Module 10 ~ Nucleic Acids

What are the physiological roles of nucleotides?

• energy currency through ATP

• signaling molecules (cAMP)

• enzyme co-factors (NAD, FAD)

• building blocks of nucleic acids

What are they physiological roles of nucleic acids?

• genetic info (DNA, RNA)

• all stages of protein synthesis (DNA, mRNA, tRNA, rRNA)

What are nucleotides?

• building blocks of nucleic acids

What three components do nucleotides share?

• ribose sugar (ribose of deoxyribose)

• nitrogenous base (purine or pyrimidine)

• phosphate(s)

What’s the difference between ribose and deoxyribose

• the difference is at the C2 carbons

• whether or not there is an hydroxyl group at C2

What form is the ribose within the nucleotides?

• cyclized form, beta-d-riboFURANose

What are the two families of nitrogenous bases?

• purines: two ring system: AG

• pyrimidines: single ring system: CUT

*planar and non-polar

Where do nitrogenous bases link?

• to the ribose through N-glycosidic bonds

• all the bases link to the C1 of the sugar

• In purines N-glycosidic bond is to N9, in pyrimidines is on the N1

What’s the difference between nucleotides and nucleosides?

• the nucleotides are phosphorylated of the nucleosides

• osine is side, ylate is tide

What type of bonds is atp?

• high energy

• the energy released from hydrolysis of these bonds drives many biological rxns

What molecule can signal transduction produce?

• cyclic AMP

• formed from ATP in a rxn catalyzed by adenylyl cyclase

What kind of processes does cyclic AMP associate with?

• with you being awake and alert

• a go signal

How does caffeine counter with cyclic AMP?

• it slows down its production, causing the “go” symbol to last longer

Are the phosphodiester bonds joining nucleotides unique?

• no they’re all identical in DNA and RNA

Can exercising change your pheno and genotype?

• Yes

What does more genomes indicate?

• the more genomes the more valuable they become

• just as phones becoming more valuable because its a communication essence

• this is called the network effect, the more we sequence the more it becomes valuable

What is the change in one nitrogenous base that causes sickle cell?

• at position 6: the change is from T to A, now it codes for valine and not glutamate

What does the sequence in the DNA determine?

• the sequence in the messenger RNA

• which determines the sequence within the protein which determines its structure and function

Although RNA is single-stranded, what can it adopt?

• complex three-dimensional structures

• the looped ends of mRNA protects it because when they’re broken down, the ends get destroyed

What are the functions of RNA?

• rRNA most abundant

• tRNA carry activated amino acids to ribosomes for protein synthesis

• mRNA code for proteins, contains triplet codons that specify sequence

• miRNA short & function in trans and post-trans regulation of gene expression

What does the presence of the hydroxyl group of RNA mean?

• that it’s more likely of you to get cleavage of the strand

• inc susceptibility to base hydrolysis at the phosphodiester linkage

Who took credit for DNA double helix and who actually discovered it?

• Watson and Crick

• Taken from Rosalind Franklin

What is the specificity of Watson-Crick base pairing largely determined by?

• hydrogen bonds

• G-C has three hydrogen bonds

• A-T has two

What are the weak forces that stabilize the double helix?

• hydrophobic effects: purine and pyrimidine rings inside

• stacking interactions: stacked form van der Waals

• hydrogen bonds: between base pairs

• charge-charge interactions: electrostatic repulsion of negatively charged phosphate groups

What are the minor vs major grooves?

• allowing for base pairs to access interactions with other molecules, proteins acting in a sequence-dependent manner

• DNA can use this to “read” sequence

What are restriction enzymes?

• makes cuts in duplex DNA

• protecting bacteria from viruses that attack it

What is palindrome?

• self complementary about a point

• where the restriction enzymes cut at

What does treating DNA from different individuals with restriction enzymes do?

• breaks it into pieces

• these pieces look different and cut at different fragments with different lengths

• this is called RFLP: Restriction Fragment Length Polymorphisms

  • can be done with PCR

What is denaturation?

• complete separation of double-stranded DNA by heat or chemical agents

• its a cooperative process

What is annealing?

• reforming the double-stranded helix from single strands

What is the melting point of Denaturation?

• the temp at which half the DNA has become single-stranded

• melting temp reflect sequence compositions, higher GC content the more stable so higher temp

What is DNA and RNA polymerase?

• primary enzyme for synthesizing nucleic acids

• synthesize in the 5’3 direction

• are both pencils and erasers

What is PCR?

• takes advantage of the ability for each DNA to serve as a template for production of a complimentary strand

• uses heat-stable enzymes

• discovered by Kary Mullis

What are DNA-histones?

• they are DNA packaging enzymes

  • pack tightly in nucleosomes

• a complexes on a beads on “string” of a double-stranded DNA

• they are basic, conservative and positives

What are the five histone proteins?

• H1

• H2A

• H2B

• H3

• H4

What histone proteins are nucleosomes composed of?

• two molecules of each…

• H2A

• H2B

• H3

• H4

*H1 binds the region of linker DNA

Are histones reversible?

• Yes

What do 3 nucleotides equal?

• 1 codon

• 1 amino acid

Who has single vs multiple chromosomes?

• Viruses and bacteria = single

• Eukaryotes = multiple

What are some key features of bacterial genome?

• closed, circular

• no introns

• have plasmids: isolated and manipulated

  • many of them are resistant to antibiotics

• contains all info required to produce every protein required by the bacteria

What are the non-coding regions that interrupt eukaryotic genes called?

• Introns

  • they are located between the coding regions

True or False: Eukaryotic chromosomes are typically circular, similar to bacterial genomes.

• False

Which two organelles in a eukaryotic cell may contain their own DNA, distinct from the nucleus?

• Mitochondria and chloroplasts

What are the repetitive DNA sequences at the ends of linear eukaryotic chromosomes called, and what is their primary function?

• Telomers

  • protect ends of chromosomes from deterioration or from fusing with neighboring chromosomes

*happens in cancer cells

Define introns and state where they are typically found.

• Introns are non-coding sequences of DNA that "intervene" or interrupt the coding regions (exons) of a gene. They are a hallmark of the eukaryotic genome

What is Epigenetics, and does it involve changing the actual DNA sequence?

• Epigenetics refers to heritable changes in gene expression that do not involve changes to the underlying DNA sequence

*turns genes off

What can we see in our modern world soon?

• manipulations to make immortal persons

• personalized medicine