Protein: Amino Acids Aulanni’am Biochemistry Laboratory

Name: Protein: Amino Acids Aulanni’am Biochemistry Laboratory
Uploaded: 2017-07-15T17:40:07+00:00
Duration: PTM40S2
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Description: Protein: Amino Acids Aulanni’am Biochemistry Laboratory

Protein: Amino Acids Aulanni’am Biochemistry Laboratory
Chemistry Departement Brawijaya University Aulani "Biokimia" Presentation 5

Aulani "Biokimia" Presentation 5
Proteins have an amino group, an acid, a hydrogen, carbon molecule and a carbon side chain. Protein means primary or first and are necessary for life. Amino means contains nitrogen (NH2). Proteins can also contain sulfur, phosphorus or iron. Aulani "Biokimia" Presentation 5

Amino Acids Aulani "Biokimia" Presentation 5

a - + H H N Carboxylic group Amino group 3 COO R group
L-Form Amino Acid Structure COO - Carboxylic group Amino group a H N 3 + H R group H = Glycine CH3 = Alanine Aulani "Biokimia" Presentation 5

N N C C H H+ H Amino H+ Carboxylic O H O H+ pKa pKa
Proton： abundant and small, affects the charge of a molecule Low High lone pair electrons pKa H H+ N H N Amino H+ High Low pKa Carboxylic C O H C O H+ Ampholyte contains both positive and negative groups on its molecule Aulani "Biokimia" Presentation 5

Acidic environment Neutral environment Alkaline environment pK2 ~ 9 NH2 H+ NH2 H+ COO- R - C - H COO- NH2 R - C - H R - C - H COOH pK1 ~ 2 5.5 +1 -1 Isoelectric point Aulani "Biokimia" Presentation 5

12 9 6 3 [OH] → Amino Acids Have Buffering Effect pH pK2 pI pK1 + pK2
pH pK2 ★ H-C-R COO- NH2 H+ Isoelectric point = pI pK1 + pK2 2 ★ pK1 [OH] → Aulani "Biokimia" Presentation 5

- + Environment pH vs Protein Charge 10 9 8 7 6 5 4 3 Buffer pH
Isoelectric point, pI + - Net Charge of a Protein Aulani "Biokimia" Presentation 5

pKa of Amino Acid Residues
Residues on amino acids can release or accept protons -COOH -COO- a + H+ pKa = 1.8~2.4 -COOH -COO- R + H+ pKa = 3.9~4.3 -Imidazole·H+ -Imidazole His + H+ pKa = 6.0 -SH -S- Cys + H+ pKa = 8.3 -OH -O- Tyr + H+ pKa = 10 -NH3+ -NH2 a + H+ pKa = 8.8~11 -NH3+ -NH2 R + H+ pKa = 10~12.5 Smaller pKa releases proton easier Only His has the residue with a neutral pKa (imidazole) pKa of a carboxylic or amino groups is lower than pKa of the R residues Aulani "Biokimia" Presentation 5

pKa of Amino Acids [OH-] pH Amino acids -COOH -NH2 -R Gly G Ala A Val V Leu L Ile I Ser S Thr T Met M Phe F Trp W Asn N Gln Q Pro P Asp D Glu E His H Cys C Tyr Y Lys K Arg R two pKa pK2 pI pK1 pK1 + pK2 2 three pKa pK3 ? pK2 ? pI ? pK1 Aulani "Biokimia" Presentation 5

Aspartic acid HOOC-CH2-C-COOH NH3+ H first +1 Isoelectric point is the average of the two pKa flanking the zero net-charged form pK1 = 2.1 HOOC-CH2-C-COO- NH3+ H second 2 = 3.0 Isoelectric point pK2 = 3.9 -OOC-CH2-C-COO- NH3+ H +1 -1 -2 -1 pK1 pK2 pK3 third pK3 = 9.8 -OOC-CH2-C-COO- NH2 H -2 [OH] Aulani "Biokimia" Presentation 5

Amino Acids Nonessential amino acids a.k.a dispensable amino acids can be made within the body Essential amino acids a.k.a indispensable amino acids must be obtained from foods Conditionally essential amino acids are needed from food sources if the building blocks to make them are not available. Aulani "Biokimia" Presentation 5

An Essential Amino Acid
Aulani "Biokimia" Presentation 5

Nonessential Amino Acids

Most amino acids are neutral with an aliphathic (single chain) or aromatic chain. Two are dibasic with two amino groups: Histidine and arginine A few are diacidic and are commonly used as components of proteins in cell membranes Aulani "Biokimia" Presentation 5

Proteins Peptide bonds connect the acid end of one amino acid with the amino end of another. They are the links that form a protein chain, which can be simple or very complex. Aulani "Biokimia" Presentation 5

Dipeptide Aulani "Biokimia" Presentation 5

1 2 2 1 NH2 COOH NH2 COOH NH2 C N COOH O H
Formation of Peptide Bonds by Dehydration Amino acids are connected head to tail NH2 COOH 1 NH2 COOH 2 Dehydration -H2O Carbodiimide NH2 C N COOH O H 2 1 Aulani "Biokimia" Presentation 5

A Tripeptide consists of three amino acids linked together. When there are three or more amino acids, the protein starts to form three dimensional shapes. Aulani "Biokimia" Presentation 5

Protein structure Remember Starch?: glucose+glucose+glucose+glucose+glucose… Meet Protein: amino acid+amino acid+amino acid+amino acid… Made of 20 different amino acids bonded together in different sequences to form many SPECIFIC proteins. Aulani "Biokimia" Presentation 5

Amino acids Essential (10) Phenylalanine Valine Threonine Tryptophan Isoleucine Methionine Histidine Arginine Leucine Lysine Conditionally essential (3) Cysteine Glutamine Tyrosine Nonessential (10) Alanine Asparagine Aspartic acid Cysteine Glutaminc acid Gluatmine Glycine Proline Serine Tyrosine Aulani "Biokimia" Presentation 5

Elemental composition of protein
% Carbon Hydrogen Nitrogen Oxygen Sulfur Phosphorous 51.0 – 55.0 6.5 – 7.3 15.5 – 18.0 21.5 – 23.5 0.5 – 2.0 0.0 – 1.5 Aulani "Biokimia" Presentation 5

Classification of amino acids
Essential amino acid One that the body is unable to make or can only make in inadequate quantities Need to be consumed from the diet 8-10 essential amino acids Nonessential amino acid One that the body can make in large enough quantities Made from essential amino acids Not necessary to consume these in the diet 10-12 nonessential amino acids Aulani "Biokimia" Presentation 5

Classification, cont. Conditionally essential amino acid. One that can become essential in certain physiologic conditions 3 of these Example: Tyrosine becomes essential in people with “Phenylketonuria (PKU)” Aulani "Biokimia" Presentation 5

Structure levels in proteins
primary structure amino acid sequence secondary structure spatial arrangement of amino acids within a polypeptide chain (a-helix, ß-sheet, unstructured turns) tertiary structure spatial arrangement of secondary structural elements quatery structure subunit interactions Aulani "Biokimia" Presentation 5

Amino acids are constituents of proteins
there are about 20 proteinogenic amino acids Aulani "Biokimia" Presentation 5

Structure of amino acids
Central carbon N H C H C OH O Different side chains make different amino acids Acid group Amino group Side chain (R) Aulani "Biokimia" Presentation 5

Likage of amino acids Aulani "Biokimia" Presentation 5

Primary structure of a protein
It is the sequence of amino acids that makes each protein different from the next Dipeptide = 2 amino acids Tripeptide = 3 amino acids Polypeptide = many amino acids Most proteins have many 100 amino acids It is the sequence of amino acids that makes each protein different from the next Dipeptide = 2 amino acids Tripeptide = 3 amino acids Polypeptide = many amino acids Most proteins have many 100 amino acids It is the sequence of amino acids that makes each protein different from the next Dipeptide = 2 amino acids Tripeptide = 3 amino acids Polypeptide = many amino acids Most proteins have many 100 amino acids It is the sequence of amino acids that makes each protein different from the next Dipeptide = 2 amino acids Tripeptide = 3 amino acids Polypeptide = many amino acids Most proteins have many 100 amino acids Peptide Bonds Aulani "Biokimia" Presentation 5

Secondary structures a-helix ß-sheet Aulani "Biokimia" Presentation 5

Secondary structure Alignment of polypeptides as a right-hand alpha helix Stabilized by hydrogen bonds between carboxyl (C=O) and imido (NH) groups Aulani "Biokimia" Presentation 5

Unstructured turns connect secondary structural elements
pronounced turn limited turn Aulani "Biokimia" Presentation 5

helices are shown in yellow, carbon backbone is shown in black
Tertiary structure helices are shown in yellow, carbon backbone is shown in black Aulani "Biokimia" Presentation 5

Tertiary structure Three dimensional folding and coiling of polypeptide into globular 3-D structure Caused by additional chemical interactions among side chains Disulfide bonds Aulani "Biokimia" Presentation 5

Quaternary structure Interactive folding of several polypeptide chains together to form a “single” functional protein Functional proteins also might incorporate minerals or other nonprotein components Final shape and components determine function of protein Aulani "Biokimia" Presentation 5

Quartery structure T-form compact structure R-form relaxed structure Aulani "Biokimia" Presentation 5

Proteins Amino acid sequences can vary resulting in almost an endless number of combinations. Each protein’s sequence is determined by the DNA As each amino acid has unique chemical characteristics and electrical charges, the resulting shapes can be very complex. Aulani "Biokimia" Presentation 5

Protein shape and function

Enzymes Proteins that catalyze (speed up) chemical reactions without being used up or destroyed in the process. Anabolic (putting things together) and catabolic (breaking things down) functions. Examples Digestion Salivary amylase Trypsin Aulani "Biokimia" Presentation 5

Hormones Chemical messengers that are made in one part of the body but act on cells in other parts of the body. Note that "steroid hormones" are not proteins! Examples Insulin CCK Some reproductive hormones Aulani "Biokimia" Presentation 5

Immune function (antibodies)
Antibodies are proteins that attack and inactivate bacteria and viruses that cause infection. Aulani "Biokimia" Presentation 5

Denaturation Protein denaturation happens when a protein changes its shape, usually uncoiling. This changes its function and properties. An egg is mostly liquid until cooked. Milk becomes yogurt or or cheese when acids or enzymes are added. Heat, acids, bases, alcohol, heavy metals, enzymes or other agents can cause denaturation. Aulani "Biokimia" Presentation 5

Protein Digestion Stomach releases HCL, which denatures (uncoils) protein strands and converts the inactive form of pepsinogen into the active form pepsin. Pepsin breaks the proteins into smaller polypeptides Pepsin is one of thousands of enzymes, which allows chemical reactions to take place in the body without being affected itself. Aulani "Biokimia" Presentation 5

Small Intestine Releases pancreatic and intestinal proteases. These hydolyze the polypeptides further into tripeptides, dipeptides and finally amino acids, which are actively transported into SI cells and then released into the blood stream. Aulani "Biokimia" Presentation 5

Protein Digestion in the GI Tract

Protein Absorption Carriers - cells of the villi of the SI have gates through which carrier substances transport the amino acids. Capillaries, which are the smallest branches of the circulatory system carry the free amino acids from the villi throughout the body. Absorption misconceptions Enzyme/amino acid supplements Aulani "Biokimia" Presentation 5

Messenger RNA from the nucleus and Ribosomes within cells assemble the free amino acids into proteins As the ribosome moves along the mRNA, an enzyme bonds one amino acid to another. 40 to 100 amino acids can be added to a growing protein strand in one second. Aulani "Biokimia" Presentation 5

Protein Synthesis DNA in the cell nucleus gives mRNA the instructions. mRNA goes into the cellular fluid and attaches itself to ribosomes transfer RNA carries free amino acids to the mRNA Ribosomes move along the mRNA allowing enzymes to bond one amino acid to another until the completed protein is finished and released. Aulani "Biokimia" Presentation 5

Protein Synthesis Aulani "Biokimia" Presentation 5

Sequencing errors Aulani "Biokimia" Presentation 5

When a cell makes a protein it is said that that gene is expressed. Nearly all the body’s cells can make all human proteins, but each type of cell makes only the kinds of proteins it needs. Aulani "Biokimia" Presentation 5

Roles of Proteins Building material Growth, a matrix of protein underlies almost all structures in the body including bones,muscles ligaments, tendons, connecting matrix between cell walls, scar tissue, hair and nails. Maintenance, GI tract cells are replaced every three days. The whole body has its cells renewed every seven years. Aulani "Biokimia" Presentation 5

Proteins as Enzymes Enzymes are usually composed of a protein, a vitamin and a trace mineral. They act as catalysts, allowing reactions to occur more quickly and efficiently. They can cause two substances to come together making a new structure or can split a compound apart. An enzyme is not affected by the chemical reactions it allows to take place. Aulani "Biokimia" Presentation 5

Roles of Proteins Enzymes Aulani "Biokimia" Presentation 5

Hormones Aulani "Biokimia" Presentation 5

Roles of Proteins Regulation of fluid balance Dependent edema may be caused when there is too much fluid between cells and not enough hydrophilic protein within the cells. Acid-base regulation, proteins act as buffers accepting and releasing hydrogen ions thus preventing acidosis or alkalosis. Aulani "Biokimia" Presentation 5

Transport Proteins Aulani "Biokimia" Presentation 5

Proteins in Immunity Antibodies are giant proteins that bind up specific invaders like viruses or antigens Antigens are substances that cause the body to produce antibodies. They may include bacteria, allergens, toxins or anything that causes an inflammatory response. Aulani "Biokimia" Presentation 5

Roles of Proteins Source of energy. The brain and nervous system must have glucose. Once the amino group is removed from the protein, the remaining carbon molecules can be used to create energy - 4 Kcal per gram or stored as fat. Other roles include being converted to other proteins or making neurotransmitters norepinephrine and epinephrine, melanin, fibrin and as precursor to the vitamin niacin. Aulani "Biokimia" Presentation 5

Roles of Proteins Other roles include being converted to other proteins or making: neurotransmitters norepinephrine and epinephrine melanin fibrin precursor to the vitamin niacin. Aulani "Biokimia" Presentation 5

Protein Metabolism Protein turnover Amino acid pool includes free amino acids from endogenous or exogenous sources Nitrogen balance Positive nitrogen balance during growth or when building new tissue Negative nitrogen balance if burned, fever, injury, infection or starvation. Aulani "Biokimia" Presentation 5

Protein Metabolism Using amino acids to make proteins. Cells can dismantle one amino acid and combine the amino group of that amino acid with carbon fragments from glucose metabolism to make another essential or nonessential amino acid needed. Aulani "Biokimia" Presentation 5

Protein Metabolism Deamination is the removal of the nitrogen containing amino group, converting it to ammonia, which is sent to the liver and converted into urea. The remaining carbon fragment may be burned or stored as fat. Amino acids can be used to make fat by removing the amino group and converting the remaining carbon fragments to fat. Aulani "Biokimia" Presentation 5

Amino Acid Pool Proteins are degraded and resynthesized continuously Several times more protein is turned over daily within the body (endogenous) than is consumed (exogenous) AA consumed in excess or unable to be used are not stored. They are: degraded into urea, uric acid, and creatinine lost in feces or sweat converted into hair and nails Aulani "Biokimia" Presentation 5

Protein Quality High-quality proteins Digestibility Animal vs. plant Amino acid composition Limiting amino acid High quality proteins or complete proteins contain all the essential amino acids in relatively the same amonts as human geing require; it may or may not contain all of the nonessential amino acids. Animal sources of protein are generally complete. Digestibility is a measure of the amount of amino acids absorbed from a given protein source. Limiting amino acid refers the idea that one of the essential amino acids is lower in content that is required. Aulani "Biokimia" Presentation 5

Protein Quality Is reflected in the amino acid score: content of individual essential AA in food content of same AA in reference pattern Based on reference pattern for age Four AA are likely to be limiting Lysine, sulfur containing (methionine plus cystine), threonine and tryptophan Aulani "Biokimia" Presentation 5

Protein Quality Reference protein Complementary proteins Aulani "Biokimia" Presentation 5

Reference Proteins Nitrogen balance studies within age groups Used data for highy digestible, high quality proteins - egg, meat, milk or fish Amino acid scoring patterns were factored in A margin of safety of 2 standard deviations to meet needs of 97.5% of the population For adults over age 19 the reference protein intake is 0.75 g/kg/day (RDA is 0.8) Range was egg to vegetable based diet Aulani "Biokimia" Presentation 5

Protein Quality Protein Digestibility Corrected AA Score compares the amino acid content of a protein with the human amino acid requirements and corrects for digestibility. Considers factors that limit digestion: cell walls, enzyme inhibitors, tannins Reveals the most limiting AA Aulani "Biokimia" Presentation 5

Protein Quality PDCAAS Protein digestibility-corrected amino acid score Aulani "Biokimia" Presentation 5

Food Labels Quantity of protein Daily Value 50 g protein 10% of a 2000 kcal diet Aulani "Biokimia" Presentation 5

Protein-Energy Malnutrition (PEM)
Acute PEM when one is recently deprived of food. Children are thin for their height. Chronic PEM from long term food deprivation. Children are short for their age. Aulani "Biokimia" Presentation 5

Protein-Energy Malnutrition
Marasmus - inadequate energy and protein over a long period of time. Often seen at 6-18 months of age. Look like little old people. Kwashiorkor - “the evil spirit that infects the first child when the second child is born.” Sudden deprivation at 18 mon to 2 yrs. Marasmus-kwashiorkor mix: edema of marasmus with wasting of kwashiorkor Aulani "Biokimia" Presentation 5

Protein-Energy Malnutrition
Infections: Antibodies needed to fight infections are degraded to provide amino acids for survival. Dysentery with concomitant diarrhea robs the body of needed nutrients. Rehabilitation: electrolytes especially potassium and sodium are given slowly over the first 2 days, then foods may be started in small quantities. Aulani "Biokimia" Presentation 5

Health Effects of High Protein
Heart disease: diet high in animal protein may contribute to a higher incidence of heart disease in the U.S. High homocysteine level possibly from suboptimal B12, B6 and/or folic acid is associated with heart disease. Cancer of the colon, breast, kidneys, pancreas and prostate is associated with high animal protein and fat diet. Adult bone loss. Calcium excretion rises as protein intake increases. Aulani "Biokimia" Presentation 5

Health Effects of High Protein Diet
Weight control helpful for some not all Any diet in which grains are severely limited should supplement with manganese 5 mg/day and selenium 200 ug Kidney disease - a high protein diet increases the load on the kidneys, which in Chinese medicine means degenerative changes will take place earlier. We are as old as our back is flexible and our kidneys function adequately. Aulani "Biokimia" Presentation 5

Recommended Intakes RDA 0.8 g/kg/day for healthy adults 8-11% - of energy intake per day 50-65 grams of protein per day or between 200 to 250 Kcal. If junk food, sugar and fat is restricted, it is difficult not to get enough protein. Aulani "Biokimia" Presentation 5

Recommended Intakes Calculate own: wt (lbs) divided by 2.2 x .8 Adequate intake - if total Calories are too low, protein will be used to meet Calorie needs Protein in abundance Aulani "Biokimia" Presentation 5

Supplements Protein supplements- very active athletes may benefit from an intake of 1 gm of protein per kg rather than .8 gm/kg of body wt. (75 gm instead of 63 gm/day - 1 1/2 oz more meat) Amino acid supplements if not balanced may lead to deficiencies of some AA thru competition with carrier enzymes Lysine up to 3 gm a day may suppress herpes infection (divided doses with meals) Aulani "Biokimia" Presentation 5

Vegetarian Diets Healthy food choices Macrobiotic diets use too much salt and can be overly restrictive. However, they contribute one excellent idea - to eat as much as possible a variety of minimally processed, organic, locally grown foods in the season in which they are grown. Aulani "Biokimia" Presentation 5

thank you Aulani "Biokimia" Presentation 5

Protein: Amino Acids Aulanni’am Biochemistry Laboratory

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