Biochemistry II

  1. Hydration Shell
    3,4 molecule thick water "shell" surrounding a molecule
  2. Clathrate cage
    The ordered water molecules, or hydration formed around a hydrophobic core
  3. Hydrophobic core
    The hydrophobic center of a clathrate cage
  4. Hydrophobic effect
    As side chains exit the ribosome the hydrophobic side chains order water molecules forming a clathrate cage, which drives formation of a hydrophobic core of the protein "molten globules", forcing the hydrophobic side chains together to decrease entropy
  5. Amphipathic
    Showing properties of both polar, and non-polar molecules
  6. Alpha Helix
    • common secondary structure of proteins.
    • 3.6 residues/turn
    • 5.4Å Pitch
    • Hydrophobic center
    • Hydrophilic outside
  7. Beta sheet
    • common secondary structure of proteins
    • Stability due to hydrogen bonding between chains
  8. Protein Domain
    Stably folded secondary structure which performs a function
  9. A collection of secondary structures which serve no function, possibly structural
    Protein Motif
  10. Active Site
    Site of the proteins function. Frequently found where two or more domains meet
  11. Where are proteins generally synthesized?
    The cytosol of the cell because it is a controlled environment
  12. How do proteins regulate activity?
    A.) Binding of effector molecules, inhibitors, allosteric.

    B.) Covalently modifying the protein.

    C.) Physically localized within the cell.

    D.) Physical amount of the protein within the cell.
  13. Why are biocatalysts used vs inorganic catalysts?
    • 1.) Greater reaction specificity
    • 2.)Milder reaction conditions
    • 3.)Higher reaction rates
    • 4.)Capacity for regulation
  14. What is the Proximity Model?
    The free rotation of reactants slows reaction rates.
  15. ΔGbinding 

    Gibbs free energy necessary for binding
  16. Types of catalysts
    Acid/Base catalysis -proton transfer

    Covalent catalysis  -change reaction path

    Metal Ion catalysis -use redox cofactors, pka shift

    Electrostatic catalysis -preferential interaction with transition state
  17. De-oxy Ribose
    Image Upload 1
  18. Purine
    Image Upload 2
  19. Pyrimidine
    Image Upload 3
  20. Adenine
    Image Upload 4
  21. Guanine
    Image Upload 5
  22. Cytosine
    Image Upload 6
  23. Thymine
    Image Upload 7
  24. Uracil
    Image Upload 8
  25. Transcription
    • Transcription: DNA->RNA
    • Replication: DNA->DNA
    • Translation: RNA->Protein
  26. Chargaff's Rule of Base Pairing
    • Adenine<--> Thymine
    • Guanine<--> Cytosine

    Image Upload 9
  27. DNA Replication:
    DNA replication travels always from 5'->3'

    Image Upload 10
  28. DNA
    • Negatively super coiled
    • Held together using:
    • 1.H-bonding
    • 2.Magnesium
    • 3.Base pairing
    • Image Upload 11
  29. Hyperchromic Effect
    Absorbance of DNA in the UV range increases ~40%

    The Hypochromic Effect describes the decrease in the absorbance of ultraviolet light in a double stranded DNA compared to its single stranded counterpart. Compared to a single stranded DNA, a double stranded DNA consists of stacked bases that contribute to the stability and the hypochromicity of the DNA.
  30. Energies of Interactions:
    • Covalent: 100KJ/Mole
    • D/D:10KJ/Mole
    • H-bond:20KJ/Mole
    • D/ID+LD: 1.5KJ/Mole
  31. Zinc Fingers Motif
    Two beta strands with an alpha helix end folded over to bind a zinc ion.

    Image Upload 12
  32. Helix Turn Helix Domain(HTH)
    • Two a-Helices joined by a short strand of amino acids
    • (Left)
    • Image Upload 13
  33. Leucine Zipper Motif
    (Considered a sub-group of Coiled-coils)

    Repeated Leucine repetitions within an alpha helix every 7 residues. 

    Image Upload 14
  34. Coiled-Coil Motif
    2 a-helixes are coiled together.

    Image Upload 15
  35. Beta hairpin Motif
    (beta-ribbon,beta-beta unit)
    • Two anti-parallel beta strands connected by a tight amino acid turn
    • Image Upload 16
  36. Greek key Motif
    • four adjacent anti-parallel strands and their linking loops. 
    • Image Upload 17
  37. Omega loop Motif
    Loop in which the first and last residues are in close proximity.

    • (Image also contains an beta-ribbon motif)
    • Image Upload 18
  38. Helix-loop helix Motif
    Alpha helices bound by a looping stretch of amino acids

    Image Upload 19
  39. Nest Motif
    Three consecutive amino acid residues form an anion-binding concavity.

    Image Upload 20
  40. Niche Motif
    Three consecutive amino acid residues form a cation-binding concavity

    • Image Upload 21
    • (Green is a calcium atom)
  41. Armadillo Repeat Domain
    Repetitive amino acid sequence of 40 residues.

    Image Upload 22
  42. Basic Leucine Zipper Domain (bZIP)
    • alpha helix with every 4th residue Leucine. 
    • Allows Dimerizatino of seperate DNA binding/transcription factors.

    Image Upload 23
  43. Cadherin repeats
    Extracellular Calcium binding domains
  44. Death Effector Domain
    Allows protein-protein binding, protein interaction domain found to regulate a variety of cellular signalling pathays.

    Image Upload 24
  45. Zinc Finger Domain
    • Collection of Zinc finger motifs which bind RNA, DNA, proteins, and lipid substrates.
    • Image Upload 25
  46. Leucine zipper Domain
    • Bind on DNA at specific sites within the promoters of genes. stimulates transcription and expresses genes.
    • Image Upload 26
  47. Okazaki Fragments
    • Short newly synthesized DNA fragments formed on the lagging strand of DNA replication.
    • Seperated by 10-nucleotide RNA primers,are unligated,
  48. Processivity
    the efficiency of an enzyme of adding nucleic acids until they fall apart
  49. Klenow Fragment
    Large protein fragment produced when DNA polymerase 1 from E. Coli is cleaved by subtilisin(protease).
  50. What is the 'O' Helix in Finger Domain?
    found in Taq DNA polymerase, Plays an important role in the enzyme's fidelity.
  51. Origin of Replication gene
  52. Cyclins
    Family of proteins that control the progression of cells through the cell cycle.
  53. Replication Fork
    • The area of the DNA that is opened by DNA helicase is known as the replication fork.
    • Image Upload 27
  54. Terminus Utilization Substrate (Tus)
    • A gene of E. Coli 
    • DNA-binding protein that binds to terminator sites, blocks replication forks.
    • Counter Helicase
  55. Operons
    • Sequences of DNA to gain access into genes
    • Genes are farther along, not located within the operon
  56. Promoters
    40bp sequences before the transcription site
  57. Rho independent-
    Rho Dependent-
    Types of Transcriptional termination.

    Rho-Dependent--Transcription terminators which require a protein called Rho factor(which exhibits RNA helicase activity) to displace Polymerase from template.

    Rho-Independent-- terminatino occurse when RNA forms a hairpin structure which displaces RNA Polymerase and ends transcription
  58. Actinomycin D
    • prevents both DNA and RNA polymerase function.
    • Clamp DNA, RNA helixes shut.
    • (Interclating Agent)
  59. Interclating agent
    Molecules that may insert between bases in DNA causing Frameshift mutation during replication.
  60. Rifamycin
    • Stops mRNA synthesis in prokaryotes not not Eukaryotes
    • prevents bases from being added
  61. Alpha Amanitin
    • Highly toxic in mushroom species.
    • α-Amanitin interacts with the bridge helix in RNA polymerase II(pol II). This interaction interferes with the translocation of RNA and DNA needed to empty the site for the next round of RNA synthesis.
  62. Taq Polymerase
  63. Types of DNA mutations
    • Substitution: CTGGAG->CTGGGG
    • Insertion: CTGGAG->CTGGTGGAG
    • Deletion: CTGGAG->CTAG
    • Framshift: "The Fat cat sat"->"Hef atc ats at"
    • --codons which are out of phase altering the gene.
  64. Codon
    Sequence of three DNA or RNA nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis.
  65. Helicase
    Opens the double helix at replication forks by disrupting hydrogen bonds that hold the two strands together.
  66. Single-strand bonding protein(SSB)
    Binds to single strands of DNA and prevents the helix from reforming before it can be used as a template for replication
  67. Topoisomerase
    Breaks one or both DNA strands preventing
  68. DNA polymerase
    Links nucleotide subunits to form a new DNA strand from a DNA template
  69. DNA primase
    Synthesizes short RNA primers on the lagging strand, begins replication of the leading strand
  70. DNA Ligase
    links Okazaki fragments by joining the 3' end of the new DNA fragment to the 5' end of the adjoining DNA
  71. DNA gyrase
    • (Topoisomerase II)
    • Relieves strain while double stranded DNA is being unwound by helicase, causes negative supercoiling of the DNA.

    Looping the template and cutting one of the double helices(holds the other).
Card Set
Biochemistry II
For my biochem II course