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97 Cards in this Set

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Amino Acid
Compound that contains an amino group and a carboxylic group
Carbohydrate
same as monosaccharide or just sugar, formula (CH2O)n
Nucleotide
A five carbon sugar, nitrogen containing ring and one or more phosphates
Lipid
polymer, poorlysoluble in water
Protein/polypeptide
Polymer of amino acids, mediate chemical reactions, provide structural support
Nucleic Acid/Polynucleotide
Polymer of nucleotides (DNA/RNA), f-n - carry genetic information
Exergonic
G negative, spontaneous
Endergonic
G positive, non spontaneous
How can non spontaneous reactions still occur?
Cells couple unfavorbale metabolic processes so that the net change in free energy is negative
Why is water molecule polar?
It has uneven distribution of charge
How many hydrogen bonds can water form?
Water can form 4 hydrogen bonds, since it has 2 hydrogen atoms to donate to H bond and 2 pairs of electrons to accept
Relative strengths of bonds in biological molecules?
Covalent-->Ionic --->H bonding--> van der Waals
Van der Waals interaction between 2 polar molecules
Dipole - dipole interaction
Van der Waals interaction between 2 nonpolar molecules
London dispersion forces
Hydrophobic
water fearing, compound that lacks polar groups and is relatively insoluble
ex. alkane
What happens to entropy when hydrophobic molecule is disolved
Entropy decreases because water is not free to form H bonding
How do hydrophobic molecules increase entropy?
Aggregate, since number of water molecules needed decreases
Hydrophobic effect
Exclusion of nonpolar substances from an aqueous solution
Amphipathic/amphiphillic
Molecules that have both hydrophilic and hydrophobic parts
What happens when amphiphillic molecules are added to water?
Polar groups orient themselves toward solvent,and nonpolar aggregate due to hydrophobic effect
Lipid Bilayer
Polar heads are exposed to solvent, nonpolar tails are inside
f-n - prevent diffusion of polar substances
Kw, ionization constant of water
10 ^-14 at 25 C
What are concentrations of [OH] and [H+] in pure water?
10 ^ -7 M
pH
- log [H+}
Acid
SUbstance that can donate a proton
Base
Substance that can accept a proton
Whats the relation between Ka and pKa
The larger acids Ka, lower it pKa, stronger acid
Buffer
System of weak acid and its conjugate base that prevents changes in pH
What happens at midpoint of titration?
pH = pK, and [acid] = [conj. base]
How do you make a good buffer?
pH needs to be within one unit of pKa
Typical pH of human body
6.9-7.4
Enzyme for H2CO3 buffer
carbonic anhydrase
Can you determine if the reactions is spontaneous from standard G?
no, need actual concentrations, cant use standard
Why are ATP bonds called high energy bonds?
Cleavage of this bonds has a large negative free energy change
WHy cleavage of ATP bonds releases free energy?
ATP hydrolysis products are more stable then reactants, less resonance stabilization
What are other forms of transfering energy?
Reducing cofactors, phosphorylated compounds, thioester ( acetyl- CoA)
Oxidizing Agent ( Oxidant)
Reduced, gains electrons
Reducing Agent (Reductant)
Oxidized, loses electrons
Standard Reduction Potential
Affinity of substance for electrons
What does large E means?
Greater E means greater potential of oxidized from to be reduced (i.e accept electrons)
Electrons flow spontaneously from substance with _ reduction potential to _ reduction potential
Lower, higher
What is G for reaction with large positive E value?
Large negative
Purines
2 rings, A and G
Pyrimidines
one ring, C and T
Nucleoside
Sugar + N base
Name sugar in DNA
2 deoxyribose
Name sugar in RNA
ribose
Phosphodiester Bond
Linkage between nucleotides in nucleic acids, phosphate group makes bonds with both carbons at 3" and 5" ends
what is attached to 5 " end?
Phosphate group
What is attached to 3 " end?
free OH group
How is the base sequence read?
From 5" end to 3 " end
How many hydrogen bonds between A and T?
2
How many hydrogen bonds between C and G?
3
`How do two polynucleotide strands relate to each other?
Antiparallel, one goes 5" - 3", other 3"- 5"
Dna ladder is right or left handed?
Right handed
What are the name of 2 grooves?
Minor and major groove
Why do phosphates bind Mg2+ ions in vivo?
Helps minimize electrostatic repulsion between 2 groups.
Describe location of base pairs?
They are located in the center of the helix, and stack upon each other
What does stability of DNA mainly depend on?
Stacking interaction, form of van der Waals interaction between adjacent base pairs
Which stacking interaction is stronger A-T or C-G?
G-C is stronger
RNA Polymerase I
transcribing rRNA genes
RNA Polymerase III
synthesizes tRNA
RNA Polymerase II
transcribes protein coding genes
Describe action of RNA polymerase
catalyzes attack of the 3" OH group of the growing polynucleotide chain on the 5" phosphate of an incoming nucleotide.
What happens to DNA molecule with high temperature?
DNA melts, base pairs begin to unstack, H bonding breaks, two strands separate
Can denatured DNA be renatured?
yes, if lower temperature
EUchromatin
Active chromatin
Heterochromatin
Inactive chromatin
Nucleosome
Complexes of DNA and proteins in the chromatin
Histones
H2A, H2B, H3, H4
Which part of histone gets covalently modified?
Tail, flexible and charged
Name covalent modifications of histones
acetylation of LYS residues, phosphorylation of Ser and HIS side chains, and methylation of LYS and ARG side chains
What is the name of the site where transcription begins?
Promoter
TATA box
AT rich sequence, usually part of eukaryotic promoter
Activator binds...
Enhancers
Silencer binds
represors
How many RNA polymerases bacteria have? eukaryotes?
1 - bacteria, 3 - eukaryotes
RNA polymerase I
Transcribes rRNA genes, which are present in multiple copies
RNA polymerase III
tRNA and small RNA's
RNA polymerase II
transcribes protein coding genes
How does the switch occurs from initiation to elongation?
C terminal domain serves as a binding place for Mediator like complex, after it becomes phosphorylted elongation begins
5" capping
three enzyme activities modify 5 " end to protect it from exonuclease
signal for 3" polyadenylation
aauaaa
what carries out splicing?
spliceosome
Why is genetic code degenerate?
More then one mRNA codon may specify an amino acid
isoacceptor tRNA
tRNA that bear the same amino acid but have different anticodons
Acceptor Stem
A segment at the 5" end of the tRNA pairs with bases near 3" end
D loop
COntains modified dihidrouridine
AMinoacyl tRNA synthetase reaction
The amino acid reacts with ATP to for aminoacyl-AMP. Activated amino acid reacts with tRNA to form aminoacyl-tRNA
A site
accomodates incoming aminoacyl-tRNA
P site
binds tRNA with growing polyeptide chain
E site
Exit, transiently binds tRNA that has been deacylated
Which codon specifies initiation of translation
AUG, methionine
What factors are required for initiation?
IF1, IF2, IF3
Does initiator enters A site?
no, IF2 sterically hinders A site forcing initiator to go to P site
WHat stops translation?
Stop codon, when stop codon is in A site, ribosome binds release factor
Chaperones
assists protein folding, recognizes hydrophobic parts