Protein Flashcards
Chemical protein structures
Primary: Amino acid sequence. DNA is the basis of AA sequence and # of AAs. AA sequence dictates what protein is made (secondary structure). Dictates protein’s identity and function.
Secondary: weak H bonds b/t carboxylic acid and amino group causes folding. a-helix and b-sheet. H and O on the carbon backbone determines the secondary protein structure.
Tertiary: final 3-D structure of a protein. Interactions b/t (R group) side chains.
Quaternary: non-covalent interactions bind polypeptides into one large protein. Not all proteins have quaternary structures. Hemoglobin is a complex 4 protein molecule.
Central Dogma
DNA makes RNA makes Protein
Protein Synthesis
what regulates what?
1) cell signaling: Cell signaling communicates the need for protein synthesis to the nucleus. Can be up or down regulated.
2) Transcription of a gene in the nucleus results in the synthesis of a strand of mRNA
3) Translation: The mRNA strand leaves the nucleus and binds to ribosomes in the cytoplasm. tRNA translates the information carried by mRNA by delivering AA in the right sequence to the ribosome, resulting in a polypeptide strand.
Peptide formation
dehydration synthesis
Classification of AA
1) Structure (side chain)
2) Net Electrical Charge
3) Polarity (side chain)
4) Essentiality
Essential AA
Phenylalanine Valine Tryptophan Threonine Isoleucine Methionine Histidine Leucine Lysine
Conditional (precursors) AAs
Tyrosine (phenylalanine) Cysteine (Methionine, Serine) Proline (Glutamate) Arginine (Glutamine, Glutamate, Aspartate) Glutamine (Glutamate, Ammonia)
Branched chain AA
Leucine
Isoleucine
Valine
Complete vs incomplete protein
complete: adequate amounts of all essential amino acids (animals sources)
incomplete: low amounts of >1 essential amino acid (rice + beans)
Limiting AA
missing or in low amounts (corn)
Factors that determine the quality of food protein
Low vs High quality
high quality: complete protein + bioavailability
low quality: incomplete protein + bioavailability
Different measures of protein quality
Biological Value: % of absorbed protein nitrogen from a test protein source that is retained in the carcass of a lab animal.
100% of N absorbed from egg protein is retained
BV= N retained/ N absorbed * 100
Why is hemoglobin structure important of the function of the protein in the body?
Hemoglobin is an example of a protein with quaternary structure and prosthetic groups (nonprotein component that contains minerals). Made up of four polypeptide chains that are combined with a iron-containing heme (prosthetic group). Heme transports the oxygen and carbon dioxide gases in the blood.
oligopeptides vs polypeptides
oligopeptides- 2-12 amino acids
polypeptides- 12 or more amino acids
Given a structure drawing of an amino acid
- explain polarity and classify the amino acid as polar or nonpolar
- classify amino acids as essential or non-essential or conditionally essential
- classify side chains: straight chain, branched, hydroxylic, sulfuric, acidic, basic, alphatic, aromatic, imino.
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Denaturation
The alteration of a protein’s three-dimensional structure by heat, acid, chemicals, enzymes or agitation. Only the secondary, tertiary and quaternary structures are affected.
Epigenetics
Alterations in gene expression that do not involve changes in the DNA sequence. Nutritional status in very early life may affect long-term health via epigenetic modifications. Babies who are malnourished during fetal life during fetal life but then experience accelerated growth in infancy or childhood may be at increase risk for CVD & T2D.
Dietary Proteins Digested, Absorbed and Circulated
Protein digestion begins in the stomach
Continues in the small intestine
AA are absorbed in the small intestine and circulated in the blood
Describe how aa and peptides are transported through enterocytes
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Catabolic pathways can metabolize protein for energy
The body must depend on AA particularly during starvation. Body can break down its own stored protein (skeletal muscle)
Stage 1: proteolysis: breaks down protein into amino acids, the liver then takes up aa where they can enter the next stage
Stage 2: Removing the nitrogen-containing amino group and using the remainder of the aa to generate substances that can enter the citric acid cycle
a-keto acid: the structure remaining after the amino group has been removed from the aa.
Transamination: the amino group from an amino acid is transfeerred to a a-keto forming a new aa.
the carbon skeleton remaining (a-keto) is used to generate ATP by entering the citric acid cycle.
deamination (produces NADH + H+): removal of amino group from an amino acid that results in the formation of an a-keto. occurs in the liver. a-ketoglutarate is formed when the amino group is removed from glutamate. Thus a-ketoglutarate can take part in transamination. The amino group group removed from the aa is converted to ammonia. which is quickly converted to urea which is released into the blood, filtered by the kidneys and excreted in the urine.
after transamination and deamination are complete the a-keto acid is ready to enter stage 3.
Stage 3: citric acid cycle. a-keto can enter at various points (unlike glucose) depending on the needs of cells the a-keto acid can be metabolized for energy or used to synthesize glucose or fatty acids. when used as energy a-keto are oxidized to produce NADH + H+ and FADH2 which enter the electron transport chain.
