1. Nucleic Acids Examples: Structure: RNA (ribonucleic acid)
single helix
DNA (deoxyribonucleic acid)
double helix
Structure:
monomers = nucleotides
DNA
RNA

2. Nucleotides 3 parts nitrogen base (C-N ring) pentose sugar (5C)
ribose in RNA
deoxyribose in DNA
phosphate (PO4) group
Nitrogen base I’m the A,T,C,G or U part!
DNA & RNA are negatively charged:
Don’t cross membranes.
Contain DNA within nucleus
Need help transporting mRNA across nuclear envelope.
Also use this property in gel electrophoresis.
Are nucleic acids charged molecules?

3. Types of nucleotides 2 types of nucleotides different nitrogen bases
Purine = AG
Pure silver!
2 types of nucleotides
different nitrogen bases
purines
double ring N base
adenine (A)
guanine (G)
pyrimidines
single ring N base
cytosine (C)
thymine (T)
uracil (U)

4. Dangling bases? Why is this important?
Nucleic polymer
Backbone
sugar to PO4 bond
phosphodiester bond
new base added to sugar of previous base
polymer grows in one direction
N bases hang off the sugar-phosphate backbone
Dangling bases? Why is this important?

5. Pairing of nucleotides
Nucleotides bond between DNA strands
H bonds
purine :: pyrimidine
A :: T
2 H bonds
G :: C
3 H bonds
The 2 strands are complementary.
One becomes the template of the other & each can be a template to recreate the whole molecule.
Matching bases? Why is this important?

6. H bonds? Why is this important?
DNA molecule
Double helix
H bonds between bases join the 2 strands
A :: T
C :: G
H bonds = biology’s weak bond
• easy to unzip double helix for replication and then re-zip for storage
• easy to unzip to “read” gene and then re-zip for storage
H bonds? Why is this important?

7. Matching halves? Why is this a good system?
Copying DNA
Replication
2 strands of DNA helix are complementary
have one, can build other
have one, can rebuild the whole
when cells divide, they must duplicate DNA exactly for the new “daughter” cells
Why is this a good system?
Matching halves? Why is this a good system?

8. Interesting note… Ratio of A-T::G-C affects stability of DNA molecule
2 H bonds vs. 3 H bonds
biotech procedures
more G-C = need higher T° to separate strands
high T° organisms
many G-C
parasites
many A-T (don’t know why)
At the foundation of biology is chemistry!!

9. From Gene to Protein How Genes Work

10. DNA gets all the glory, but proteins do all the work!
The “Central Dogma”
Flow of genetic information in a cell
How do we move information from DNA to proteins?
transcription
translation
DNA
RNA
protein
trait
To get from the chemical language of DNA to the chemical language of proteins requires 2 major stages:
transcription and translation
DNA gets all the glory, but proteins do all the work!
replication

11. from DNA nucleic acid language to RNA nucleic acid language
Transcription
from DNA nucleic acid language to RNA nucleic acid language

12. DNA RNA RNA ribose sugar N-bases single stranded lots of RNAs
uracil instead of thymine
U : A
C : G
single stranded
lots of RNAs
mRNA, tRNA, rRNA, siRNA…
transcription
DNA
RNA

13. Transcription Making mRNA transcribed DNA strand = template strand
untranscribed DNA strand = coding strand
same sequence as RNA
synthesis of complementary RNA strand
transcription bubble
enzyme
RNA polymerase
coding strand 3 A G C A T C G T 5 A G A A A G T C T T C T C A T A C G
DNA T 3 C G T A A T 5 G G C A U C G U T 3 C
unwinding G T A G C A
rewinding
mRNA
RNA polymerase
template strand
build RNA 53 5

14. RNA polymerases 3 RNA polymerase enzymes RNA polymerase 1
only transcribes rRNA genes
makes ribosomes
RNA polymerase 2
transcribes genes into mRNA
RNA polymerase 3
only transcribes tRNA genes
each has a specific promoter sequence it recognizes

15. Matching bases of DNA & RNA
Match RNA bases to DNA bases on one of the DNA strands C U G A G U G U C U G C A A C U A A G C
RNA
polymerase U 5' A 3' G A C C T G G T A C A G C T A G T C A T C G T A C C G T

16. Eukaryotic genes have junk!
Eukaryotic genes are not continuous
exons = the real gene
expressed / coding DNA
introns = the junk
inbetween sequence
introns come out!
intron = noncoding (inbetween) sequence
eukaryotic DNA
exon = coding (expressed) sequence

17. mRNA splicing Post-transcriptional processing
eukaryotic mRNA needs work after transcription
primary transcript = pre-mRNA
mRNA splicing
edit out introns
make mature mRNA transcript
eukaryotic RNA is about 10% of eukaryotic gene.
intron = noncoding (inbetween) sequence
~10,000 bases
eukaryotic DNA
exon = coding (expressed) sequence
pre-mRNA
primary mRNA
transcript
~1,000 bases
mature mRNA
transcript
spliced mRNA

18. Splicing must be accurate
No room for mistakes!
a single base added or lost throws off the reading frame
AUGCGGCTATGGGUCCGAUAAGGGCCAU
AUGCGGUCCGAUAAGGGCCAU
AUG|CGG|UCC|GAU|AAG|GGC|CAU
Met|Arg|Ser|Asp|Lys|Gly|His
AUGCGGCTATGGGUCCGAUAAGGGCCAU
AUGCGGGUCCGAUAAGGGCCAU
AUG|CGG|GUC|CGA|UAA|GGG|CCA|U
Met|Arg|Val|Arg|STOP|

19. from nucleic acid language to amino acid language
Translation
from nucleic acid language to amino acid language

20. How does mRNA code for proteins?
TACGCACATTTACGTACGCGG
DNA 4
ATCG
AUGCGUGUAAAUGCAUGCGCC
mRNA 4
AUCG ?
Met Arg Val Asn Ala Cys Ala
protein 20
How can you code for 20 amino acids with only 4 nucleotide bases (A,U,G,C)?

21. mRNA codes for proteins in triplets
TACGCACATTTACGTACGCGG
DNA
codon
AUGCGUGUAAAUGCAUGCGCC
mRNA
AUGCGUGUAAAUGCAUGCGCC
mRNA ?
Met Arg Val Asn Ala Cys Ala
protein

22. WHYDIDTHEREDBATEATTHEFATRAT WHYDIDTHEREDBATEATTHEFATRAT
1960 | 1968
Cracking the code
Nirenberg & Khorana
Crick
determined 3-letter (triplet) codon system
WHYDIDTHEREDBATEATTHEFATRAT
WHYDIDTHEREDBATEATTHEFATRAT
Nirenberg (47) & Khorana (17)
determined mRNA–amino acid match
added fabricated mRNA to test tube of ribosomes, tRNA & amino acids
created artificial UUUUU… mRNA
found that UUU coded for phenylalanine

23. The code Code for ALL life! Code is redundant Start codon Stop codons
strongest support for a common origin for all life
Code is redundant
several codons for each amino acid
3rd base “wobble”
Why is the wobble good?
Strong evidence for a single origin in evolutionary theory.
Start codon
AUG
methionine
Stop codons
UGA, UAA, UAG

24. How are the codons matched to amino acids?3 5
DNA
TACGCACATTTACGTACGCGG 5 3
mRNA
AUGCGUGUAAAUGCAUGCGCC
codon 3 5
UAC
Met
GCA
Arg
tRNA
CAU
Val
anti-codon
amino acid

25. Protein Synthesis in Prokaryotes
Bacterial chromosome
Protein Synthesis in Prokaryotes
Transcription
mRNA
Psssst… no nucleus!
Cell
membrane
Cell wall

26. Prokaryote vs. Eukaryote genes
Prokaryotes
DNA in cytoplasm
circular chromosome
naked DNA
no introns
Eukaryotes
DNA in nucleus
linear chromosomes
DNA wound on histone proteins
introns vs. exons
Walter Gilbert hypothesis:
Maybe exons are functional units and introns make it easier for them to recombine, so as to produce new proteins with new properties through new combinations of domains.
Introns give a large area for cutting genes and joining together the pieces without damaging the coding region of the gene…. patching genes together does not have to be so precise.
introns come out!
intron = noncoding (inbetween) sequence
eukaryotic
DNA
exon = coding (expressed) sequence

27. Translation in Prokaryotes
Transcription & translation are simultaneous in bacteria
DNA is in cytoplasm
no mRNA editing
ribosomes read mRNA as it is being transcribed

28. Translation: prokaryotes vs. eukaryotes
Differences between prokaryotes & eukaryotes
time & physical separation between processes
takes eukaryote ~1 hour from DNA to protein
no RNA processing