Flashcards

Biochemistry 1

Timo Struik English 39 cards

Cards in this deck (39)

1—Biochemistry 1
Bio-Pharmaceutical Sciences
Leiden University
2(poly)Peptide structures can take four different forms. Explain every form.g
3Amino acid residues are exclusively D or L stereoisomers?L stereoisomers
4An amino acid consists of five chemical groups. What are they?1. The chiral center, the alpha-carbon atom.
2. Carboxyl group.
3. Amino group.
4. R group
5Designate the carbon atom with the right Greek-letter and number of the amino acid shown below.C-1, the carboxyl group
C-2, alpha, alpha-carbon/chiral center
C-3, Beta
C-4, Gamma
C-5, Delta
C-6, Epsilon, attached to positively amine-group
6Explain the Titration curve of an amino acid?Left the fully protonated form. The carboxyl group of glycine loses its proton in the first stage of the titration. This bends the curve 'till the half deprotonated form is formed in the middle of the picture. In the second stage the positively charged amino group is deprotonated what bends the curve again. At pH of 5.97 Glycine is a zwitterion. Also the pI. pI = 0.5(pK1 + pK2).
7Explain what homologs are.Homologs or homologous proteins are members of the same protein family and share a common ancestor. Similair protein with same function found in eukaryotes and prokaryotes.
8Explain what horizontal gene transfer is related to proteins.An example of horizontal gene transfer is the recent rapid spread of antibiotic-resistance genes in bacterial populations.
9What function do the amino acids have with a polar, uncharged R group to the protein structure or funciton?The R groups are more soluble in water, so they R groups contributes to the water solubility of the protein. Furthermore the R groups form H-bond. Cysteine can form a disulfide bond and becomes a cystine, two linked cysteine molecules by a disulfide bond. A disulfide bond is strongly hydrophobic and plays a special role in structure of many proteins by forming covalent bonds between polypeptide chains
10What function do the amino acids have with a positively charged R group to the protein structure or function?These R groups are the most hydrophilic. Histidine plays an important role in many enzym-catalyzed reactions by serving as proton donor/acceptor.
11What function do the amino acids have with negatively charged R group to the protein structure or function?The R groups are acidic, they have an extra carboxyl group.
12What function have the amino acids with a nonpolar aliphatic R group to the protein structure?The side chains cluster together within proteins, stabilizing protein structure by means of hydrophobic interactions.
13What function have the amino acids with an aromatic R group to the protein structure or funciton?All can participate in hydrophobic interactions. The hydroxyl group of tyrosine can form H-bond ,and its an important functional group in some enzymes. Tryptophan and Tyrosine absorb UV-light and to a much less extent Phe.
14What is the difference between paralogs and orthologs?Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution.
Paralogs are genes related by duplication within a genome. Orthologs retain the same function in the course of evolution, whereas paralogs evolve new functions, even if these are related to the original one.
15What is the differents between peptides, dipeptides, oligopeptides, polypeptides and proteins?They all consist of amino acids.
A dipeptide is formed of two amino acid by condensation of the alpha-aminogroup and the alpha-carbon group to a peptide bond.
When a few(<30) amino acids are joined in this fashion, the structure is called an oligopeptide.
When many amino acids are joined, the product is called a polypeptide.
We speak of proteins when a polypeptide has a moleculer weight above 10 kDa.
16When an amino acid sequence of a peptide, polypeptide or protein is displayed what end is placed on the left and what on the right?When an amino acid sequence of a peptide, polypeptide or protein is displayed, amino terminal(N-terminal) end is placed on the left, the carboxyl-terminal(C-terminal) on the right.
17Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...The amino acid is called alanine, Ala, A with a nonpolar, aliphatic R group
18Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...The amino acid is called arginine, Arg, R with a positively charged R group.
19Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...The amino acid is called Asparagine, Asn, N with a polar, uncharged R group.
20Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...The amino acid is called Aspartate, Asp, D with a negatively charged R group
21Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...The aminio acid is called Cysteine, Cys, C with a polar, uncharged R group.
22Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...The amino acid is called Glutamate, Glu, E with s negatively charged R group.
23Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Glutamine, Gln, Q with a polar, uncharged R group.
24Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Glycine, Gly, G with a nonpolar, aliphatic R group.
25Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Histidine, His, H with a positvely charged R group.
26Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Isoleucine, Ile, I with a nonpolar aliphatic R group.
27Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Leucine, Leu, L with a nonpolar, aliphatic R group
28Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Lysine, Lys, K with a positively charged R group
29Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Methionine, Met, M with a nonpolar, Aliphatic R group
30Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Phenylalanine, Phe, F with a aromatic R group.
31Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Proline, Pro, P with a nonpolar aliphatic R group
32Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Serine, Ser, S with a polar uncharged R group
33Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Threonine, Thr, T with a polar uncharged R group
34Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Tryptophan, Trp, W with a aromatic R group.
35Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Tyrosine, Tyr, Y with a aromatic R
36Which amino acid is shown below? What is the 3-letter and one-letter code? The R group is ...This amino acid is called Valine, Val, V with a nonpolar, aliphatic R group
37Why do amino acids act like acids and bases?An amino acid is a zwitterion. Amino acids have two groups, the -COOH group and the -NH3+ group, that can yield protons.
Substances with a dual nature are amphoteric and are often called ampholytes.
38Why do amino acids have two possible forms?Because of the tetrahedral arrangement of the bonding orbitals around the alpha-carbon atom, four groups can occupy two unique spatial arrangements, and thus amino acids have two possible stereoisomers.
39—