Exam 2

biochem

Nucleotide synthesis precursors

is chrosimate for aromatic amino acids

Nucleotide synthesis ribose addition

added in the first step by Ribose-5-phosphate pyrophoskinase adding to the C1 of ribose making %-phosphoribosyl-alpha-pyrophosphate(PRPP)

Nucleotide synthesis first common purines and pyrimidines made

Carbamoyl-P and Aspartate

How are the various forms of THF made and/or interconverted

they exist in different oxidation states and are interconverted by NADPH oxidation or reduction

Purine synthesis committed step

is the formation of phosphoribosyl-amine from PRPP with glutamate as the nitrogen donor.

How is a balance between AMP and GMP achieved

Both are made from IMP and AMP inhibits the first step of IMP→AMP and GMP inhibits the first step of IMP→GMP. This nets a proper balance of AMP and GMP

Antagonist of folic acid metabolism

methotrexate impair purine synthesis and therefore cell division.

How does methotrexate impair purine synthesis

binds to dihyrofolate reductase inhibiting folate metabolism. Thus not allowing THF to be made a cofactor in purine synthethis

Nucleotide

bases + sugar + phosphates

Nucleoside

bases + sugar, but no phosphates

Nucleoside diphosphate

There are specific kinases, adenylate kinase and guanylate kinase, for the formation of ADP and GDP. Both use ATP as the phospho donor. These same kinases also act on dAMP and dGMP.

Nucleoside diphospate rxn

(d)NMP+ATP

Nucleoside triphosphate

Nucleoside diphosphate kinase is a nonspecific enzyme that converts any nucleoside diphosphate (ribo or deoxyribo) to a nucleoside triphosphate with any nucleoside triphosphate as the phospho donor

Nucleoside triphosphate rxn

(d)NDP+ATP

What is PRPP

adds a phosphoribosyl group from PRPP to form AMP,GMP and IMP

Two major phosphoribosyltransferases

adenine (APRT) and hypoxanthine-guanine(HGPRT)

Lesch-Nyhan disesase

is caused by complete deffeciency of HGPRT. Uric acid accumulation resulting in gouthy arthritis this is from purine not being salvaged and only degraded

Tautomerization affects base pairing

The shift in structure determines whether the nitrogen or oxygen is an hydrogen-bond acceptor or donor. The oxygens and nitrogen determine base-pairing properties.

Tautomerization affect on mutations

structural changes are frequent causes of mutations.

What bonds in nucleotides and nucleic acids are unstable and under what conditions?

Glycosidic linkages can be unstable in acid but are stable under alkaline conditions

Bases for Purine are

guanine adenine

Bases for pyrimidines

cytosine uracil thyamine

What are nucleosides

bases linked to sugar via glycosidic linkage

glycosidic linkage and its stability in purines and pyrimidines

stable and unstbale

Anti configuration

no base over the sugar and the nucleoside is fully extended

Syn configuration

has base over the sugar

Pyrimidines can ____ rotate by linkage

not due to steric hindrance from the oxygen

Purines can ____ rotate by linkage

freely

Bio function of adenosine

acts as a local hormone and circulates in the bloodstream and influences blood vessel dilation, smooth muscle contraction, neuronal discharge, neurotransmitter release, and fat metabolism

Accumulation of adenosine causes

sleepyness as it binds to neuron receptors

What does caffeine due

analog for adenosine blocking it from reaching nueron accepts and causing sleepyness

Degradative enzyme bonds with what during attack?

Nucleases degrades by attacking either side of the phosphate

Types of degradative enzymes

Endo (inside) Exo (outside)

Nucleic acid stability in acid

not stable in acid (pH below 2.3)

Nucleic acid stability in alkali

not stable in pH above 10

Why are nucleic acids not stable in acid or alkali

H bonding is disrupted

Nucleic acid sequencing by the Sanger method

using a restriction enzyme (cuts dna) adding deoxynucleotides and determining what has been found .

454 Tech process

done by adding primer and DNA to bead. These beads are placed in wells and add one nucleotide. Wash if unbound and repeat 500 cycles. IF bound a light is emitted. Pyrophosphate is release and the first rxn of sulfate reduction is reversed to form ATP and Sulfate. ATP plus luciferin enzyme emits light.

A-DNA

Bases are not stacked perfectly onto one another.Occurs only in dehydrated DNA and DNA:RNA- hybrids

B-DNA

Second most common biologically

Z-DNA

Requires alternating purine and pyrimidines on one strand,Guanine is anti position. Pyrimidine is strained to continue bond.It has a distorted DNA backbone in a zig zag pattern(left handed orientation)

Z-DNA can also occur if

Methylation of C allows formation even if purines and pyrimidines do not alternate

Cruciforms

inverted repeat on a single strand can base pair .

Hoogsteen base pairs

hydrogen-bonding can also involve the five-membered ring. Some alternate bonding creates the base pairs

Triplexes are formed

In slightly acid conditions, C can be protonated, and H-bond differently, and C can only have two H-bonds with G. These interactions leave atoms that normally H-bond free to form additional H-bonding, and allow triplex formation

Quadruplex factors

G-rich, cyclic, and have Hoogsteen base interactions . Certains cations (K+, Na+, Ca++) favor these structures via the O6 carbonyl group

Location of quadruplex structures

in telomeres, Ig gene rearrangements, in gene regulatory regions, , and some human diseases

What is denaturation

destablizing of hydrogen bonds resulting in strand seperation

Factor of denaturation

ph above 10 or below 2.3, extreme temp, ionic strength

What is renaturation

Denatured DNA will restore if disrupting agents are removed. Temp just below melting

Time it takes for renaturation

usually slow the first step to find the proper register takes a while second step is much faster

DNA tertiary structures are ?

supercoils,topoisomerases and gyrases

Supercoil

formed by circular DNA, normal DNA has 10bp per helical turn adding twist creates it

Negative supercoil

adds twist in the direction of the unwinding(one less helical turn than expected)

Positive supercoil

adds twist in the direction of winding( one helical turn more than expected)

Biological DNA is _____

supercoiled

Topoisomerases

change the linking number and are important in replication

Topo I

cuts one strand,  lets the other strands pass through the break and reseals the DNA

Topo II

breaks a double strand , and lets another double strand pass through it

Gyrases

in DNA it adds negative supercoils, is a type II topoisomerase

Structures of higher order DNA are present in ______

all forms of life

Structure of tRNA and rRNA both are

single stranded but can have double stranded regions and extensive secondary structures.

tRNA sec structures

73-94 nucleotides, the accecptor stem is where the amino acids is linked. The 3’ end of all t RNA is CCA

tRNA teritary structure is formed from

H- bonding to the D- loop and the variable and TwC loop. Involves variant residues in the loop and often includes odd bases.

tRNA structure is ____

L shaped. This maximizes hydrophobic interactions between the stacked base pairs.

Structure is ____ and

important; not sequence

Nucleic acid syn occurs in

5’ to 3’ direction

Bidirectional

starts specific site( origin of replication). Replication occurs in both direction. Two replication forks

Helicase role

drive the unwinding of DNA and are ATP-dependent, does not break phosphodiester bonds. Once separated SSB( has 10 helicases) keeps the strands separated.

Semi discontinuous synthesis

Strands are made as the replication fork moves. The 5’-3’ is the leading strand and it is synthesized continuously.

Lagging strand

synthesis occurs after movement of the replication fork

Leading strand

synthesis occurs during replication fork movement

Okazaki fragment

1000-2000 bases in length. Requires an RNA primer

DNA polymerase properties

base pairing rule governs synthesis, elongation in the 5’ – 3’ direction. ALL DNP require a free 3’-OH to build on ( can not make the first phosphodiester bond)

DNP I,II,V function to

repair DNA

DNP I activity

3’ to 5’ exonuclease and 5’ to 3’. First removes nucleotides from the 3’ end of an elongating chain .

5’ to 3’ acts on

on double stranded DNA to remove  distorted(mispaired) segments in front of the replication fork. Also removes the primer that initates DNA synthesis

Core enzyme

simplest form that can polymerase DNA.

Core enzyme subunits

3 subunits alpha,epsilon, and thetha. The other subunits increase DNP activity and processivity.

Telemore replication

Form protective caps at the end of chromosomes.Short 5-8bp. RNA-dependent DNA polymerase that restores this missing sequence. The enzyme contains the RNA that serves as a template. In humans is 450 nucleotides long

Point mutation

single base change(substation) or instertion/deletion of one or more bases.During DNA replication

Transition mutation

a type of mutation that switches the base purine of  a base pair with another purine. Same with pyrimidine. IE A to G would be changed to an A to T base pair and C to G base pair.

Transition mutation is a type of

point mutation

Mutagen mutations

Base analog can be incorporated into DNA and be designed to cause mispairing by modifying the base

Spontaneous mutation

rxns with reactive oxygen species, S-adenosylmethionine (spontaneous), formaldehyde(an aldehyde)

Alanine synthesis

Synthesized by a glutamate-alanine transaminase in all organisms

Pyruvate family precursors

pyruvate (Valine), α-Ketobutyrate (Isoleucine) and an α-ketoacid (leucine)

Valine and Isoleucine share

enzyme for their last 4 rxns( one methyl group different)

Role of thiamine pyrophosphate

adds 2 carbons to valine and isoleucine. 2C is provided by pyruvate

Leucine mimicks

1st rxn of TCA cycle(addition of acetyl-CoA)

Serine synthesis

Oxidation of 3-PG to alpha keto acid

keto acid transaminated →3 phosphorserine

finally dephosphorylated

Glycine synthetis steps

made from serine (3C) to (2C) one step

Glycine syn

glycine →(cleaved by glycine cleavage enzyme) CO2,NH3,NADH, and N5,N10-methylene THF

Cysteine syn

proceeds from serine.

replace -OH with -SH

1)hydroxyl is activated by acetyl-CoA

2)H2S replaces acetyl group

Major donor of sulfur in bacterial rxns

Cysteine

Sulfur Assimilation

Sulfur in the enviroment is available in the oxidized form of sulfate

Sulfate is reduced after activation by ATP to form

ADS and PAPS

What reduces Sulfate to sulfite

Thioredoxin

What reduces Sulfite to Sulfide

NADPH

Phenyalanine syn

both have prephenate as an intermediate and share 1)the first step in removing C02 and -OH

2) transamination (glutamate is the donor)