Biology 2581B Study Guide - Quiz Guide: Protein Structure, Beta Sheet, Amine
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For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. Proteins are ______________ built from amino acids, which each have an amino group and a _____________ group attached to the central _______________. There are twenty possible _______________ that differ in structure and are generally referred to as âR.â In solutions of neutral pH, amino acids are _______________, carrying both a positive and negative charge. When a protein is made, amino acids are linked together through _______________, which are formed by condensation reactions between the carboxyl end of the last amino acid and the ___________________ end of the next amino acid to be added to the growing chain.
| a: amino | b: ionized | c: polypeptides |
| d: alpha-carbon | e: length | f: protein |
| g: carbon | h: noncovalent | i: R group |
| j: carboxyl | k: peptide bonds | l: side chains |
m: hydroxide
Instructions
BACKGROUND
The amino acid sequence for a protein that is associated with the onset of Huntington's Disease in humans is 582 amino acids long and is provided below. This disease is autosomal dominant and results in a prolonged degeneration of nerve cells in the brain.
INSTRUCTIONS
For this assignment, use any method you determine most feasible (i.e. programming in MATlab, R script, Crystal Ball, Witchcraft/Hocus Pocus, etc.) to decipher the amino acid composition of this protein and answer the 15 questions associated with this protein and its associated amino acid structure.
You will be calculating proportions (percentages - %) for this assignment. Calculate all proportions to 1 decimal place and make sure you have rounded up or down correctly. If unsure, use a spreadsheet program such as Excel to display your proportional calculations to 1 decimal place.
Spelling matters (Incorrect spelling will be graded as such - incorrect).
Huntington Disease Associated Protein Amino Acid Sequence
The first amino acid below ('m') represents the amino (NH3) terminus of this protein. The last amino acid in this sequence represents the carboxy (COOH) terminus and is the very last 'c' at the bottom of this protein sequence structure. The amino acids are numbered individually across the rows (left to right) beginning from the amino terminus (#1) to the carboxy terminus (#582).
| mvskreniat | hhlyqawdpv | pslspattga | lisheklllq | inperelgsm | syklgqvsih |
| svwlgnsitp | lreeewdeee | eeeadapaps | spptspvnsr | khragvdihs | csqfllelys |
| rwilpsssar | rtpailisev | vrsllvvsdl | fternqfelm | yvtltelrrv | hpsedeilaq |
| ylvpatckaa | avlgmdkava | epvsrllest | lrsshlpsrv | galhgilyvl | ecdllddtak |
| qlipvisdyl | lsnlkgiahc | vnihsqqhvl | vmcatafyli | enypldvgpe | fsasiiqmcg |
| vmlsgseest | psiiyhcalr | glerlllseq | lsrldaeslv | klsvdrvnvh | sphramaalg |
| lmltcmytgk | ekvspgrtsd | pnpaapdses | vivamervsv | lfdrirkgfp | cearvvaril |
| pqflddffpp | qdimnkvige | flsnqqpypq | fmatvvykvf | qtlhstgqss | mvrdwvmlsl |
| snftqrapva | matwslscff | vsastspwva | ailphvisrm | gkleqvdvnl | fclvatdfyr |
| hqieeeldrr | afqsvlevva | apgspyhrll | tclrnvhkvt | tc | CARBOXY TERMINUS |
I need these decoded in order to answer the following questions:
a.) What is the name of the least abundant amino acid in this protein and what proportion of the total amino acids in the protein does this individual amino acid represent?
b.) What is the proportion of essential amino acids included in this protein sequence?
c.)How many Tryptophan residues are present in this protein sequence?
d.) The amino acid sequence from residues 73-85 is represented by the amino acids EEEWDEEEEEEAD, how would you generally classify this small region of the protein
e.) Two amino acids are present in the same proportion in this protein, which two are those?
f.) How many positively charged amino acids are present in this protein?
g.)Which class of amino acids is the most abundant in this protein?
h.) What amino acid(s) is/are present at locations 572 and 582 in the Huntington Disease protein (Full Amino Acid Name(s))
i.) What type of structure could form between these amino acids that could help stabilize this protein's structure?
j.) How many valine residues are present in this protein?
k.)Which class of amino acids is least abundant in this protein?
l.) How may negatively charged amino acids are present in the Huntington disease protein?
m.) How many Aspartic Acid residues are present in this protein and what proportion do they represent of the total amino acids in this protein?
n.)Summed together, how many hydrophilic amino acid residues are present in this protein?
o.)What is the sequence of amino acids from positions 487-492 (First letters only)?
p.) How would you classify this area of the Huntington protein based on these amino acids?
Protein Structure
a.Different function of proteins and examples:
b. Protein building blocks:
1. atomic composition of building block:
2. "parts" or "functional groups" of the building block:
c. Importance of side chain (R group):
d. Hydrophobic amino acids characteristics:
e. Hydrophilic amino acids characteristics:
f. Charged amino acids characteristics
Copy and complete the table below regarding the characteristics and which groups in the polypeptide interact together at each structural level of the protein.
| characteristics | groups interacting | ||
|---|---|---|---|
| Primary structure | |||
| Secondary structure | |||
| Tertiary structure | |||
| Quartenary structure |
Value: 2
Choose the correct statement(s). You may choose more than one answer.
[mark all correct answers]
a. Proteins are the building blocks of amino acids.
b. Enzymes are a type of protein.
c. Quartenary structure consists of two or more polypeptide chains interacting.
d. Amino acids are made of carbon, hydrogen, nitrogen and phosphorus.
e. The primary structure of a protein is formed due to the interaction of side groups.
Value: 3
Put the following statements regarding the structural levels of a protein formation in the correct order.
Below is a sequence of events. Place them in the order they should occur, number 1 being the first item. Select the step number from the drop down next to each item.
Items to order:
1. Individual amino acids are bonded together via peptide bonds.
2. Two or more polypeptide chains interact via bonds.
3. Hydrogen bonds form between neighboring amino acids within a polypeptide chain allowing the chain to coil or form pleated sheets.
4. Side groups (R) of the individual amino acids interact with each other allowing the protein to assume its three dimensional shape.
Value:4
Put the following statements regarding the structural levels of a protein formation in the correct order
| Individual amino acids are bonded together via peptide bonds. | 1 2 3 4 |
| Two or more polypeptide chains interact via bonds. | 1 2 3 4 |
| Hydrogen bonds form between neighboring amino acids within a polypeptide chain allowing the chain to coil or form pleated sheets. | 1 2 3 4 |
| Side groups (R) of the individual amino acids interact with each other allowing the protein to assume its three dimensional shape. | 1 2 3 4 |
Value: 5
Hydrophobic amino acids will be found _______________.
a. In the interior (inner core) of a protein, away from the watery environment.
b. in the interior of a plasma membrane.
c. Both A and B
d. Neither
Value: 6
A protein's function is defined by ____________.
a. enzymatic reactions
b. it's shape.
c. chain of nucleotides.
d. the presence of carbon and hydrogen.
Value: 7
Which of the following is NOT considered a protein function?
a. transport of substances across membrane
b. enzymatic reactions
c. provides structural support
d. carries genetic information