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Protein
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:
Amino acids in proteins are covalently joined together by peptide (amide)
bonds … with many hundreds of amino acids in a single protein
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-AspartateGlutamate-GLY-ALA-PHE-LEU- . . . to a MW up to 9,999.
Protein: MW 10,000 or greater.
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 . . .
Tertiary structure
refers to how the
different secondary
structures interact to
produce the threedimensional
structure of the
protein
Leucine Zipper
Zinc-finger
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)
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.
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
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
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)
Purines and
pyrimidines are
components of the
nucleotides
Very useful
molecules!
Note the nitrogens
So . . . How do we use all these things to make proteins?
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.
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
signal transduction pathways
which ultimately result in the
activation of the actual DNAbinding proteins.
We eat protein in order to get the amino acids so we can build our own proteins . . .
Of the different amino acids:
Alanine
Glycine
Hydroxylysine
Methionine
Tyrosine
Asparagine
Glutamine
Proline
Phenylalanine
Valine
Aspartic Acid
Glutamic Acid
Hydroxyproline
Serine
Arginine
Histidine
Isoleucine
Threonine
Cysteine
Lysine
Leucine
Tryptophan
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…
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
(mixed)
~ 60 g/day male
~ 50 g/day female
Japanese Diet
(vegetarian)
~ 75 g/day male
~ 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.
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
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
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.
DRI
0.8 g/kg; 1.0 - 1.4 g/kg with exercise
10% to 35% calories (4 kcal/g)
Nitrogen balance studies indicate that more is needed with exercise
...
. . . labeled infusion studies on the use of amino acids for synthesis
and metabolism indicate a decrease in proteolysis / with a
maintenance of synthesis 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 American consumes > 2X DRI already, modifying
dietary content of protein also is of dubious benefit…
DRI
Another way to look at the DRI for protein is to look at the
indispensable amino acids; RDA for Adults:
Histidine
Isoleucine
Leucine
Lysine
Methionine + Cysteine
Phenylalanine + Tyrosine
Threonine
Tryptophan
Valine
mg/kg/day
14
19
42
38
19
33
20
5
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
- Mastication in mouth
Bolus w/ saliva/mucus
- Denature in stomach
Chyme w/ acids
Pepsinogen
- Pancreatic enzymes
carboxypeptidases
aminopeptidases
trypsin
chymotrypsin
Proteases are somewhat
specific . . .
Chymotrypsin cleaves a
peptide at Tyr (and few others)
Proteases
Where the action really happens
Villi
Duodenum
(small intestine)
Absorption from lumen
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
Brush Border
To venous circulation
There are a variety of different sodium-dependent and sodiumindependent 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.
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 . . . . . . . . . .