Biochemistry II

3,4 molecule thick water "shell" surrounding a molecule

The ordered water molecules, or hydration formed around a hydrophobic core

The hydrophobic center of a clathrate cage

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

Showing properties of both polar, and non-polar molecules

• common secondary structure of proteins.
• 3.6 residues/turn
• 5.4Å Pitch
• Hydrophobic center
• Hydrophilic outside

• common secondary structure of proteins
• Stability due to hydrogen bonding between chains

Stably folded secondary structure which performs a function

Protein Motif

Site of the proteins function. Frequently found where two or more domains meet

The cytosol of the cell because it is a controlled environment

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.

• 1.) Greater reaction specificity
• 2.)Milder reaction conditions
• 3.)Higher reaction rates
• 4.)Capacity for regulation

The free rotation of reactants slows reaction rates.

Gibbs free energy necessary for binding

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

• Transcription: DNA->RNA
• Replication: DNA->DNA
• Translation: RNA->Protein

• Adenine<--> Thymine
• Guanine<--> Cytosine

DNA replication travels always from 5'->3'

• Negatively super coiled
• Held together using:
• 1.H-bonding
• 2.Magnesium
• 3.Base pairing
• 

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.

• Covalent: 100KJ/Mole
• D/D:10KJ/Mole
• H-bond:20KJ/Mole
• D/ID+LD: 1.5KJ/Mole

Two beta strands with an alpha helix end folded over to bind a zinc ion.

• Two a-Helices joined by a short strand of amino acids
• (Left)
• 

(Considered a sub-group of Coiled-coils)

Repeated Leucine repetitions within an alpha helix every 7 residues. 

2 a-helixes are coiled together.

• Two anti-parallel beta strands connected by a tight amino acid turn
• 

• four adjacent anti-parallel strands and their linking loops. 
• 

Loop in which the first and last residues are in close proximity.

• (Image also contains an beta-ribbon motif)
• 

Alpha helices bound by a looping stretch of amino acids

Three consecutive amino acid residues form an anion-binding concavity.

Three consecutive amino acid residues form a cation-binding concavity

• 
• (Green is a calcium atom)

Repetitive amino acid sequence of 40 residues.

• alpha helix with every 4th residue Leucine. 
• Allows Dimerizatino of seperate DNA binding/transcription factors.

Extracellular Calcium binding domains

Allows protein-protein binding, protein interaction domain found to regulate a variety of cellular signalling pathays.

• Collection of Zinc finger motifs which bind RNA, DNA, proteins, and lipid substrates.
• 

• Bind on DNA at specific sites within the promoters of genes. stimulates transcription and expresses genes.
• 

• Short newly synthesized DNA fragments formed on the lagging strand of DNA replication.
• Seperated by 10-nucleotide RNA primers,are unligated,

the efficiency of an enzyme of adding nucleic acids until they fall apart

Large protein fragment produced when DNA polymerase 1 from E. Coli is cleaved by subtilisin(protease).

found in Taq DNA polymerase, Plays an important role in the enzyme's fidelity.

oriC

Family of proteins that control the progression of cells through the cell cycle.

• The area of the DNA that is opened by DNA helicase is known as the replication fork.
• 

• A gene of E. Coli 
• DNA-binding protein that binds to terminator sites, blocks replication forks.
• Counter Helicase

• Sequences of DNA to gain access into genes
• Genes are farther along, not located within the operon

40bp sequences before the transcription site

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

• prevents both DNA and RNA polymerase function.
• Clamp DNA, RNA helixes shut.
• (Interclating Agent)

Molecules that may insert between bases in DNA causing Frameshift mutation during replication.

• Stops mRNA synthesis in prokaryotes not not Eukaryotes
• prevents bases from being added

• 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.

• 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.

Sequence of three DNA or RNA nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis.

Opens the double helix at replication forks by disrupting hydrogen bonds that hold the two strands together.

Binds to single strands of DNA and prevents the helix from reforming before it can be used as a template for replication

Breaks one or both DNA strands preventing

Links nucleotide subunits to form a new DNA strand from a DNA template

Synthesizes short RNA primers on the lagging strand, begins replication of the leading strand

links Okazaki fragments by joining the 3' end of the new DNA fragment to the 5' end of the adjoining DNA

• (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).