DNA-binding proteins are proteins that are composed of DNA-binding domains and thus have a specific or...
DNA-binding proteins are proteins that are composed of DNA-binding domains and thus have a specific or general affinity for either single or double stranded DNA. Protein X is one such protein that binds to double stranded DNA. What residues are most likely to be located in the DNA binding site of protein X and why?
Homework Answers
Protein X such as histone proteins are major DNA binding proteins. They most likely contain basic amino acid residues. This is because DNA contains acidic phosphate groups which has more affinity towards basic amino acids such histidine, lysine and arginine.
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DNA-binding proteins are proteins that are composed of
DNA-binding domains and thus have a specific or...
DNA‑binding domains recognize and bind to specific DNA sequences. Complete the sentences. The homeodomain is also...
DNA‑binding domains recognize and bind to specific DNA sequences. Complete the sentences. The homeodomain is also called the homeobox domain. Not all words will be used. Two terms will be used more than once. A 1.) contains a metal ion in coordination with two cysteine and two histidine residues or with four cysteine residues. DNA–protein binding generally occurs in the 2.) of DNA. The 3.) , found in eukaryotes, contains a small DNA‑binding region similar to the helix‑turn‑helix motif....
Select the correct statement about DNA binding proteins. For proteins that have a helix-turn-helix motif, one...
Select the correct statement about DNA binding proteins. For proteins that have a helix-turn-helix motif, one of the alpha helices fits directly into the minor groove of DNA There are two classes of zinc finger motifs found in DNA binding proteins. One is characterized by pairs of cysteines and histidines (the C2H2-type). The second is the Cx-type. The function of both classes is to coordinate zinc. The leucine zipper motif has leucines at alternating residues of an alpha-helix. The hydrophobic...
Viruses are composed of O proteins, RNA and ribosomes O single stranded DNA O double stranded...
Viruses are composed of O proteins, RNA and ribosomes O single stranded DNA O double stranded DNA and RNA Single stranded RNA O RNA or DNA, but never both, and a protein coat
HP1 is a DNA binding protein that interacts with a specific sequence (TGCTTATTC). You want to...
HP1 is a DNA binding protein that interacts with a specific
sequence (TGCTTATTC). You want to analyze, by a Dnase I
footprinting assay, the effect on DNA binding of the interaction
between HP1 and its 6 binding partner PA. In each assay, you
combine a radiolabeled fragment of DNA that binds to HP1 and a
specific combination of proteins. After incubation with DNase I,
each reaction mixture was resolved by gel electrophoresis, and then
exposed to film. The autoradiogram showing...
1. The figure below shows a DNA double helix and its nucleotide sequence. A. A homodimeric...
1. The figure below shows a DNA double helix and its nucleotide
sequence.
A. A homodimeric helix–turn–helix protein binds to a DNA
fragment containing this sequence. Its preferred half-site is
AACAC. Show where the two recognition helices in the protein
contact the DNA.
B. Are protein–DNA contacts primarily in the major or the minor
groove of DNA? What parts of the nucleotides contact the amino acid
side chains of the protein to provide most sequence specificity?
What kind of bond...
1. A biochemist is attempting to separate a DNA-binding protein (protein X) from other proteins in...
1. A biochemist is attempting to separate a DNA-binding protein (protein X) from other proteins in a solution. Only three other proteins (A, B, and C) are present. The proteins have the following properties: pl (isoelectric point) Size Mr Bind to DNA? protein A 7.4 protein B 3.8 protein C 7.9 protein X7.8 82,000 21,500 23,000 22,000 yes yes no yes What type of protein separation techniques might she use to protein X from the other proteins. Give a flow...
5. (12 Points) We learned that larger proteins may have specific domains that contribute to catalytic...
5. (12 Points) We learned that larger proteins may have specific domains that contribute to catalytic activity of an enzyme. In most cases, the independent isolated domains can be separated and will remain folded in solution. In the context of a full length protein, these domains are interconnected within the protein by flexible loops. An example enzyme protein (EX-FL) has a peptide bond cleaved between two residues to produce two fragments, a peptide fragment (20 residues in length, EX-pep) and...
Proteins have different parts, or domains, that have different functions. What is the function of an...
Proteins have different parts, or domains, that have different functions. What is the function of an SH2 domain? A. Binds to a phosphorylated tyrosine on itself B. Binds to a phosphorylated tyrosine on a different protein C. binds to a proline rich sequence in another protein D. Binds to a kinase
(2) In isolation, a DNA-binding protein binds to its regulatory sequence with a Kd of 1.0 M. Another DNA binding protein binds to another sequence on the same DNA a few bases away with a Kd of 5....
(2) In isolation, a DNA-binding protein binds to its regulatory sequence with a Kd of 1.0 M. Another DNA binding protein binds to another sequence on the same DNA a few bases away with a Kd of 5.0 HM when alone. The two proteins each have a domain which binds to the other with an interaction energy of -2.7 kcal/mole: (a) Draw the thermodynamic box which represents all four states of this system (b) what are the affinities for each...
Please answer all.... Thank you! 57) An enzyme binding site with a specific shape can bind...
Please answer all.... Thank you!
57) An enzyme binding site with a specific shape can bind only those having a complementary shape; thus, the shape of the protein molecule determines the specificity of the binding site the affinity of the binding site the saturation of the binding site the counding strength of the binding site Two of the above are correct. 58) A cell is what it is because of the instructions it receives concerning the types of proteins (enzymes...
Select the correct statement about DNA binding proteins. For proteins that have a helix-turn-helix motif, one of the alpha helices fits directly into the minor groove of DNA There are two classes of zinc finger motifs found in DNA binding proteins. One is characterized by pairs of cysteines and histidines (the C2H2-type). The second is the Cx-type. The function of both classes is to coordinate zinc. The leucine zipper motif has leucines at alternating residues of an alpha-helix. The hydrophobic...
Viruses are composed of O proteins, RNA and ribosomes O single stranded DNA O double stranded DNA and RNA Single stranded RNA O RNA or DNA, but never both, and a protein coat
HP1 is a DNA binding protein that interacts with a specific
sequence (TGCTTATTC). You want to analyze, by a Dnase I
footprinting assay, the effect on DNA binding of the interaction
between HP1 and its 6 binding partner PA. In each assay, you
combine a radiolabeled fragment of DNA that binds to HP1 and a
specific combination of proteins. After incubation with DNase I,
each reaction mixture was resolved by gel electrophoresis, and then
exposed to film. The autoradiogram showing...
1. The figure below shows a DNA double helix and its nucleotide
sequence.
A. A homodimeric helix–turn–helix protein binds to a DNA
fragment containing this sequence. Its preferred half-site is
AACAC. Show where the two recognition helices in the protein
contact the DNA.
B. Are protein–DNA contacts primarily in the major or the minor
groove of DNA? What parts of the nucleotides contact the amino acid
side chains of the protein to provide most sequence specificity?
What kind of bond...
1. A biochemist is attempting to separate a DNA-binding protein (protein X) from other proteins in a solution. Only three other proteins (A, B, and C) are present. The proteins have the following properties: pl (isoelectric point) Size Mr Bind to DNA? protein A 7.4 protein B 3.8 protein C 7.9 protein X7.8 82,000 21,500 23,000 22,000 yes yes no yes What type of protein separation techniques might she use to protein X from the other proteins. Give a flow...
5. (12 Points) We learned that larger proteins may have specific domains that contribute to catalytic activity of an enzyme. In most cases, the independent isolated domains can be separated and will remain folded in solution. In the context of a full length protein, these domains are interconnected within the protein by flexible loops. An example enzyme protein (EX-FL) has a peptide bond cleaved between two residues to produce two fragments, a peptide fragment (20 residues in length, EX-pep) and...
Proteins have different parts, or domains, that have different functions. What is the function of an SH2 domain? A. Binds to a phosphorylated tyrosine on itself B. Binds to a phosphorylated tyrosine on a different protein C. binds to a proline rich sequence in another protein D. Binds to a kinase
(2) In isolation, a DNA-binding protein binds to its regulatory sequence with a Kd of 1.0 M. Another DNA binding protein binds to another sequence on the same DNA a few bases away with a Kd of 5.0 HM when alone. The two proteins each have a domain which binds to the other with an interaction energy of -2.7 kcal/mole: (a) Draw the thermodynamic box which represents all four states of this system (b) what are the affinities for each...
Please answer all.... Thank you!
57) An enzyme binding site with a specific shape can bind only those having a complementary shape; thus, the shape of the protein molecule determines the specificity of the binding site the affinity of the binding site the saturation of the binding site the counding strength of the binding site Two of the above are correct. 58) A cell is what it is because of the instructions it receives concerning the types of proteins (enzymes...
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