Old people (structure and function of DNA)

Franklin / Wilkins had picture if DNA x-ray diffraction

Watson and Crick determined double helix structure
Griffith – kills mice w/ heat killed s cell and live r cell (?? Is moving from s to r? Hereditary thing
Avery – eliminated protein and RNA in experiment to heat killed s cell to kill more mice
Hershey-Chase – radio active isotopes to label protein and DNA injected bacteria to cell.

Structure of DNA:
All DNA molecules are made up of:
1. a 5-sugar molecule (deoxyribose)
2. a phosphate group
3. a nitrogenous base (Adenine, Thymine, Guanine, Cytosine)

The sugar molecule of one DNA molecule covalently bonds to the phosphate group of another on
the 5’ carbon. Another phosphate is bonded to the succeeding sugars 3’ carbon. The phosphate
group and Sugar molecule forms the sugar-phosphate backbone (hydrophilic) which looks like the
staircase of the double helix. The nitrogenous bases face the insides of the double helix
(hydrophobic) and complementary nitrogenous bases form a hydrogen bond. This bond is called a
hydrogen bond. A nucleotide is a subunit of DNA strand that consists of == a sugar, a phosphate
group, a nitrogenous base ==.DNA strands are anti parallel because each has a 5’ end and a 3’ end.
The 5’end of one strand is opposite of the 5’ end of the opposing strand.

Nitrogenous base pairing happens in both DNA and RNA. Hydrogen bonds are formed between
Nitrogenous bases when they have found their complementary nitrogenous base.
IN DNA: But in RNA:
A <3 T A <3 U << Thymine doesn’t exist. It is replaced by uracil.
C <3 G C <3 G

Thymine and Cytosine are Pyrimidines

Adenine and Guanine are Purines -> double ring of Carbon and Nitrogen.

STEPS IN DNA REPLICATION:

1. Helicase (enzyme) separates DNA strand and SSB attaches to prevent DNA strands from
Reannelling.
2. The Y shaped region where complementary bases are paired is called the replication fork.
3. The double helix consists of two antiparallel DNA strands with complementary 5’ to 3’
strands running in opposite directions. Polymerase enzymes can synthesize nucleic acid
strands only in the 5’ to 3’ direction, hooking the 5’ phosphate group of an incoming
nucleotide onto the 3’ hydroxyl group at the end of the growing nucleic acid chain. Because
the chain grows by extension off the 3’ hydroxyl group, strand synthesis is said to proceed in
a 5’ to 3’ direction
4. DNA polymerase cannot simply begin copying the DNA < needs a place to start
5. RNA polymerase (primase) first copies a short stretch of the DNA strand
6. DNA polymerase starts at the 3’ end of the RNA primer,
7. DNA polymerase adds complementary nucleotides to template (randomly floating).
8. Covalent bonds form between deoxyribose sugar + phosphate group so backbone grows
9. When DNA polymerase is done, it falls off.
10. Hydrogen bonds form between complementary bases.
11. Other polymerase can only copy a short stretch of DNA before it runs into the primer of the
previously sequenced fragment. It is forced to repeatedly release the DNA strand and slide
further upstream to begin extension from another RNA primer.
12. The sliding clamp helps hold this DNA polymerase onto the DNA as the DNA moves through
the replication machinery. The sliding clamp makes the polymerase secure on DNA.
13. The short stretches of DNA that make up the lagging strand are known as Okazaki fragments.
14. RNA primers must be removed and the Okazaki fragments must be joined together to create a
continuous DNA strand.
15. Removal of the RNA primer. RNAse H, which recognizes RNA-DNA hybrid helices,
degrades the RNA by hydrolyzing its phosphodiester bonds
16. sequence gap created by RNAse H is then filled in by DNA polymerase which extends the 3’
end of the neighboring Okazaki fragment
17. Okazaki fragments are joined together by DNA ligase that hooks together the 3’ end of one
fragment to the 5’ phosphate group of the neighboring fragment

Role of protein in organisms:

 Proteins (amino acids) grow and repair tissues
 They do everything in living cell
 Catalyze bio and chemical reactions within living cell
 Store chemical compounds
 Protective proteins – immune response of the organism,
 Facilitated diffusion
 Repairs body

Transcription (nucleus) – first step to protein synthesis where RNA copies DNA

**transcription only happens on a specific gene (part of DNA) genes are split into sections the
transcribed is called the exons, and the not used section is the intron.
RNA polymerase binds to a promoter (a sequence on DNA) and DNA unwinds.  at the
promoter RNA polymerase finds complementary nitrogenous bases to the single stranded DNA 
Thymine however, is replaced by Uracil on a mRna strand.  Complementary bases are found
until they reach the termination signal (sequence of nucleotide that marks end of gene) RNA
polymerase releases DNA and new RNA strand mRNA strand moves to cytoplasm

Codons are 3 nitrogenous bases that code for a certain amino acid (20). The DNA is read from a 3’
to 5’ end while because of the anti parallel nature it is transcribed in the 5’ to 3’ end (same as DNA
replication) .

Translation (cytoplasm) – 2nd step to protein synthesis where RNA  protein!

So the mRNA is floating around in the cytoplasm, and Ribosome (made up of rRNA with 50’s
subunit and 30’s subunit) binds to the mRNA strand and finds the start codon AUG  tRNA that
has the anti codon floats around and enters at the Accepter site  anti codon of tRNA binds to its
complementary codon at peptidyl site  next tRNA that recognizes codon comes in at the A site,
and tRNA move one codons distance  the amino acids on previous tRNA forms a peptide bond
(condensation synthesis) with the new coming amino acid and then connects to new tRNA  old
tRNA moves to E site and falls off  the cycle repeats until they reach the stop codon  amino
acid chain = polypeptide = primary structure of protein!

Role of RNA’s in protein synthesis:

mRNA – Carry strands of instruction from DNA template

rRNA – makes up ribosome (site for protein synthesis)
tRNA – carries amino acids, has complementary anti codons, makes protein

Stages of Protein structure (Amino Acids determine final shape!)

Primary Structure (1D) – sequence of covalently (peptide =condensation) bonded amino acids
Secondary Structure (2D) – segments of polypeptides fold and become stable. Hydrogen bonds
between amino group of one and Carboxylic group of another. R group interact = adjacent coils or
folded strands. Coils are Alpha Helix. Ladder like is Beta sheet.
Tertiary Structure (4D) – domain formation of proteins. Beta sheets fold up to make shape
 Ionic bonds – some r groups are very charged so attraction
 Hydrogen bonds – keep its shape
 Hydrophobic interaction – uncharged R group tend to loop and stay away from
water (Hydrophobic)
 Disulfide bonds – covalent linkages between an r group w/ sulfur and another
Quaternary Structure – two or more polypeptide chains forming a complex. Arrangement of
multiple folded protein molecules. Ionic interactions and disulfide bonds keep it together.

Ribosomes are attached to rough Endoplasmic Reticulum  gives ribosome’s a great surface to
synthesize on a large scale.
Golgi Apparatus controls flow of substances cell. Carbohydrates are added to protein in the end.
Final product moves to cell membrane where it is excreted and can be used.

DNA RNA similarities DNA RNA differences

 1 sugar, phosphate group, nitrogenous base
 Has complementary bases to pair with
 It’s sugar is linked to phosphate at 5 prime
base linked to 1’ carbon
 Shares ACG
 Contains genetic information
 RNA single stranded
 RNA much shorter
 RNA has uracil instead of Thymine
 DNA doesn’t have different types
 DNA in nucleus only
 RNA in nucleus and cytoplasm
 RNA involved in protein synthesis
The sugar phosphate backbone is highly polar = hydrophilic. Bases neutral = hydrophilic.
Antiparallel strands = have opposite chemical polarity. Antiparallel unzips leading strand and
lagging strand because DNA can only synthesis in 5’ to 3’ direction.

DNA Replication Enzymes:

Helicase – unwinds DNA strands
Primase – synthesizes a short stretch of RNA primers to replication can start
Ligase – links short DNA chains or parts together a.k.a. the gat at the replication fork. Bonds by
phosphydiester bonds.

Role of DNA:
Protein synthesis – helicase unwinds and 1 strand is used as template. Semi-conservative
Cell reproduction – needs to have same genetic information. DNA contains information and
through semi-conservative replication, the same exact info is copied.
Genetics –
Evolution – DNA has genetic code for development of an organism. Mutations occur in genetic
coding making organism traits change. Environment allows organisms w/ good mutations to live.
Natural selection = these mutants live longer, reproduce, pass trait on, organisms evolve.