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Condensed course notes for fundamentals of nutrition (nutr3210) includes all lab and lecture info. Perfect for studying for exam.
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PROTEIN STRUCTURE AMINO ACID CLASSIFICATIONProtein: Source of energy (if needed), Substrate for Glucose Synthesis, Provides AAs for Essential AA: (Indispensable) Not made by the body or can’t be made quickly
protein synthesis. In humans there are 21 proteinogenic AAs (includes selenocysteine) enough to meet demands. 9 AAs (lys, thr, iso, leu, met, phe, trp, val, and his)
(AA that is incorporated into a protein during translation). 9 AAs are “essential”. Conditionally Essential: Not normally required in the diet in a healthy individual, but
protein in our diets: % protein of animal-derived foods generally higher than plants become essential under specific contexts
AA Structure: building block of proteins. Can be considered a monomer. Alpha-carbon, Phenylketonuria: (genetic) inborn error of metabolism whereby a person is unable
Amino Terminal (Amine Functional Group), Side Chain (variable composition, which may to breakdown Phe into Tyr. build-up of Phe in the body causes mental retardation.
or may not contain functional groups), Carboxyl Terminal (Carboxylic Acid Functional The solution is to limit Phe in diet and supplement with Tyr
Group-contains a carbonyl carbon) Liver disease (cirrhosis): impairs Phe and Met catabolism. Tyr and Cys are
AA Enantiomers: D vs. L enantiomers. All standard AAs exist as enantiomers (except for synthesized from Phe and Met, respectively. Tyr and Cys become indispensable in
glycine). L form naturally occurring. D form made from post-translational modifications this context
Zwitterions: At physiological pH, AAs are ionized→ Protonated amine group, Non-Essential :(Completely Dispensable)- Can be synthesized in the body and are
Deprotonated carboxyl group. No overall charge (except R group). This increases polarity not essential in the diet
and Makes AAs more water soluble Basic AAs: Polar, +ve charge on NH3 group on side chain enables DNA binding
peptide bonds: (amide bonds) Connects AA’s. type of covalent chemical bond. The Important in histone proteins, which bind DNA. Lysine- Essential, Simple straight
carboxyl group of one AA reacts with amino group of another AA, releasing H2O chain, Absent from grain products. Arginine- Conditionally Essential, Newborn
(condensation reaction) To break a peptide bond, Just add H2O (hydrolysis reaction) infants unable to synthesize arginine, Non-essential in healthy adults Histidine-
Protein Synthesis: From AA to Protein. 2 AAs = Dipeptide, 3 AAs = Tripeptide, ~50 AAs = Essential Ring structure, Used to produce histamine (inflammation)
Oligopeptide, >50 AAs = Polypeptide, 1 or more polypeptides (biologically active protein)
Primary Structure: Determined by the DNA sequence. refers to a polypeptide chain of
AAs. AAs are held together by peptide bonds. Translation is helped by chaperone proteins
in the cell. A polypeptide chain has a carboxyl and amino terminus (Counting of AAs
always starts from the amino end)
Secondary Structure: determined by the H-bonds that create a stabile structure. Doesn’t
involve side chains, only backbone atoms. Two “types” : α-helix - amino group makes a H-
bond with a carboxyl group 4 AAs down the chain, creating a helical shape in polypeptide
chain. β-pleated sheets - amino group makes a H- bond with a carboxyl group in the
folded back polypeptide chain, parallel or anti-parallel. Acidic & Neutral AAs: Acidic AA (-ve charge on side chain carboxyl group), are polar.
Tertiary structure: corresponds to the arrangement of secondary structures. Involves Aspartate- Non-essential, Transaminated to oxaloacetate (Krebs). Glutamate-
interactions between AA side chains. Consists of a single polypeptide chain. Non-essential, Transaminated to α-ketoglutarate (Krebs), Used to produce GABA
Hydrophobic AAs tend to be placed towards the centre of a protein to help ensure the (neurotransmitter). Asparagine- Non-essential. Glutamine- Non-essential
protein is water soluble (ex, disulfide bonds can form between cysteine AAs.) Important in AA catabolism because it is a carrier of nitrogen (to liver & kidney)
Quaternary Structure: corresponds to a combination of 2 or more tertiary structures that
are required to make a functional protein. When proteins combine, the individual
proteins are subunits. Forms a multi-subunit complex (i.e., multiple polypeptides e.g.,
insulin, immunoglobulins).
native protein: a protein in its normal 3D configuration.
denatured protein: loses its bioactivity. heat, salt treatment, detergents, pH (stomach
acid). affects 2°, 3°, and 4°structures (but not 1°).
Neutral AAs: Neutral AAs (no charge on side chain), Non-polar, Aliphatic (C & H
PROTEIN DIGESTION atoms joined in straight or branched chains). Glycine- Non-essential, No
Mouth: No enzymatic digestion, Mechanical breakdown enantiomers, Used primarily to produce porphorin (a component of heme, which is
Stomach: produces "Gastric juice". HCl is secreted from parietal cells; its release is found in hemoglobin). Alanine- Non-essential, Important role in glucose-alanine
triggered by gastrin, acetylcholine, and histamine. HCl has two functions- 1. Denatures Branched Chain AA: Neutral aliphatic AAs (no charge on side chain), Non-polar. All
proteins -disrupts hydrogen bonds and Electrostatic bonds, 2. Activates pepsin are branched. Leucine, Isoleucine, Valine - All are essential, Not catabolized in the
Pepsinogen, which is an inactive zymogen, is secreted chief cells of the stomach. HCl liver, so high levels found in circulation, Promotes protein synthesis
causes a conformational change in pepsinogen, allowing it to then autoactivate itself.
Activated to pepsin in an acidic pH, inactive at a neutral pH. Pepsin is an endopeptidase,
i.e., in other words, it cleaves peptide bonds within the polypeptide chain. Generates
mostly oligopeptides and some free AAs
Pancreas: Pancreatic juice containing zymogens (inactive digestive proenzymes).
Small Intestine: Zymogens activated, Enzymes break-down peptides, Absorption of AAs
Hydroxylated AA: OH-group on side chain is important for protein phosphorylation,
Polar AAs, Tyrosine can also be classified as “hydroxylated”, but is grouped with
aromatic AA, OH group on side chain is important for phosphorylation. Serine- Non-
Essential. Threonine- Is Essential
Sulfur-containing AA: Contain a sulfur-group, Non-polar. Cysteine- Non-essential,
Made from methionine, “Spares” methionine when cysteine consumed in the diet,
Used to form disulfide bonds, Used in glutathione synthesis (oxidant defence
AA absorption: Most AAs are absorbed in upper small intestine through Facilitated system). Methionine- Essential, Methionine is limiting in legumes
diffusion OR Active transport (>60% of AAs are absorbed this way, Sodium-dependent
transporters (indirect ATP requirement)). Essential AAs are absorbed faster than non-
essential AAs. Competition for absorption exists between AAs. Free AAs have no
absorptive advantage (i.e., protein supplements) over AAs in foods
Facilitated diffusion: Does not require Na+ or ATP. Will not concentrate against gradient
Active transport: Na-dependent, Requires ATP Concentrate against gradient
AAs used in Small Intestine: AAs are either transported out of the intestinal cell or used
directly within the enterocyte for: 1. Energy 2. Synthesis of new protein. 30-40% of
essential AAs are used in the small intestine
Example: glutamine highly used in intestinal enterocytes to: Generate energy for the cell, Aromatic AA: Contain aromatic rings, Non-polar (except tyrosine because of the OH
Stimulate cell proliferation (replace shed enterocytes), Increase synthesis of heat shock group in its side chain). Phenylalanine- Essential, Used to make Tyr. Tyrosine- Non-
proteins (chaperones), Drive mucus production, helps prevent bacterial translocation essential, "Spares" . Phe- Used to synthesize neurotransmitters. Tryptophan-
Liver: is very effective at taking up AAs from circulation. uses ~20% of the AAs to Make Essential, Used to synthesize serotonin, Used for niacin (vit B3) synthesis. Proline-
new proteins, new enzymes, albumin and other transport proteins, peptide hormones. Important for collagen production (extracellular matrix), Aliphatic side chain
Liver catabolizes the remaining 80% of AAs, where: NH3sent to the urea cycle, Carbon
skeleton sent to Kreb’s cycle (for energy) or used for gluconeogenesis or lipogenesis.
BCAAs are not taken up by liver, and instead are anabolic signals for tissues like muscle
, PROTEIN CATABOLISM
Reactions of Protein Catabolism: Constant turnover between protein synthesis 3B) GLUTAMATE REGENERATION: Releases amino group from glutamine side chain (i.e.,
and breakdown. The body is very efficient at AA reutilization during protein deamination). Active in liver in the fed state (amino group used for urea synthesis). Active
breakdown. Most AAs derived from protein breakdown are reused to make new in the kidneys during fasting (amino group secreted as NH4+). Bi-directional reaction
protein, while a little bit is catabolized. @ physiological pH we see NH4+ ***but different enzymes for forward & reverse reactions…Make glutamine in muscle
Fate of NH3(NH4+) from AA catabolism: NH4+ is toxic and needs to be converted →travel in blood to deliver amino group to liver / kidneys -→regenerate glutamate
into something safe for transport between organs. Muscle (or other non-hepatic
tissue) --> Glutamine & alanine (Amino group transporters) --> Fasted or Fed
3 differences between fasted and fed state: 1. Fasted state involves the formation
of both glutamine and alanine, while the fed state is primarily glutamine. 2. Fed
state involves both the liver and kidneys. 3. Fed state mainly involves the
excretion of the amino group as urea, whereas the fasted state mainly involves 4) UREA CYCLE: Toxic NH4+ is converted to less toxic urea in the liver. Urea transported to
the excretion of the amino group as ammonium (NH4+) directly. kidneys for excretion. Fasted state: 80-90% of urinary N will be in form of NH4+. Fed
Why the difference between fed and fasted? Catabolizing an α-ketoacidleads to state: 80-90% of urinary N will be in form of urea. NH4+from oxidative deamination and
the production of bicarbonate (HCO3-). Bicarbonate is a weak base that reacts glutamate regeneration from glutamine. Aspartate condenses with citrulline and donates
with a H+(if this happens, no change in pH). an amino group. Urea cycle uses HCO3-, thereby preventing alkalosis. Urea cycle requires
Fed state encourages alkalosis: High dietary protein intake increase amino acid energy (ATP). Defects in any of the enzymes in the urea cycle leads to developmental
catabolism, which leads to an increase in HCO3-(because H+is used up). This can neurotoxicity due to a build-up of NH4+in the body.
increase pH a bit (to ~7.8) α-ketoacids enter the Kreb’s cycle in all cells, resulting In the fed state: non-liver protein catabolism leads to glutamine formation (from
in CO2production; however, @ physiological pH the CO2is actually HCO3-. glutamate). Glutamine is transported to the liver, where it delivers an amino group for
Response- 1. The liver converts the amino group to urea in a process that uses urea production. Urea is then transported to the kidneys and excreted in urine
HCO3-. 2. Catabolism of sulfur-containing AA produces a bit of sulphuric acid to In the fasted state: non-liver protein catabolism leads to glutamine formation (from
neutralize pH. glutamate) and alanine (from pyruvate). Glutamine is transported directly to the kidneys,
longer-term fast or starvation: minor amounts of protein are catabolized to while alanine is sent to the liver (for gluconeogenesis). In the kidneys, glutamine is
release glucogenic amino acids (for gluconeogenesis). However, the primary converted to glutamate and the removed amino group is excreted in urine as NH4+.
source of energy is fat (TAG). The breakdown of TAG leads to the production of PROTEIN QUALITY
acidic ketone bodies (which the brain can use for energy during starvation).long- AA composition: Any protein that provides all essential AA is considered “high quality”.
term fasting encourages a slight acidosis (pH can drop to 7.0)! (nutritional ketosis) Animal protein > plant protein. For example, grains are limiting in lysine, legumes are
Response: The amino group is brought directly to the kidneys thus bypassing the limiting in sulfur-containing AA (methionine).
urea cycle where HCO3-is used up. This means that HCO3-can be used to Digestibility: Some proteins are more digestible than others. More digestible, means
neutralize the weak acidosis state caused by ketone bodies higher quality. Animal protein > plant protein. Some materials, like hair, have a great
Important AAs in nitrogen metabolism: Glutamate- important in AA catabolism, amino acid balance but are indigestible.
common end product of transamination reactions, α-ketoacid for glutamate is Presence of toxic factors: Less toxic factors means higher quality. Animal protein > plant
alpha-ketoglutarate. Aspartate- Donates an amino group in the urea cycle, α- protein. Plants contain thousands of phytochemicals. For example, soybeans contain
ketoacid for asparatate is oxaloacetate. Alanine- Inter-organ nitrogen carrier inhibitors that interfere with trypsin, thus preventing protein digestion.
(goes to liver), α-ketoacid for alanine is pyruvate. Glutamine- Most abundant AA Species consuming the protein: Humans, pigs and chickens have similar protein needs.
in the body, Inter-organ nitrogen carrier (goes to liver & kidneys), Can donate an Ruminants have bacteria in the rumen that can make all AAs, so none are considered
amino group to other reactions essential (remember that ruminants can use low quality protein sources).
4 reactions move nitrogen from catabolized protein between organs for excretion Protein Efficiency Ratio (PER): = gain in body mass (g)/total protein intake (g)
1) TRANSAMINATION: transfer of an amino group to an AA carbon skeleton (i.e., Official method in Canada for the evaluation of protein quality. At 10% “perfect protein”
α-ketoacid) catalyzed by “aminotransferases”. most AA undergo transamination you get 2g of rat growth per gram intake ***(whole egg is optimal to get a value of 2.0),
(except lysine, proline, and threonine). Pyridoxal phosphate - (active form of Vit Gelatin = 0 (no tryptophan); Wheat = 0.6 (little lysine); Raw soy = 0.5 (trypsin inhibitors) ;
B6), coenzyme that holds NH3 group during transfer. Bi-directional reactions, Cook soy = 1.7. Pros- Simple, Cheap, Very sensitive to AA balance, digestibility, toxic
Active in all tissues, Always produces an AA (usually glutamate) and α-ketoacid. At factors. Cons- Rats are not humans, Growth, not maintenance. You don’t know WHY
least 1 transaminase exists for each AA, with each using glutamate/alpha- Protein requirements: vary with life stage. Higher protein requirements in Infancy,
ketoglutarate as one of the pairings. Most abundant aminotransferases in the childhood, and in teenagers, During pregnancy and lactation. Recommendations for
liver- Glutamate pyruvate transaminase (GPT) (also known as ALT), Glutamate protein requirements based on ANIMAL sources of protein. Plant sources may be less
oxaloacetate transaminase (GOT) (also known as AST) Glutamate and alpha- digestible due to differences in the nature of protein and other components (fibre). If
ketoglutarate play key roles in amino acid metabolism these recommendations used plant sources of protein, the values would be higher.
Atkins Diet :(most criticized) (C:F:P = 3:64:33). Different phases where macronutrient
content varies. CHO intake very low, while fat and protein intake very high (~ 30%
protein). no attention to type of CHO or fat consumed.
South Beach diet: (C:F:P = 30:40:30). Different phases where macronutrient content
varies. For CHO intake there is an emphasis on low GI foods. Protein is consistent
throughout the various phases (~30%)
Evaluation of High Protein Diets: All high protein diets NOT created equal. Few LONG
term (> than 1 year) studies of high protein diets. Observed Clinical Results- short term
2) OXIDATIVE DEAMINATION: Glutamate is the main AA to undergo oxidative weight loss is comparable to other diet approaches. Some studies show improved insulin
deamination. Because glutamate is the main product of transamination. Amino sensitivity with high protein as compared to high CHO diets. Conflicting results with
group is released from the glutamate backbone. Reaction favours the formation of respect to effect on cardiovascular health. A moderate increase in protein appears to be
alpha-ketoglutarate. A process that is very active in all tissues in the body. Uses of cardioprotective, but high protein may be a concern in the long-term. People with kidney
free NH4+ are tissue-dependent: In extrahepatic tissue (EHT), the NH4+ is used in diseases should avoid high-protein diets
the synthesis of glutamine. In the liver, NH4+ is used for urea synthesis Protein Supplements: Supplements help to ensure that the correct balance of AAs are
In kidneys, NH4+ is excreted directly as is into urine delivered to the muscle. HOWEVER, this would be the same if a person ate a high quality
3A) GLUTAMINE PRODUCTION: Formation of glutamine (primary inter-organ protein (eggs, meat, fish). Most protein supplements deliver high levels of BCAAs. BCAAs
nitrogen carrier). Muscle produces ~90% of the glutamine found in the body. are rapidly absorbed and delivered to the muscle. Anabolic response of the muscle to a
Glutamine synthetase. Glutamine is the most abundant AA in blood. In the fed protein meal diminishes after 40 years of age (improved with BCAA supplements)
state, primarily travels to liver. In the fasted state, primarily travels to kidneys Marasmus: Protein and Energy Deficiency. 8-10% protein (so just a bit below what is
needed). everything is in balance, the body switches to starvation mode. Characterized by
a complete loss of body fat and muscle, peeling skin, uneven pigmentation. Increased
susceptibility to infection and disease
Kwashiorkor: Protein deficiency. Only 1-2% protein in the diet. Typically seen in
developing countries. High CHO foods (e.g., tuber cassava). characterized by enlarged
abdomen, ‘burns’ on the skin and diarrhea. Increased susceptibility to infection, disease.
Decreased plasma proteins causes an osmotic imbalance in the gut (edema), leading to a
swelling of the gut. Liver is enlarged due to the inability to export fat from the liver (VLDL)
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