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| Learning Biochemistry With Val by ValentineMary(m): 12:50pm On Aug 05, 2016 |
As much as I am a physics enthusiast, I am deeply concerned on how the biological scientist has been relegated leaving the physics and ICT guys to be having a swelled day. So I want to bring back biochemistry in a cool and easy way. I know what u think, that biochemistry is for saddist and old men with white hair. Well that's not exactly true. It is a very interesting subject. So this thread is going to be in series starting from simple to a little advanced biochemistry. Enjoy.  |
| Re: Learning Biochemistry With Val by ValentineMary(m): 2:30pm On Aug 05, 2016 |
Biochemistry is simply the study of the chemistry of living things. Any other additional definition is jara. It studies plants, bacterias, protozoa, mammals, etc. But it mostly study it at the cellular level because it is at this level that many of the metabolic reactions are determined from energy production, food digestion, hormonal action, genetic inheritance, etc. There are several biomolecules that are building blocks in all cells viz 1. Amino acid 2. carbohydrate 3. nucleic acid 4. lipids Every structure in ur body is made up of these biomolecules. Now let us look at them and their characteristics. [b] AMINO ACIDS These are the building blocks for protein, there are thousands of amino acid in nature but only 20 are common in proteins viz: alanine, glycine, valine, leucine, isoleucin, glutamine, asparigine, glutamic acid, aspartic acid, lysine, arginie, methionine, cysteine, proline, histidine, phenylalanine, tyrosine, tripthophane, serine, and theronine. Don't bother about memorizing the names now. . These molecules are important because proteins are very important for living things. They make up our hormones, enzymes, food, etc a single protein may have about 1,000 amino acid sequence and they must be at the right position else bye bye to a normal life. for example sickle cell is caused by a substitution of valine instead of glutamine at position 6 of the beta chain haemoglobin.One significant thing in the structure of all amino acid is the presence of an amino group and a carboxylic group. CARBOHYDRATES These are also called sugars, they have the general formular C x (H2O) y · They are the most common biomolecules in the cell and are primary source of energy due to their abundance.They are used to make ourwooden tables, papers, etc. But in the cell they help with structure. There are several types which can be grouped based on number of carbon atoms or chains of sugars attached together. According to number of carbon atoms they are: 1. Three carbon sugars: The only 2 molecules that belong to this group are triglyceraldehyde and dehydroxyacetone. They are the most simple carbohydrates. 2. Four carbon sugars: These ones are more numerous than the ones above eg erthyrose and therose. They are vital in many reactions in our body. 3. five carbon sugars: These have 5 carbons and are extremely important to living things eg ribose is used to make DNA. example include ribose, xylose, xyloluose, arabinose, etc. 4. six carbon sugar: These are the most common in living things eg glucose, fructose, mannose, galactose, etc 5. seven carbon sugar: This is extremely rare in nature eg sedoheputulose. They can also be grouped into monosaccharide if they have only 1 sugar, disaccahride if they have 2 eg lactose, maltose, triscaharride if they have 3 eg raffinose, polysaccaharide if they have plenty eg starch. In futher lectuers we would see how these molecules are important. NUCLEIC ACID Without these molecules life as we know it would not exist. They make up our DNA and RNA. They include adenine, guanine, thymine, uridine and cytidine. But molecules like uridine are found only in RNA while thymine is found only in DNA. These molecules are also arranged in a particular order just like amino acid if there is a distortion it would lead it genetic defect. The RNA is responsible for protein synthesis (we would look at this later on). The DNA splits to give RNA which is read in the cells in code to give protein. So a defect in DNA would lead to adefect in protein. That's why genetic defect could be fvcking dangerous. LIPIDS These ones are different from the rest because they don't form giant molecules like the rest. That's why they ain't polymers.  They aid in transportation of many molecules and are large energy storage molecules which also help as insulators against heat. They are also insoluble in water and polar solvent but are soluble in non polar solvent like benzene. Examples include fatty acids, acyl glycerol, sphingolipids, cholesterol, etc. Fatty acids are grouped based on the number of carbon atoms they contain. They also have a COOH group attached to the end. they include 1. lauric acid (12 carbon atoms) 2. myristic acid (14 carbon atoms) 3. palmitic acid (16 carbon atoms) 4. stearic acid (18 carbon atoms) 5. arachic acid (20 carbon atoms) Fatty acid joined to phosphoglycerol to give acyl glycerol with the elimination of a phosphate group. If it is 1 then it is mono acyl glycerol, if it is 2 then it is diacyl glyceol, and if it is 3 it is triacyl glycerol. Cholesterol are forned from an entirely different reaction involving acetyl coA. So this is the introduction to biochemistry as we have outlined the biomolecules. Next time we go deeper. |
| Re: Learning Biochemistry With Val by johnydon22(m): 9:10am On Aug 06, 2016 |
Bring it on Val. . . we are waiting |
| Re: Learning Biochemistry With Val by Krasid(m): 5:39pm On Aug 06, 2016 |
Nice write-up.I would love to learn more about Nucleic acid.Plus, how come lipids is not a polymer but is classified along with Carbohydrates, Protein, and Nucleic acid as biological macromolecules.It would be really helpful in a course I am studying next semester.Thanks. |
| Re: Learning Biochemistry With Val by ValentineMary(m): 7:20pm On Aug 06, 2016 |
Krasid:Lipid is not a polymer because it can't form long chains like others. That's why we don't call it macromolecules rather bio molecules.I would update later on glyco biology, protein chemistry and nucleic acid chemistry. |
| Re: Learning Biochemistry With Val by Nobody: 10:10pm On Aug 07, 2016 |
....I wanted to create a thread like this but I am way too lazy lol  Ride on, OP |
| Re: Learning Biochemistry With Val by Edenoscar(m): 1:10am On Aug 08, 2016 |
following |
| Re: Learning Biochemistry With Val by ValentineMary(m): 4:56pm On Aug 08, 2016 |
Sorry for the delay guys. CARBOHYDRATES I know we did carbohydrates before but that was a summary today we would do it in details. Carbohydrates have basically 2 structures viz the fisher and Howart structure. The Fisher structure is linear while the Howart structure is cyclic in nature adopting either the furanosal or pyranose structure. The furanosal structure have 4 carbons in the ring and an oxygen molecule while pyranose has 5 carbon and an oxygen molecule in the ring. Now in the Fisher structure have 2 families the aldose (CHO) and the ketoses (C=O). Carbohydrates can be drawn in their fisher or howart structure. Carbohydrates can either be in the D or L configuration depending on how they rotate light.The D configuration bends light to the right while the L bends light to the left. Also they can exist in the alpha or beta configuration based on the orientation of the -OH group of the first carbon. So don't get scared if u see sh*it like alpha-D- glucose. In a 2D drawing it is alpha if the OH in the first carbon (anomeric carbon) is faced downward and beta if upward. Example of aldose sugar include erythrose, glyceraldehyde, lyxose, glucose, galactose, maltose, etc while examples of keto sugars are fructose, sorbose, xylulose, dihydroxylacetone, erythrulose, etc. Now we have some sugar derivatives which are gotten when a compound or groups of compounds are attached to a sugar. example glucose-6-phosphate can be gotten when the hydrogen of the OH group of carbon 6 in glucose is replaced with PO 3 2- (this molecule is very essential for energy production from glucose. Another is N-acetyl-beta-D-glucosamine which can be gotten when the OH group in carbon 2 of glucose is replaced with NHCOCH3. This is the basic monomer for chitin (exosekelton for insects). How are disaccharides formed  They are formed from a simple condensation reaction involving 2 monosacharrides. They form basically 2 types of bonds the alpha and beta bonds. The aplha or beta depends on the orientation of the OH group as discussed earlier eg maltose forms alpha 1>4 glycosidic bond because 2 molecules of glucose joined with the anomeric alpha carbon bonding to carbon 4 of the other glucose. Now get this maltose= glucose + glucose sucrose= glucose + fructose lactose = glu + galactose. PS: Humans can't eat food containing a beta glycosidic bond. That's why many humans can't take raw milk (are u suprised?) though we can take it as kids but as we grow, we lose the ability because we lose the enzyme for breaking the beta bond. Polyscahharides are formed from a very complex reaction. The most popular being the calvin cycle. They are joined by glycosidic bonds to point infinity They are stored as starch in plants by alpha 1>4 and 1>6 glycosidic bond and glycogen in animals by thde same type of bonds but the difference is that in starch u only see aplha 1>6 bond after 24-30 glucose but in glycogen it is after 8-12 glucose. That means glucose is more packaged than starch.Starch is our main source of food. But the plants also have cellulose which are carbohydrates linked by beta bonds. They make up most percentage of wood (now u see why we can't eat wood even though they are carbohydrates) I love carbohydrates so much because they are our main source of food thus they sustain our lives. But next time we would look at a more important life sustaining compound responsible for the evolution of life. The nucleic acid or rather DNA and RNA. |
| Re: Learning Biochemistry With Val by ValentineMary(m): 2:52pm On Aug 09, 2016 |
Nucleic acid This is by far the most important group of bio molecules they are the energy currency in the cell, they carry information from generation to generation, they have enzymatic roles (RNA), etc. This is the bio molecule responsible for life as we know it, without it, we would not have lives neither are we going to look alike as humans It is composed of basically 5 types of nitrogenous bases and a phospho ribose sugar. These bases are guanine, adenine, tymine, uracil and cytidine. These 5 can be grouped basically into 2 groups. 1. Purine: Guanine and adenine 2. pyrimidine: uracil, cytidine and thymine. Pyrimidine ALWAYS binds to purin in DNA. That is adenine binds with thymine with a double bond while guanine binds with cytosine with a triple bond thus the guanine-cytosine bond is stronger. Uridine is found only in RNA and RNA are single strands so they don't form bonds. And thymine is found only in DNA. These nucleic acid are also the primary source of energy to the cell. ATP being the most comon is adenosine tri phosphate which many of us who did elementary biology are familiar with. It is simply adenine bond to a ribose and a triphosphate group. We also have others like GTP (guanine tri phosphate), ADP (adenine di phosphate), AMP (adenosine mono phosphate), etc The DNA is a double helix structure that carries genetic info. The structure was discovered by James Watson and Francis Crick but not without help from Rosalind Franklin and Maurice Wikins. The structure can be unwound and wound back again. When unwound so as to be read and converted to RNA for protein synthesis, the unwinding begins at the adenine thymine bond because it is weaker before it gets to the stronger guanine cytosine bond. The Chagaff's rule clearly makes known how DNA works in living things. CHARGAFF RULES 1. DNA compoitions varies from one organism to the other. 2. DNA specimen from different tissues of the same specie has the same composition 3. DNA composition is constant throughout life 4. The number of adenine equals that of thymine while that of guanine equals that of cytosine in DNA. DNA could exist either in the A, B or Z form. But the most common in humans are the B form. We also have some 3 stranded DNA called hoogsteen DNA (but this is a little advanced for this stage) RNA are the bio molecules responsible for protein synthesis. They also play enzymatic role in cells. We have 3 types of RNA viz: mRNA (messenger RNA), tRNA (transfer RNA) and rRNA (ribosoal RNA). The method for how they synthesize protein is quite easy. Messenger RNA carries the codes to the ribosome, transfer RNA interpretes the RNA code while ribosomal RNA brings the amino acid specific for each code (remember that amino acids are the building block for proteins) eg AUG (adenine uracil guanine) code for methionine (3 nucleotides code for 1 amimo avod). This leads us to the central dogma of molecular biology viz DNA>RNA>protein. But there are exceptions when reverse transcriptase is involved. Have a nice day. |
| Re: Learning Biochemistry With Val by linztech: 4:46pm On Aug 10, 2016 |
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| Re: Learning Biochemistry With Val by emilfischer(m): 6:45am On Aug 11, 2016 |
ValentineMary:actually it tryptophan not tryptophan love this post keep it up |
| Re: Learning Biochemistry With Val by ValentineMary(m): 10:28am On Aug 18, 2016 |
Waw it's been a while I updated. Sorry for the delay guys. Let's look at protein chemistry. Protein Protein is responsible for almost every proces in thr body. From metabolic reaction, to locomotion and even gene replication. As we learnt earlier, amino acid is the building block for proteins and they are grouped into several parts according to their chemical structure. 1. Aliphatic amino acid: These are straight chain amino acids which can contain a branch at certain points. They are insoluble in water but soluble in non polar solvents like benzene. viz: Glycine (gly), alanine (ala), proline (pro), valine (Val) , leucine (leu), isoleucine (ile), and methionine (met).2. Aromatic group: These contain a benzene ring. Viz phenylalanine (phe), tyrosine (tyr), and tryptophane (trp). 3. Polar group: These ones are soluble in water. Serine (ser), theronine (thr), cysteine (cys), asparagine (asn), and glutamine (gln). 4. Positively charged group: These cintain an extra -NH3 + group that makes them positively charged. Lysine (lys), histidine (his), and arginie (arg). 5. Negatively charged: This contains an extra COO- group that confers a negetive charge on it. Aspartate (asp) and glutamate (glu). These are the grouping on the 20 common amino acids found in protein. We also have thousands of other amino acid but we would not deal with those now. Amino acid are also classified based on how they appear in our diet and body. The essential amino acids are amino acids that are naturally lacking in our body and we need to take it in our diet viz His, ile, leu, lys, met, phe, thr, try, val, gly, cys, pro, gln, and arg. Non essential are already in our body so no further need for it being in our diet. Ala, Asn, asp, glu, and ser. Protein function based on their 3D structure. Thus how protein folds is very important to how they behave. The types of structures protein have are primary structure, secondary structure, tertiary structure and quaternary structure. The primary structure of protein involves the -NH2 of an amino acid binding to the COOH of another amino acid to form a planer rigid structure. They form a peptide covalent bond this is fvcking hard with a carboxyl terminus and an amino terminus. The secondary structure of protein are in 2 forms, the alpha helix and beta confirmation structure. Though the beta structure is rare, the alpha structure is more predominant. It was discovered by Pauling and Corey based on the orientation of polar groups such as COO and NH. Pauling and Corey also proposed the beta structure (bad guys) based on peptide backbone arrangment. Here it is more like a zig zag rather than helical structure. These are common in globular proteins. The overall 3D arrangement of all atoms in a protein is referred to as tetiary structure. While some proteins contain 2 or more sepeate polypeptide chains which can w identical or different, this constitutes the quaternary structure. We would not go details info protein 3D structures now so as to keep it easy. |
| Re: Learning Biochemistry With Val by ValentineMary(m): 5:03pm On Aug 18, 2016 |
Lipid chemistry These are a group of compounds that don't dissolve in water. Unlike other bio molecules treated above, they don't form polymers because they can't make long chains but they are very important in cell functions. They help as energy reservoir, they help against mechanical injuries, they aid as transporters in cell, etc. We have severak types of lipids like fatty acid, triacyl alycerol, sphingolipid, cholesterol, and so many lipid derivatives. Fatty acids: These are derivatives of hydrocarbons except that they have a COOH group at their end. They range from C4 - C 36 and can either have a double or single bond. The longer the carbon chain, the less soluble they are in water. The most common are even numbers but the longer the chain, the more energy it stores (we would look at this proper when we start metabolism) examples include 12 carbon is Lauric acid 14 carbon is myristic acid 16 carbon is palmitic acid 18 carbon is stearic acid 20 carbon is arachidic acid 24 carbon is lignoceric acid 16 carbon with double bond at position 9 is palmitoleic acid 18 carbon with double bond at position 9 is called oleic acid 18 carbon with double bond at positions 9 & 12 is linoleic acid 18 carbon with double bond at positions 9, 12 & 15 is called linolenic acid 20 carbon with double bonds at positions 5, 8, 11, & 14 is called arachidonic acid PS: These double bond always appear in the cis configuration to allow proper packaging in cells. They form micelles when dissolved in water. Triacyl glycerol: These are esters of the reaction between fatty acid and glycerol. They are derived from a phosphoglycerol. they are named based on the fatty acid attached to it. Eg if 3 palmitic acid molecules is attached to it, u call it tripalmitine, if it is 1 steric acid at position 1 and 2 arachidic acid, u name it 1-steroyl diarachidic glycerol. They are hydrophobic molecules (water hating). They are also good energy stores. Cholesterol is mainly derived from a compound known as acetylcoA. They are our main and only source of vit D. Their metabolism is quite complex so I would not talk about that now. |
| Re: Learning Biochemistry With Val by ValentineMary(m): 5:42pm On Aug 20, 2016 |
I'm sorry folks I have to stop this thread because it seems the mods are not comfortable with it as they always bring down my post each time I update unless I beg them. |
| Re: Learning Biochemistry With Val by mkmyers45(m): 2:24am On Aug 23, 2016 |
Please continue your posts. The antispam bot is just on the fritz |
| Re: Learning Biochemistry With Val by ValentineMary(m): 8:56am On Jan 13, 2017 |
Hello guys, so I got pissed and abandoned this thread. But I don calm down so let's proceed. |
| Re: Learning Biochemistry With Val by ValentineMary(m): 12:41pm On Jan 14, 2017 |
Since we are done with biomolecules, let us go to what makes biochemistry different from biology. PATHWAYS Okay what are pathways It is a mechanism by which the body carries out metabolism which is the sum total of catabolism and anabolism. Catabolism is the breakdown of materials in the body system while anabolism is the build up. So for your body to use the sugars, proteins, lipids, nucleotides, etc. So we would start would the most elementary pathway in biochemistry Glycolytic pathway also known as glycolysis. This is a pathway that converts glucose into pyruvate which would further be metabolised based on the nature of the organism. Aerobic organisms and anaerobic organisms have different routes. Okay let us get to work Glucose is taken into the cell via is immediately phosphorylated by hexokinase to give glucose 6-phosphate . This reaction consumes 1 ATP. The ATP is the phosphoryl group donor. Glucose 6-phosphate is isomerised to fructose 6-phosphate via the enzyme glucose 6-phosphate isomerase. This step is reversible. Next up, fru 6-phosphate is converted to fru 1,6-bisphosphate via the enzyme phospho fructo kinase I (PFK 1). Okay this enzyme is fucking important as we would see in following lectures. Fru 1,6-bisphosphate is cleaved to give glyceroaldehyde 3-phosphate and dihydroxyl acetone phosphate. The dihydroxyl acetone phosphate is converted to glyceroaldehyde 3-phosphate. This brings us to the end of the preparatory phase. It is called such because ATP is invested into the pathway. Now we go to the harvesting phase where ATP is harvested. Pls note that this reaction now takes twice for each step because if u recall glyceroaldehyde 3-phosphate is now double . So glyceroaldehyde 3-phosphate is acted upon by the enzyme glyceroaldehyde 3-phosphate dehydrogenase to give 1,3-bisphospho glycerate. Here NADPH (nicotine adenine dinucleotide phosphate hydrogen) is invested. Then 1,3-bisphospho glycerate is acted upon by phospho glycero kinase in which 2 ATP molecules are harvested and 3-phospho glycerate. Now 3-phospho glycerate is acted upon by 3-phospho glycero mutate which converts it to 2-phoso glycerate by moving the phosphoryl group from carbon 3 to carbon 2. Now enolase acts upon 2-phosopho glycerate to give phospho enol pyruvate (PEP) by the removal of a water molecule. And finally PEP is acted upon by pyruvate kinase to give pyruvate with the removal of 2 ATP. *swipes sweat off face * Now notice that the ATP invested is 2 and the ones gotten is 4. Thus the net ATP is 2. And note that ATP is the energy currency in the. So this pathway is utilised by cancer cell for energy metabolism thus they grow fast. But we would look at that in future lectures . So that is all about glycolysis. Questions are welcomed. Bye.
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| Re: Learning Biochemistry With Val by Nobody: 8:48pm On Jan 17, 2017 |
oh God... this is complex. |
| Re: Learning Biochemistry With Val by bqlekan(m): 11:18am On Jan 18, 2017 |
As an industrial chemist, sometimes the complexity of biochemistry baffles me. Thanks I will pass |
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