DNA Replication and Protein Synthesis

YOUR NOTES

UNIT 2 NOTES
DNA (deoxyribonucleic acid)
DNA Functions
• Stores genetic information and copies itself (replication) to pass on the information
• Contains genes (instructions to make proteins)
• Instructs cell’s activities
DNA Structure
• DNA is a polymer of nucleotides
• Chromosomes (DNA strand + associated proteins ie. Histones wrap DNA around like a spool = condensed chromatin)
↓
genes (sections of a chromosome that codes for a protein)
↓
nucleotides (3 parts: phosphate, deoxyribose sugar, and nitrogen base)
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Double helix shape - Held together by weak hydrogen bonds
Found only in NUCLEUS
4 different bases N- bases: adenine – thymine can only bond together cytosine – guanine

Nucleotide bases have one of the following structures:
Purines: have a double Nitrogen-ring = adenine and guanine
Pyrimidines: have a single Nitrogen-ring = thymine, cytosine, and uracil
# of purines = # of pyrimidines

DNA Replication
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Means of copying genetic information to be passed on (meiosis)
Ensuring all cells carry same genetic information (mitosis)
Occurs in cell nucleus. (before cell division)

STEPS:
1.
Unzipping: DNA strand unwinds
• DNA helicase (enzyme) breaks H-bonds between N-bases
= unzipping

2.

Complementary base pairing
• DNA polymerase (enzymes) bonds the complementary DNA nucleotides into position with their partners on each side of the DNA strand called the template or parent strand. (Nucleotides free floating in nucleus)
- H- bonds between N- bases
- Covalent bonds between  and sugar of each nucleotide

3.

Joining of adjacent nucleotides.
• 2 new sugar-phosphate backbones form when the enzyme DNA polymerase forms covalent bonds between new nucleotides. End up with 2 identical strands which are semi-conservative where there is one old strand and one new strand of DNA (composed the original “parent” and a new “daughter” strand).

4.

“Proof reading”: enzyme DNA polymerase checks for any mistakes
→ mistakes = MUTATIONS - mutations can occur due to chemicals, UV rays…

GENETIC ENGINEERING
= the direct manipulation of genes for practical purposes
Genetic Engineering APPLICATIONS:
1. Protein Production via Recombinant DNA (rDNA)
= replacing genes from one organism with genes from another organism
• Bacteria, such as E. coli are often used
Example using insulin gene (from humans)
I. restriction enzymes are used to cut out the insulin gene from human DNA molecule
II. plasmid is removed from a bacteria – cut with same restriction enzymes
9 an extra ring of DNA found in some bacteria
III. insulin gene is inserted into the plasmid
IV. recombined DNA plasmid is put back into bacteria
V. as bacteria divides the recombined DNA is replicated
- new gene causes bacteria to behave differently ie. Change sewage into less toxic forms, detoxifying toxic spill (ie oil), get rid of pests in plants.
Human growth hormone (HGH) to treat stunted growth
Dissolve blood clots in heart attack patients.
Tissue plasminogen activator (TPH)
2. GMO’s – genetically modified organisms
3. Gene therapy – alteration of afflicted individuals’ genes (of the same species)
• could help with genetic diseases like cystic fibrosis, Alzheimer’s, some cancers, AIDS
• Problems costly, human genes are hard to manipulate, difficult to get the new gene in the right spot, ethically questionable to experiment on humans, leads to Eugenic engineering (“designer babies”)
4. Better / safer vaccines – flu, HIV
5. Transgenic organisms – organisms modified with DNA from another organism

PROTEIN SYNTHESIS
What is the connection between DNA and protein?
• Remember: DNA can’t leave the nucleus but protein synthesis occurs in the cytoplasm …
How?
• protein message must be carried from the nucleus → cytoplasm → ribosomes
RNA Structure
• Single straight polymer of nucleotides
• RNA is a polymer of nucleotides
• Ribose sugar, nitrogen base, and phosphate
• Linear (not helix)
• A, C, G, U - uses uracil (U) rather than thymine (T)
• Made in nucleus but functions (works) in the cytoplasm for protein synthesis
• 3 types of RNA – mRNA, tRNA, rRNA
N-bases = adenine, uracil (instead of thymine) guanine, and cytosine
RNA - made in nucleus, but functions outside of the nucleus
Function:
• aids in protein synthesis
• uses DNA strand as the template to make its strand using complimentary base pairing
Test Yourself – Create a Venn Diagram to compare and contrast DNA and RNA using these terms
Deoxyribose
A with T
C with G
A with U
Double Stranded
Located in the nucleus and cytoplasm Found in the nucleus
Monomers contain nitrogen
Nucleotides contain phosphate
Ribose
Single stranded
3 types of RNA: all help in protein synthesis
1.
messenger RNA (mRNA) - carries transcribed message from DNA to ribosome (nucleus to cytoplasm)
2.
Transfer RNA (tRNA) - carries the amino acid that will base pair with mRNA to make polypeptide
3.
ribosomal RNA (rRNA) - makes up the ribosome (along with proteins)

Overview of gene expression
Replication (DNA to DNA) ê Transcription (DNA to mRNA) ê Translation (mRNA to protein)

Steps of Protein Synthesis:
Step 1:Transcription
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DNA code (gene) has instructions to make a particular protein
Instructions are copied into mRNA in the nucleus

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Steps of Transcription
A. Helicase opens the section of DNA (the gene)
– Begins at INITIATION site
– Continues until TERMINATION site
B.. complementary RNA base pairs attach to form the mRNA strand (RNA polymerase forms the
RNA sugar-phosphate backbone and checks for mistakes)
• Transcription occurs in the nucleus – makes mRNA, tRNA, and rRNA
C. complementary mRNA detaches & leaves the nucleus through the nuclear pore and goes to the cytoplasm

Step 2: Translation
Info:
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The mRNA code is made up of groups of three nucleotide bases known as codons.
Each codon codes for a specific amino acid.
Please note that there is more than one codon for each amino acid:
• CODONS – mRNA base triplets
• Translation occurs in cytoplasm only at a ribosome (a large and a small subunit made up of rRNA and proteins)
– rRNA is made in the nucleolus
• tRNA is found free-floating in the cytoplasm
• tRNA structure:
» tRNA molecule is a small piece of RNA that has a specific aa attached to one end
» at the other end, an anticodon (3 bases that will complement mRNA codon)
3 STEPS in Translation
A. Initiation (means “start”)
– ribosomal subunits come together and mRNA attaches
– an INTIATOR (start) codon (always AUG) turns on the process
B. Elongation (what is getting bigger?)
– tRNA anticodon (with specific aa) matches up with the mRNA codon
– Each tRNA leaves to find another aa as mRNA over one codon & another tRNA brings the next aa
– aa’s continually peptide bond building a polypeptide
C. Termination
– When ribosomal unit reaches any ‘Terminator’ codon, the message is to STOP translation
• There are 3 stop codons (UAA, UAG, UGA)
– None of these have matching tRNA anticodon
– Ribosome subunits split in 2 again

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Still translation but not a step:
Polyribosome – often several ribosomes work together on one protein
• Each ribosome makes a section of the protein
• This is done for very large proteins. This enables these large proteins to be made faster.
• Also called a polysome

Mutations (B8)
A mutation is a permanent change in DNA.
• it may occur spontaneously during DNA replication or
• it may be caused by MUTAGENS (environmental agents) causing an increased rate of mutations.
3 types of mutagens:
a) Chemical – food additives, hallucinogenic drugs, asbestos, DDT, manufactured chemicals, pesticides, etc.
b) Radiation – some is natural (cosmic rays, UV)
c) Biological – bacteria and viruses such as human pampiloma virus (HPV) that causes warts or hepatitis B and C which cause liver damage and cancer.

3 common point (gene) mutations:
1. Substitution – not as serious. One nucleotide is substituted for another. v This may or may not change the AA
Ex) G is substituted for T
ATG CCT TAC
ATG CCG TAC
2. Deletion – Serious. One nucleotide is deleted so all the codons are changed from that point on.
– The reading frame is shifted
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Ex) T in the first codon is deleted
ATG CCT TAC
AGC CTT AC .
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Insertion – Serious. One nucleotide is randomly added so all the codons are changed from that point on.
– The reading frame is shifted.
– Ex) A is inserted in the first position on the second codon
ATG CCT TAC
ATG ACC TTA C
(this last codon is incomplete and does not make sense)

Genetic Code: Many aa’s can be represented by more than one codon (degenerative nature)
Ex. leucine: if substitution is last base, it would result in no change due to the 4 codons (CUU, CUC, CUA, & CUG) that all code for leucine

Why can mutations cause genetic disorders?
-chemical reactions occur in “pathways”
A

→

Enzyme AB

B

→

Enzyme BC

C

→

Enzyme CD

D→

If enzyme BC were mutated pathway would stop (C & D not produced)
Ex. sickle cell anemia
– Point mutation A-T changed to T-A (substitution)
– GAG (glutamate) become GTG (valine).
Ex. cystic fibrosis caused by a deletion of AA phenylalanine
Ex. Huntington’s – insertion of multiple copies of CAG or glutamine
– Point insertions rare -usually result of gene therapy.
How can you detect where a mutation occurred?: ìRadioactively labeling one nucleotide can allow us to see if a change has occurred in the DNA or RNA
– Radioactive thymine used to see changes in DNA
– Radioactive uracil used to see changes in RNA
It is important where and when a mutation occurs
1. somatic mutation - in the body cell
• may affect the individual but are not passed on to offspring
• ex. many cancers
2. germinal mutation - occurs in the sex cells (egg/sperm).
• inheritable and may be good (rare) or bad
• have driven evolution.
• Ex. hemophilia

Chromosomal Mutations
= a mutation of all or part of a chromosome
• deletions: end of a chromosome breaks off or 2 simultaneous breaks in a chromosome leads to a loss of a segment
• duplications: a chromosomal segment is repeated. Can occur when a segment that has broken off attaches to its homologue or unequal crossing over can occur.
• inversions: a segment of a chromosome is turned around 180°. This leads to an altered gene.
• translocations: movement of a segment of a chromosome from one chromosome to another, non homologous chromosome.