Proteins pt.1

Dietary goal of carbohydrates

increase intake of non-digestible CHO

Recommended CHO intake by Health Canada

45-65%

Recommended fat intake by Health Canada

25-35%

Recommended protein intake by Health Canada

10-30%

What is the essential carbohydrate

No specific “essential” CHO

Dietary goal of lipids

• decrease total fat intake (especially saturated and industrial trans fat)

• increase monounsaturated (MUFA) and ω-3 fats; Mediterranean diet high in MUFA b/c of olive oil

• improve ω-6/ω-3 ratio

General purpose of protein

• Provides amino acids (AAs) for protein synthesis

• Source of energy (if needed); body tries to avoid on a huge extent as it doesn’t want to lose proteins

• Substrate for glucose synthesis; main purpose

Average consumption in North America of protein in calories

~16% of daily calories

Types of AAs in humans

• 21 proteinogenic AAs (includes selenocysteine)

• All but selenocysteine are part of the standard genetic code

• Non-proteinogenic AAs also exist (e.g., some neurotransmitters like GABA), but these are not used to make protein

• 9 AAs are considered “essential” or “indispensible” for humans

Proteinogenic AA

refers to an AA that is incorporated into a protein during translation

Where are proteins found in our bodies

Mainly blood (RBC), connective tissue, eye lens

Amino Acid Structure

this can be considered the monomer

Types of amino acids in the body

1. Standard Amino Acid

2. Non-Standard Amino Acid

Standard Amino Acids

• All are used to make protein

• 20 AAs are encoded in the genetic code (except for selenocysteine)

Non-Standard Amino Acids

• Many exist in the body, but they are rarely used to make

proteins

• Usually formed by post-translational modification of other AAs or as intermediates in the metabolic pathways of standard AAs

• For example, the GABA neurotransmitter is a metabolite of the amino acid glutamate

*don’t talk about in this course

AA Enantiomers

•D vs. L enantiomers

•All standard AAs exist as enantiomers; except for glycine

•L configuration of AAs is naturally occurring

•D configuration of AAs is made through post-translational modifications; mainly used by bacteria

How are AAs Zwitterions

•At physiological pH, AAs are ionized; Protonated amine group and Deprotonated carboxyl group

•No net charge (except R group)

•This increases polarity; i.e., makes AAs more water soluble

How are peptide bonds formed in AAs?

Condensation Reaction (removal of water)

• The carboxyl group of one AA reacts with amino group of another AA, releasing H2O

How do you break a peptide bond

Add H2O (hydrolysis reaction)

Protein Synthesis: From AA to Protein

• 2 AAs = Dipeptide

• 3 AAs = Tripeptide

• approx. 50 AAs = oligopeptide

• >50 AAs = polypeptide

• 1 or more polypeptide(s) = a biologically active protein

*Correct folding assisted by chaperone proteins

Misfolded proteins result in:

metabolic diseases, diabetes, obesity

• results in accumulation of misfolded proteins

Are peptide and proteins interchangeable

No, peptides are linear and biologically non-functional

Primary Structure of proteins is determined by

• DNA sequence

Primary structure of proteins characteristics

• Primary structure refers to a polypeptide chain of AAs

• held together by peptide bonds; translation is helped by chaperone proteins in the cell

• A polypeptide chain has a carboxyl and amino terminus; always start counting from amino end

Secondary structure of proteins is determined by

the hydrogen bonds that create amore stable structure

• bonds don’t involve side chains only backbone atoms

Two types of secondary structure proteins and their characteristics

α-helix

• An amino group makes a hydrogen bond with a carboxyl group 4 AAs down the chain, creating a helical shape in the polypeptide.

β-pleated sheets

• An amino group makes a hydrogen bond with a carboxyl group in the folded back polypeptide chain.

• Can be parallel or anti-parallel.

Tertiary structure

• corresponds to the arrangement of the secondary structure in 3D space

• consists of one polypeptide chain which allows for most protein to be biologically active

• Involves interactions between AA side chains (near or far); ex. disulfide bonds can form between cysteine AAs

• Hydrophobic AAs tend to be placed towards the centre of a protein to help ensure that the protein is water soluble

Quaternary Structure of Proteins

• corresponds to a combination of 2 or more tertiary structures that are required to make a functional protein

• individual structures are referred to as “subunits”

• Forms a multi-subunit complex (i.e.,multiple polypeptides); e.g., insulin, immunoglobulins

• Not all proteins need a quaternary structure to be biologically active, but some do

Native Protein

corresponds to a protein in its normal 3D conformation where they are biologically active

How can proteins be denatured

• heat

• salt treatment

• detergents

• pH (stomach acid)

What happens when a protein is denatured

• loses its bioactivity

• affects 2°, 3°, and 4° structures (but not 1°); ex. disulphide, alpha-helices, beta-sheets etc.

Different ways to classify AA

• Essential versus not essential

• Basic, acidic, or neutral

• Polar versus non-polar

Essential AA (Indispensable)

Not made by the body or can’t be made quickly enough to meet demands

Types of essential AAs

1. lys

2. thr

3. iso

4. leu

5. met

6. phe

7. trp

8. val

9. his

Conditionally essential AAs

Not normally required in the diet in a healthy individual but become essential under specific contexts

ex. a genetic problem (phenylketonuria) or development of disease Cirrhosis

Phenylketonuria

an inborn error of metabolism whereby a person is unable to breakdown Phe into Tyr

• A build-up of Phe in the body causes intellectual disability

• The solution is to limit Phe in the diet and supplement with Tyr (conditional essential)

Liver disease (cirrhosis)

impairs Phe and Met catabolism

• Tyr and Cys are synthesized from Phe and Met, respectively

• Tyr and Cys become indispensable in this context

• Tyr and Cys become conditionally essential

Non-Essential AAs (or Completely Dispensable)

Can be synthesized in the body and are not essential to obtain from the diet

Basic AAs include:

• lysine

• arginine

• histidine

Properties of Basic AAs

• Polar

• +ve charged on NH3 group on side chain enables DNA binding

• important in histone protein, which interact with DNA

Lysine

•Essential

•Limiting in grain products; small abundance

•Involved in the production of carnitine, which is important for fatty acid metabolism

Arginine

•Conditionally Essential in preterm infants unable to synthesize arginine, until gut and intestinal tract can produce

•Non-essential in healthy adults

Histidine

•Essential

•Ring structure

•Used to produce histamine (inflammation)

Acidic and Neutral AAs include:

• Aspartate

• Glutamate

• Asparagine

• Glutamine

• Glycine

• Alanine

Properties of acidic AAs

• -ve charge on side chain carboxyl group

• polar

Aspartate

•Non-essential

•Important for amino acid catabolism as it’s involved in transamination

•Transaminated to oxaloacetate (Krebs)

•A “source” of nitrogen in the urea cycle

Glutamate

•Non-essential

•Important for amino acid catabolism

•Transaminated to α-ketoglutarate (Krebs)

•Used to produce GABA (neurotransmitter)

Asparagine

• non-essential

Glutamine

•Non-essential

•Important in AA catabolism because it is an inter-organ carrier of nitrogen (to the liver & kidney)

Properties of Neutral AAs

• no charged on side chain

• non-polar

• Aliphatic: C&H atoms joined in straight or branched chains

Glycine

•Non-essential

•No enantiomers

•Used primarily to produce porphorin (a component of heme, which is found in hemoglobin); allows RBC to carry O2 around body

Alanine

•Non-essential

•Important in AA catabolism because it is an inter-organ carrier of nitrogen (to liver & kidney)

•Important role in the glucose-alanine cycle

Branched Chain AAs include:

• Leucine

• Isoleucine

• Valine

Characteristics of branched chain AAs

• no charge on side chain

• non-polar

• all are branched

• All are essential

• Not catabolized in the liver, so high levels found in circulation

• Promote protein synthesis; bypasses liver so its goes to muscle for signalling

• BCAA levels are high in protein supplements

Hydroxylated AAs include:

• Serine

• Threonine

Characteristics of Hydroxylated AAs

• OH-group on side chain is important for protein phosphorylation

• polar AA

• also includes Tyrosine, but is grouped with aromatic AAs

• Ser is non-essential and Thr is essential

• OH group on side chain is important for post-translational phosphorylation of proteins

Sulfur-containing AAs include:

• Cysteine

• Methionine

Properties of sulfur-containing AA

• non-polar

• contain a sulfur-group

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 system)

Methionine

•Essential

•1st step in the synthesis of all proteins

•Methionine is limiting in legumes

Aromatic AAs include:

• Phenylalanine

• Tyrosine (only polar aromatic AA)

• Tryptophan

• Proline

Phenylalanine

•Essential

•Used to make Tyrosine

Tyrosine

•Non-essential

•“Spares” Phe

•post-translational modification of proteins

•Used to synthesize neurotransmitters

Tryptophan

•Essential

•Used as precursor to make serotonin (mood)

•Used for niacin (Vit B3) synthesis

Proline

•Non-essential

•Important for collagen production (extracellular matrix)

•Aliphatic side chain

Where does post-translational modification take place

in polypeptide chains, not free AA

• most proteins require some type of modification before they are biologically functional

Types of post-translational modifications

• phoshorylation

• hydroxylation

• gamma-carboxylation

• iodination

• ADP-ribosylation

Phosphorylation by kinase enzymes include:

– Serine-OH

– Threonine-OH

– Tyrosine-OH

*The OH group is where phosphorylation takes place

Phosphorus dependent

Hydroxylation (creation of new hydroxyl group):

• Lysine → hydroxylysine (very important in elastin subunits,

needs copper (copper dependent); associated with aortic rupture)

• Proline → hydroxyproline (very important in collagen subunits, needs Vit C (vitamin C dependent); associated with scurvy)

Gamma-carboxylation

• Required for calcium homeostasis and blood clotting

• Certain proteins are modified to become Ca2+ binding proteins

• Another carboxyl group is added to glutamate

• Vitamin K dependent

Iodination

– Critical in the formation of thyroid hormones

– Crucial for regulation of the metabolic rate

– About 2 billion humans are iodine deficient

– Iodine dependent

ADP-ribosylation

– Adding ADP-ribose to an acceptor protein

– Critical for DNA repair and regulation of protein function

– Dependent on Vit B3 (niacin); niacin dependent

– Niacin used to form NAD+. When NAD+ is broken down in the cell, ADP-ribose and nicotinamide are the products.