Lecture 3 and 4: From Amino Acids to Proteins Part I and II Flashcards
Side chains or a-R groups determine
- the proprieties of amino acids
- hydrophobicity of the protein
- conformation of the protein such as beta or alpha
Isoelectric point (pI)
-the pH of a solution at which the net charge of a protein becomes zero.
Ex: pI of Asp is 3.38 so when the pH is 3.4, the net charge is zero
Acidic amino acids use formula:
Basic amino acids use formula:
pI= (pkaC + pkaR)/2 pI= (pkaN + pkaR)/2
The higher
you lose
The lower
you gain
The secondary structure of proteins is governed by
Hydrogen bonds
Essential amino acids
- you must take from eating and are not made by the body
- vitamins, eating foods that contain sugar etc
Nonessential amino acids
-are synthesized by the body
Phenylalanine and tyrosine are precursors of :
dopamine, epinephrine, and norepinephrine
Glutamate dehydrogenase
biosynthesis of L-glutamate (glutamic acid)
Glutamine synthase
biosynthesis of glutamic acid to glutamine
What amino acids and sugars are in the body?
D sugars and L amino acids
Peptides and Proteins are made up of
- chains of amino acids
- linked together by amide bonds
Start codon
Methionine (AUG)
Stop codons
- Theres 3
- UAG, UGA, UAA
Alanine
-formed from pyruvate in muscle. Transported to liver and then reconverted to pyruvate
Urea cycle
- metabolic cycle that helps to convert highly toxic ammonia into urea which is then excreted out the body in urine
- with the help of amino acids and enzymes
Amino acids
- play a role in the synthesis of carbohydrates and lipids
- their catabolism generates energy
Transcription
DNA -> mRNA
Translation
mRNA -> proteins
3 steps in protein synthesis
- Initiation (start of sequence)
- Elongation (adding on amino acids)
- Termination (ending sequence)
The human genetic code is composed of how many codons?
64
1 start codon
3 stop codon
Primary Struture
The number and order of the amino acid residues in a polypeptide
- sequence of amino acids
- Ex: Met-Ala-Leu-etc
FASTA format
-quick easy way to write sequence of amino acids using one letter
Forms of insulin
- Preproinsulin
- Preinsulin
3.Insulin
-using modification proteolysis
Example of proteolytic post-translational modification
Proteolysis
breakdown of proteins into amino acids with the help of enzymes such as protease
- purpose-protein maturation
- involved enzyme Proteases
Glycosylation
modification of a protein or organic molecule by adding a sugar molecule (carbohydrate)
- involves enzyme: protein glycosyl transferase
purpose: protection of cell surface - important post-translational modification
Lipid attachment
-involves enzyme: lipid transferase
anchors proteins to membrane for regulation
Phosphorylation
- addition of phosphate to an organic compound
- involved in cell signaling and change in charge
- involves enzyme: kinase, phosphatase
Acetylation
- addition of acetyl group to an organic compound
- involves enzyme: acetylase
- purpose: change charge binding, histone and gene regulation
Which type of post-translational modifications dictate a protein to be located at the cell membrane or secreted out of the cell? A. Cleavage of N-terminal signal peptide B. Acetylation C. Ubiquitination D. Phosphorylation
A. Cleavage of N-terminal signal peptide
Secondary structure
- the folding of segments of polypeptide into geometrically ordered units (-helix or -sheet)
- governed by hydrogen bonds
Tertiary structure
the assembly of secondary structural units into larger functional units such as the mature protein and its component domains
- starts to become loops (3D)
- governed by non-covalent bonds and disulfide bridges
Quaternary Structure
the number and types of polypeptide units of oligomeric proteins and their spatial arrangement
- incorporates multiple of the tertiary structure (multiple loops)
- composed of 4 subunits
- Dimers, Trimers, tetramers
Structural proteins examples
collagen, fibronectin, laminin, proteoglycans, proteoglycans, keratins, actin and myosin
Functional proteins
enzymes, carrier proteins, receptors for signal transduction, antibodies, transcription factors, chaperons, growth factors
Hemoglobin A1c (HbA1c) Test
- a test used to measure the levels of hemoglobin glycationin the past 3 months.
- for diabetes
Fibrous proteins:
Collagens, keratins, and elastins. These are mostly in the extracellular matrix
Globular proteins
enzymes, transporters, chaperon
- most enzymes
Type 1 diabetes
deficiency in insulin bc body attacks insulin producing cells
treatment is insulin
Type 2 diabetes
low insulin or insulin resistance
treatment is exercise, diet, glucose lowering medicine
Protein turnover
-Proteins are continuously synthesized and degraded - Proteins are degraded into free amino acids (catabolism) by two major pathway: the ubiquitin-proteasome pathway
and lysosomal proteolysis pathway
- Some proteins are short lived (min) and some are long lived
- Each day, humans turn over 1% to 2% of their total body protein, principally muscle proteins
CORN
L- amino acid configuration
Carboxylic acid
R group
Amine group
D-amino acid is counter clockwise
Krebs Cycle purpose
to make NADH and ATP
Example of proteolytic post-translational modification
Insulin
Glycosylation
an important post-translational modification of proteins that confers biological activity to proteins
Glycosylation is a complex modification of proteins and
affect their
- Solubility
- Stability,
- Cellular localization,
- Trafficking and clearance
Oxidative phosphorylation
Complexes I, III, and IV act as proton pumps creating a proton gradient across the membrane, which is negative on the matrix side. The proton motive force generated drives the synthesis of ATP as the protons flow back
into the matrix through the ATP synthase enzyme
Dimerizing receptor
systems that lead ultimately to down stream
phosphorylation of DNA-binding proteins and thus regulation of
gene expression
Ion channels such as acetylcholine receptor
- this channel is closed because side chains project into the channel and block it. When a ligand binds, it leads to a clockwise rotation of the helices, which rotates the side chains and opens the channel. In the acetylcholine receptor, only two of the five subunits can bind acetylcholine
Two types of proteins degradation
- ATP-Independent Degradation
2. ATP & Ubiquitin-Dependent Degradation
ATP-Independent Degradation
This is specific to blood circulating proteins. First they are deglycosylated then degraded by lysosomes in the liver cells
ATP & Ubiquitin-Dependent Degradation
requires ATP
and ubiquitin and ubiquitinating enzymes
