Lecture 3 and 4: From Amino Acids to Proteins Part I and II Flashcards
1
Q
Side chains or a-R groups determine
A
- the proprieties of amino acids
- hydrophobicity of the protein
- conformation of the protein such as beta or alpha
2
Q
Isoelectric point (pI)
A
-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
3
Q
Acidic amino acids use formula:
Basic amino acids use formula:
A
pI= (pkaC + pkaR)/2 pI= (pkaN + pkaR)/2
4
Q
The higher
A
you lose
5
Q
The lower
A
you gain
6
Q
The secondary structure of proteins is governed by
A
Hydrogen bonds
7
Q
Essential amino acids
A
- you must take from eating and are not made by the body
- vitamins, eating foods that contain sugar etc
8
Q
Nonessential amino acids
A
-are synthesized by the body
9
Q
Phenylalanine and tyrosine are precursors of :
A
dopamine, epinephrine, and norepinephrine
10
Q
Glutamate dehydrogenase
A
biosynthesis of L-glutamate (glutamic acid)
11
Q
Glutamine synthase
A
biosynthesis of glutamic acid to glutamine
12
Q
What amino acids and sugars are in the body?
A
D sugars and L amino acids
13
Q
Peptides and Proteins are made up of
A
- chains of amino acids
- linked together by amide bonds
14
Q
Start codon
A
Methionine (AUG)
15
Q
Stop codons
A
- Theres 3
- UAG, UGA, UAA
16
Q
Alanine
A
-formed from pyruvate in muscle. Transported to liver and then reconverted to pyruvate
17
Q
Urea cycle
A
- 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
18
Q
Amino acids
A
- play a role in the synthesis of carbohydrates and lipids
- their catabolism generates energy
19
Q
Transcription
A
DNA -> mRNA
20
Q
Translation
A
mRNA -> proteins
21
Q
3 steps in protein synthesis
A
- Initiation (start of sequence)
- Elongation (adding on amino acids)
- Termination (ending sequence)
22
Q
The human genetic code is composed of how many codons?
A
64
1 start codon
3 stop codon
23
Q
Primary Struture
A
The number and order of the amino acid residues in a polypeptide
- sequence of amino acids
- Ex: Met-Ala-Leu-etc
24
Q
FASTA format
A
-quick easy way to write sequence of amino acids using one letter
25
Forms of insulin
1. Preproinsulin
2. Preinsulin
3.Insulin
-using modification proteolysis
Example of proteolytic post-translational modification
26
Proteolysis
breakdown of proteins into amino acids with the help of enzymes such as protease
- purpose-protein maturation
- involved enzyme Proteases
27
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
28
Lipid attachment
-involves enzyme: lipid transferase
| anchors proteins to membrane for regulation
29
Phosphorylation
- addition of phosphate to an organic compound
- involved in cell signaling and change in charge
- involves enzyme: kinase, phosphatase
30
Acetylation
- addition of acetyl group to an organic compound
- involves enzyme: acetylase
- purpose: change charge binding, histone and gene regulation
31
```
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
32
Secondary structure
- the folding of segments of polypeptide into geometrically ordered units (-helix or -sheet)
- governed by hydrogen bonds
33
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
34
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
35
Structural proteins examples
collagen, fibronectin, laminin, proteoglycans, proteoglycans, keratins, actin and myosin
36
Functional proteins
enzymes, carrier proteins, receptors for signal transduction, antibodies, transcription factors, chaperons, growth factors
37
Hemoglobin A1c (HbA1c) Test
- a test used to measure the levels of hemoglobin glycationin the past 3 months.
- for diabetes
38
Fibrous proteins:
Collagens, keratins, and elastins. These are mostly in the extracellular matrix
39
Globular proteins
enzymes, transporters, chaperon
- most enzymes
40
Type 1 diabetes
deficiency in insulin bc body attacks insulin producing cells
treatment is insulin
41
Type 2 diabetes
low insulin or insulin resistance
| treatment is exercise, diet, glucose lowering medicine
42
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
43
CORN
L- amino acid configuration
Carboxylic acid
R group
Amine group
D-amino acid is counter clockwise
44
Krebs Cycle purpose
to make NADH and ATP
45
Example of proteolytic post-translational modification
Insulin
46
Glycosylation
an important post-translational modification of proteins that confers biological activity to proteins
47
Glycosylation is a complex modification of proteins and
| affect their
* Solubility
* Stability,
* Cellular localization,
* Trafficking and clearance
48
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
49
Dimerizing receptor
systems that lead ultimately to down stream
phosphorylation of DNA-binding proteins and thus regulation of
gene expression
50
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
51
Two types of proteins degradation
1. ATP-Independent Degradation
| 2. ATP & Ubiquitin-Dependent Degradation
52
ATP-Independent Degradation
This is specific to blood circulating proteins. First they are deglycosylated then degraded by lysosomes in the liver cells
53
ATP & Ubiquitin-Dependent Degradation
requires ATP
| and ubiquitin and ubiquitinating enzymes
