products/reactants  This does contribute to the rate of the reaction but is difficult to control 3. Enzyme activity may be altered via association with another molecule or protein  This is a short term way to control  E.g. Allosteric regulation, covalent modification, association with a regulatory protein Allosteric Enzyme  Allosteric enzymes has a different (allosteric) site where a molecule (effector) can bind non-covalently to effect it’s activity (i.e. inhibit or activate)  When the effector binds, the active site changes shape to alter the enzyme activity  Often allosteric enzymes are multimeric and contain more than one subunit  There is a distinction between these subunits as regulatory subunits have binding sites which activate or inhibit a protein’s activity (through an allosteric site), while catalytic subunits help the proteins catalyze chemical reaction (through the active site)  The equilibrium of the enzyme’s state depends on the tightness of binding and the concentration of effector present Pyrimidine Biosynthesis in Bacteria  Aspartate carbamoyltransferase catalyzes the first reaction of pyrimidine biosynthesis in E. coli  As the concentration of end product increases, the entire metabolic pathway is turned ff by inactivating the first enzyme of the pathway (Aspartate carbamoyltransferase)  This is necessary because resources (energy) are conserved as a preventative measure to not make more product than necessary  This type of regulating mechanism in multi-step pathways that functions like a negative feedback loop is known as feedback inhibition Covalent Modification  A mechanism of activation or inhibition of enzyme activity by the covalent bonding a molecule  The most common form of covalent modification is by the addition of a phosphate group  Protein kinase is an enzyme which phosphorylates another enzyme or protein  Protein phosphorylase is an enzyme which removes phosphate groups from enzymes or proteins  Side chains with OH groups (serine, threonine and tyrosine) generally have phosphate added to them  You cannot predict whether phosphorylation will activate or inhibit enzymes Topic 12: Carbohydrate Metabolism Carbohydrate Metabolism  Carbohydrate metabolism encompasses 4 key bodily actions: glycogen synthesis and breakdown, glycolysis and fermentation, gluceogenesis, and the pentose phosphate pathway Carbohydrate Storage as Glycogen  Glycogen synthase catalyzes the conversion of glucose-1-phosphate to glycogen using UTP (Equivalent to ATP in energy) as an energy source  Glycogen phosphorylase catalyzes the breakdown of glycogen to glucose-1-phosphate by way of phosphorylation (P)i  Coupled UTP hydrolysis is required to convert glucose-1-phosphate into glycogen Allosteric Regulation in Skeletal Muscle  In skeletal muscle cells, glucose-6-phosphate allosterically activates glycogen synthase, while AMP activates glycogen phosphorylase  ATP and glucos
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