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Description
Flashcards by Timo Struik, updated more than 1 year ago
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Created by Timo Struik
almost 6 years ago
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| Question | Answer |
| Biochemistry 1 Bio-Pharmaceutical Sciences Leiden University | |
| (poly)Peptide structures can take four different forms. Explain every form. | g |
| Amino acid residues are exclusively D or L stereoisomers? | L stereoisomers |
| An 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 |
| Designate 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 |
| Explain 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). |
| Explain 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. |
| Explain 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. |
| What 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 |
| What 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. |
| What 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. |
| What 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. |
| What 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. |
| What 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. |
| What 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. |
| When 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. |
| Which 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 |
| Which 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. |
| Which 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. |
| Which 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 |
| Which 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. |
| Which 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. |
| Which 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. |
| Which 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. |
| Which 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. |
| Which 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. |
| Which 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 |
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Which amino acid is shown below? What is the 3-letter and one-letter code?
The R group is ...
Image:
Lysine (binary/octet-stream)
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This amino acid is called Lysine, Lys, K with a positively charged R group |
| Which 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 |
| Which 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. |
| Which 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 |
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Which amino acid is shown below? What is the 3-letter and one-letter code?
The R group is ...
Image:
Serine (binary/octet-stream)
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This amino acid is called Serine, Ser, S with a polar uncharged R group |
| Which 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 |
| Which 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. |
| Which 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 |
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Which amino acid is shown below? What is the 3-letter and one-letter code?
The R group is ...
Image:
Valine (binary/octet-stream)
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This amino acid is called Valine, Val, V with a nonpolar, aliphatic R group |
| Why 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. |
| Why 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. |
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