Biology Chapter on Proteins

Protein Overview

• Proteins are made of 20 different amino acids (AA).
• Amino acids are composed of C, H, O, and N atoms.
• They have an amine group (NH2), an acid group (COOH), and a unique side chain.
• The side chain differentiates one AA from another in size, shape, and electrical charge. These differences create unique chemical structures.
• Amino acids join via peptide bonds to form proteins.
• The peptide bond is between the amine group of one amino acid and the acid group of the next.
• Each AA has an electrical charge affecting its shape (e.g., globular, strips, coiled).
• Shape enables specific tasks; like acting as catalysts (enzymes), transporting oxygen (hemoglobin), and forming connective tissue (collagen).

Essential, Non-essential, and Conditionally Essential Amino Acids

• Non-essential amino acids: The body can synthesize these.
• Dispensable amino acids: Alanine, asparagine, aspartic acid, glutamic acid, and serine are examples.
• Essential amino acids: These are not made by the body and must be obtained from the diet.
  • Histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine are essential.
• Conditionally essential amino acids: These are normally non-essential but become essential under certain conditions (e.g., disease or stress). An example would be tyrosine.

Amino Acid Chains & Structures

• Proteins consist of linked amino acids with various sequences.
• These amino acids are connected by peptide bonds.
• Dipeptide: two linked amino acids.
• Tripeptide: three linked amino acids.
• Polypeptide: multiple amino acids linked together.
• Primary Structure: The sequence of amino acids in a protein.
• Secondary Structure: The shape that a polypeptide chain takes, determined by weak electrical attractions within the chain. The patterns, like helices (coils) and sheets (folds) give the protein part of its three-dimensional structure. This creates stability.
• Tertiary Structure: The unique, three-dimensional shape of a protein, determined by interactions between the amino acid side chains.
• Quaternary Structure: The arrangement of multiple polypeptide chains in a protein. These chains are stabilized via the interactions between their side chains.

Protein Digestion and Absorption

• Protein digestion begins in the mouth with chewing.
• Saliva prepares the food for swallowing.
• In the stomach, hydrochloric acid (HCl) denatures proteins, exposing peptide bonds for enzymes to break down proteins.
• HCl activates pepsin from pepsinogen, crucial for the breakdown.
• The small intestine and pancreas contain enzymes that further break down polypeptides & dipeptides, into single amino acids.
• Proteases, peptidases digest peptides into individual amino acids.
• Intestinal cells absorb amino acids into the bloodstream, carrying them to the liver and then the body for use.
• Enzymes are optimal functioning in specific pH environments inside the body.
• Their denaturation occurs outside of their ideal range which affects digestion.

Protein in the Body

• The human body has more than 1 million kinds of proteins, but only a few thousand have been studied well.
• Each protein has a specific function determined during protein synthesis based on an amino acid sequence specified by heredity.

Protein Synthesis

• Protein synthesis relies on adequate dietary protein and essential amino acids.
• DNA serves as the template to produce messenger RNA (mRNA).
• Messenger RNA (mRNA) carries instructions to the cell's protein-making machinery (ribosomes).
• Transfer RNA (tRNA) collects amino acids from the body's pool/cell fluid and brings them to the ribosomes.
• Ribosomes use the information in mRNA to arrange amino acids in a specific sequence forming the protein.
• Transcription: The mRNA is created from the DNA template.
• Translation: The mRNA, using the information on the nucleotide sequence, is used by the ribosome to create the protein.

Sequencing Errors

• Genetic errors altering protein AA sequences can cause disorders like sickle cell anemia.
• Sickle cell anemia arises when valine replaces glutamic acid in the hemoglobin protein resulting in unusual hemoglobin function.
• This affects the ability of red blood cells to carry oxygen effectively due to shape alterations.

Roles of Protein

• Building Materials: Proteins are crucial for building & repairing tissues (blood, muscle, skin, etc.) and replacing damaged cells. Collagen is particularly important in bone, ligaments, tendons.
• Hormones: Some hormones, like insulin and glucagon (regulating blood sugar) and thyroxine (regulating metabolism), are proteins.
• Enzymes: Proteins act as catalysts, speeding up chemical reactions in the body.
• Acid-Base Regulators: Proteins help maintain the proper balance of acids and bases in body fluids.
• Fluid Balance: Proteins help regulate fluid balance within cells and tissues. Leaking of proteins leading to edema.
• Transporters: Proteins transport nutrients and other molecules throughout the body. Hemoglobin transports oxygen; lipoproteins carry lipids.
• Antibodies: Proteins that defend the body against disease. They recognize and neutralize foreign invaders (antigens). Memory underlies immunizations.
• Energy Source: Proteins can be broken down to provide energy if carbohydrate & total energy intake is insufficient.
• Other roles: proteins also involved in blood clotting, vision, and other critical bodily functions.

Protein Metabolism and Turnover

• Protein turnover: Proteins within cells are continuously being made and broken down.
• An amino acid pool exists where amino acids are constantly changing.
• Amino acids used to make new body proteins or other nitrogen-containing compounds.
• Amino acids can be used directly for energy production and the rest stored as fat.
• Nitrogen balance: Healthy individuals are in a state of equilibrium (protein synthesis = protein degradation).
• People in growing stages or pregnancy have positive nitrogen balance (protein intake greater than excretion).

Using Amino Acids to Make Other Compounds

• The body uses amino acids as building blocks for other molecules:
  • Tyrosine: forms norepinephrine, epinephrine, melanin, and thyroxine.
  • Tryptophan: forms niacin and serotonin.

Using Amino Acids to Make Fat

• If energy and protein intake exceed body needs and adequate carbohydrate intake is present, amino acids are converted to fat for storage.

Deaminating Amino Acids

• Deamination is the removal of the amino group to produce ammonia and a keto acid.
• The keto acid can be used in energy production, glucose synthesis, or fat production.
• Ammonia is converted to urea for excretion.

Using Amino Acids to Make Proteins and Essential Amino Acids

• The body breaks down existing proteins to obtain missing essential amino acids. Non-essential amino acids are synthesized from available intermediates.
• Essential amino acids, which can't be manufactured by the body, are obtained from the diet.
• The liver is key in synthesizing non-essential amino acids. Transamination reactions and keto acids are central processes in this synthesis.

Converting Ammonia to Urea

• Ammonia is a toxic waste product of protein metabolism.
• The liver converts ammonia to urea, a less toxic substance.
• Urea is excreted by the kidneys.

Excreting Urea

• The kidneys filter urea from the blood.
• Urea is part of waste products excreted in urine.

Protein in Food

• Quality is influenced by digestibility and amino acid composition.
• High-quality proteins contain all essential amino acids and are mostly from animal sources, and some from soy protein.
• Low-quality proteins lack one or more essential amino acids and are sourced from plant products.

Protein Quality and Digestibility

• Protein quality is evaluated using PDCAAS which measures the digestibility corrected amino acid score.
• Protein digestibility depends on the protein source (animal vs. plant) and preparation methods (cooking with moist heat)

Food Labels: Protein

• Food labels must include the quantity of protein in grams.
• They might include %DV values depending on the country, including Canada or the US.
• PDCAAS is used to evaluate protein quality, reflecting digestibility & amino acid composition.

Health Effects of Protein

• High intake of animal protein can increase the risk of heart disease.
• Replacing animal protein with plant protein may reduce this risk.
• Protein, itself, doesn't directly cause cancer. However, certain protein-rich foods might have different impacts.
• Increased protein intake can increase calcium excretion, potentially affecting bone health.
• Protein intake and fibre can help with weight control. Individuals with kidney disease require individualized protein intake based on the disease state.

Protein Deficiency

• Inadequate protein intake can cause slowed growth, impaired brain and kidney function, weakened immunity, and poor nutrient absorption.
• Inadequate protein (and/or energy) intake leads to protein-energy malnutrition (PEM).

Protein-Energy Malnutrition (PEM)

• PEM is a widespread problem due to starvation or hunger.
• Two major types of PEM are Kwashiorkor and Marasmus.
• Kwashiorkor is characterised by edema, skin rash (sometimes hair discoloration) and fatty liver.
• Marasmus is characterized by wasting of fat reserves, weakness, and extremely low energy.

Vegetarian Diets

• Several types of vegetarianism exist: vegetarian, partial vegetarian, pesco-vegetarian, lacto-ovo vegetarian, lacto vegetarian, ovo vegetarian, vegan, and fruitarian.
• Motivations for choosing a vegetarian diet can include health concerns, environmental concerns, animal cruelty concerns.

Positive Health Aspects of Vegetarianism

• Vegetarians often maintain a healthier body weight due to greater amounts of fiber, lower fat intake or possibly other dietary factors.
• Lower SFA intake has been positively correlated with lower cardiovascular issues.
• Diets with less red or processed meat appear to reduce cancer risk.

Possible Negative Aspects of Vegetarianism

• Depending on the type of vegetarian diet, there can be concerns over deficiencies in nutrients like iron, B12, calcium or vitamin D. Careful planning and possible supplementation may be necessary to circumvent these issues. Fortified products can sometimes overcome these nutrient deficiencies.

Nutrients of Interest (Protein, Fat, Minerals, Vitamins)

• Protein: Quality, amount, preparation (timing & technique), complete vs incomplete proteins.
• Fat: Omega-3 fatty acids, EPA/DHA.
• Minerals: Iron (Heme vs. Non-Heme, absorption considerations), Zinc, Calcium (for those who avoid milk products).
• Vitamins: B12 and D (fortification may be crucial).

Planning a Vegetarian Meal

• Emphasis on whole foods instead of processed, planning complete meals (carbohydrate, protein, and fat components).
• Including fortified foods (to alleviate possible vitamin/mineral deficiencies).

Nutritional Genomics

• Nutrigenomics/nutrigenetics study the relationship between nutrients & genes.
• Some genomic testing is controversial due to lack of definitive clinical or scientific validity.
• The goal is to personalize recommendations based on an individual's genes and environment, potentially optimizing health outcomes.

Genomics Primer

• The human genome contains an estimated 20,000-25,000 protein-coding genes.
• Gene expression is the process of using genetic information in DNA to make proteins.
• Examining gene expression patterns may help understand disease development.
• Gene expression doesn't guarantee trait expression.
• Nutrients can activate or silence genetic expression.

Epi-genetics

• Epi-genetics examines how environmental factors affect gene expression.
• Methylation is a crucial epigenetic process in which a methyl group is added to DNA or protein. Methylation can alter gene expression, which affects protein production.
• Ongoing research explores how different nutrients influence gene expression.

Genetic Variation & Disease

• Individuals have different genetic variations.
• Genetics can influence responses to dietary interventions (e.g., some may respond differently to the same nutritional changes).
• Genetic factors contribute to diseases like heart disease.

Gene Disorders

• Single gene disorders arise from mutations in a single gene.
• Missing or malfunctioning proteins cause specific metabolic disorders and often require specific dietary interventions.
• Examples of single-gene disorders include PKU.

Multi-gene Disorders

• These disorders are influenced by multiple genes.
• Many risk factors for a disease are influenced by multiple genes and/or environmental issues.
• Common examples are heart disease.
• Research often examines genetic variations (SNPs) to understand these issues better.

Summary

The notes above include a comprehensive summary about proteins and related concepts, drawing from the provided text. The main points regarding the role of proteins in the body, digestion, absorption, types of proteins, health implications, and implications for certain dietary choices are covered. Each concept or topic is expounded on using accurate details.