Protein

1. Protein

2. Protein Huge molecules made up of 20 different amino acids which are joined together in a specific order… Each different protein is made up of a different number of amino acids that are arranged in a different order… Acid part of the amino acid molecule: -COOH Amino part of the amino acid molecule: -NH3 Here are two of the 20 common amino acids:

3. Amino acids in proteins are covalently joined together by peptide (amide) bonds … with many hundreds of amino acids in a single protein

4. The order of the amino acids in the protein determines the ultimate structure (and function) of the protein … each different protein has a different order of amino acids and different sizes of proteins have different numbers of amino acids… Peptide: a few amino acids joined together… Dipeptide: Glycine-Alanine Tripeptide: Valine-Leucine-Isoleucine Tetrapeptide: Proline-Phenylalanine-Tyrosine-Tryptophan- Pentapeptide: Serine-Threonine-Cysteine-Methionine-Asparagine Polypeptide: Glutamine-Lysine-Arginine-Histidine-Aspartate-Glutamate-GLY-ALA-PHE-LEU- . . . to a MW up to 9,999. Protein:MW 10,000 or greater.

5. Primary structure of a protein is the order in which the amino acids are joined together . . . Secondary structure refers to how the amino acids interact to produce different shapes . . .

6. Tertiary structure refers to how the different secondary structures interact to produce the three-dimensional structure of the protein Leucine Zipper Zinc-finger

7. The different kinds of structural shapes in a protein are held together by a variety of different forces: Charge interactions - positive and negative amino acids attract - like charges repel Disulfide bonds – two sulfur-containing amino acids can covalently bond: RC-SH + HS-C-R’ → 2H+ + R-C-S=S-C-R’ Hydrophobic interactions – hydrophobic amino acids will attract to each other (eg. Leucine) Multivalent metal coordination – metal ions bonding with multiple amino acids in a single protein (heme, zinc fingers)

8. Quaternary structure refers to the structural interactions between more than one tertiary structure Two alpha-heme molecules join to two beta-heme molecules to produce the protein hemoglobin.

9. Some quaternary structure interactions alter the function of a protein. HSP90 ER Estrogen receptors can exist in the monomer steroid-binding form as well as in the dimer DNA binding form – notice the role of the leucine-zipper motif and the zinc-finger motif

10. There are literally thousands and thousands of different proteins; each one with a different order of amino acids, a different shape, and a different function: Enzymes to perform chemical reactions . . . Actin and myosin (and others) contractile proteins . . . Collagen and fibrin for connective tissue . . . Antibodies for binding to foreign or “non-self” shapes . . . DNA-binding molecules to regulate transcription/translation

11. Amino acids also are used to make • - Purines/pyrimidines: Guanine, Cytosine, Adenine, Thymine, & Uracil from which we make DNA, RNA, ATP, GTP . . . • - Peptide hormones/growth factors: insulin, glucagon, GH, IGF, LH, FSH, PDGF, . . . • - Glutathione (antioxidant) • - Cytokines, Interleukins . . . • - NRG – we recycle the high energy compounds ATP, GTP, UTP, UDP as we use them (dephosphorylate/phosphorylate)

12. Purines and pyrimidines are components of the nucleotides Very useful molecules! Note the nitrogens

14. So . . . How do we use all these things to make proteins?

15. Sequence of DNA molecules codes for a sequence of amino acids of a protein. Different sequences of DNA molecules (genes) code for different proteins. Transcription of DNA sequence into mRNA sequence is tightly controlled by a variety of transcription factors (proteins) than can initiate, enhance, or repress transcription; transcription factors that are in turn controlled by metabolic, hormonal, of other signaling processes.

16. In the previous slide, transcription was activated by the signaling molecule (estrogen) binding to the actual transcription-activator proteins – resulting in dimerization and DNA binding. Other signaling molecules (growth hormone, calcium / diacyl-glycerol, interleukins, various growth factors, and a host of others) can activate transcription by activating an enzyme cascade which ultimately results in activation of the actual DNA-binding protein.

17. We eat protein in order to get the amino acids so we can build our own proteins . . . Of the different amino acids: Alanine Asparagine Aspartic Acid Arginine Cysteine Glycine Glutamine Glutamic Acid Histidine Lysine Hydroxylysine Proline HydroxyprolineIsoleucine Leucine MethioninePhenylalanine Serine Threonine Tryptophan Tyrosine Valine The ones highlighted in red are commonly considered to be essential amino acids; However; the α-keto or hydroxy-acid version of leucine, isoleucine, valine, tryptophan, methionine, phenylalanine can be transaminated to their amino acid “counterpart”, leaving lysine, threonine, and histidine as being absolutely indispensable…

18. According to the DRIs we need to eat 0.8 g protein of average quality for every kg of body weight every day N.A. Diet ~ 60 g/day male (mixed) ~ 50 g/day female Japanese Diet ~ 75 g/day male (vegetarian) ~ 60 g/day female Vegetable; lower quality (different ratio of amino acids) than meat - therefore you must eat more to meet your minimum nutritional need for essential amino acids in the appropriate ratio – the remainder of “extra” aa are simply oxidized for NRG (predominantly in the liver) with a caloric yield of 4 kcal/g.

19. Protein Quality - Amino Acid Score: In terms of quality, eating proteins that are similar in amino acid content to human protein would be the best – the following table came from Goodhart & Shils: Modern Nutrition in Health & Disease ~1990… AA Human Protein “Content Ratio” Isoleucine 10 Leucine 11 Lysine 9 Methionine (+Cysteine) 14 Phenylalanine (+Tyrosine) 14 Threonine 6 Tryptophan 3 Valine 14 Amino Acid scoring based on reference patterns of amino acid needs are a more “modern” concept – from Advanced Nutrition in Human Metabolism, 2005 Infants Children & Adults Histidine 23 18 Isoleucine 57 25 Leucine 101 55 Lysine 69 51 Methionine + Cysteine 38 25 Phenylalanine + Tyrosine 87 47 Threonine 47 27 Tryptophan 18 7 Valine 56 32

20. According to some people, our nutritional requirements for amino acids increases with exercise: we need to eat more protein every day (From Japanese “RDA”) Kcal/day g/day male g/day female 2250/1800 ~ 70 ~ 60 2550/2000 ~ 70 ~ 60 3050/2400 ~ 85 ~ 70 3550/2800 ~ 100 ~ 85

21. Muscle weight gain in one month highest published rates: (males) 1 kg/10 weeks to 4 kg/16 weeks) Using 1 kg/4 weeks of muscle gain @ ~ 70% water = 0.3 kg dry-weight muscle gain @ ~ 50% of dry weight is protein = 0.15 kg protein gain 0.15 / 28 = 0.0054 kg / day = increased nutritional requirement specifically for muscle hypertrophy Thus ~ 5 g/day is sufficient to satisfy muscle hypertrophy Obviously, gaining muscle mass through heavy resistance training does not take much of an increase in amino acid intake.

22. DRI 0.8 g/kg 10% to 35% calories (4 kcal/g) 1.0 g/kg to 1.4 g/kg for moderate to stressful exercise? Nitrogen balance studies indicate that more is needed with exercise… However, on the basis of labeled infusion studies, the use of amino acids for synthesis and metabolism may actually be more efficient following repeated exercise; leading to a reduction in the dietary protein requirement… Therefore the IOM recommendation for 1.2 – 1.4 g/kg with moderate to stressful exercise may be somewhat dubious Because average US consumes > 2X DRI already, modifying dietary content of protein is of dubious benefit…

23. DRI Another way to look at the DRI for protein is to look at the indispensable amino acids; RDA for Adults: mg/kg/day Histidine 14 Isoleucine 19 Leucine 42 Lysine 38 Methionine + Cysteine 19 Phenylalanine + Tyrosine 33 Threonine 20 Tryptophan 5 Valine 24

24. Obviously, in order to obtain the amino acids there must be a process to get them out of the steak we ate and into our blood stream where they can be picked up by our very hungry cells. This process is, of course, called Digestion and Absorption

25. - Mastication in mouth Bolus w/ saliva/mucus - Denature in stomach Chyme w/ acids Pepsinogen - Pancreatic enzymes carboxypeptidases aminopeptidases trypsin chymotrypsin

26. Proteases are somewhat specific . . . Chymotrypsin cleaves a peptide at Tyr (and few others)

27. Proteases

28. Where the action really happens Villi Duodenum (small intestine)

29. Absorption of nutrients occurs across the brush border of the epithelial cells. Amino acids are transported across the cell membrane by sodium co-transporters and then “released” to be taken up into the venous circulation Absorption from lumen Brush Border To venous circulation

30. There are a variety of different sodium-dependent and sodium-independent transporter proteins for acidic, basic, and neutral amino acids and di- and tri-peptides. Only about 30% of amino acids are absorbed as free amino acids; most are absorbed as peptides. The peptides are then hydrolyzed to produce the free AAs.

31. Amino acids are “transported to the liver” through the portal vein and are picked up by the liver (and the rest of the body’s cells for those that the liver doesn’t get) for processing . . . Liver releases amino acids to the venous circulation and they are transported to the rest of the body through the arterial circulation . . . . . . . . . .