BIOCHEM MODULE 1 BIOCHEM C785

DNA & RNA
Central DOGMA – DNA -> RNA -> protein
 Nucleic Acid – function to encode inheritable information and pass it on through generations.

RNA – less stable, temporary nucleic acid.
o Easily made
o Degrades rapidly outside of the nucleus
Three types of RNA
1. rRNA (ribosomal) – composed of small and large sub units – binds to mRNA.
2. mRNA (messenger) – single strand copy of DNA – contains codons that specify type and order of amino
acids in the polypeptide.
3. tRNA (transfer) – cloverleaf shape, carries amino acid on one end and anti-codon on other end to transfer.

 Transcription – when the cell makes an RNA copy of a section of DNA and carries the information out of the
nucleus to the rest of the cell.
o Primary enzyme involved is RNA polymerase
- Works to separate two DNA strands at the promoter (transcription start site). It then creates
a short DNA-RNA hybrid that matches the correct RNA nucleotides to the DNA sequence it is
transcribing. RNA is then released as a single stranded molecule.
o mRNA – to form mature RNA a cap is placed on the 5’ end during transcription and a poly-A tail is
placed on 3’ end after transcription termination. (This process protects mRNA from degradation
once it leaves the nucleus).
- Then splicing occurs – introns are cut out and remaining exons are joined together to form
mature RNA that is now ready for translation.
 Translation – when RNA leaves the nucleus and the information is then used to make proteins by forming a
protein chain using peptide bonds.
o Translation always starts with AUG codon.
o Translation ends when ribosome encounters a STOP codon. Here, the ribosome then binds to a
release factor protein which terminates translation.

DNA contains:
 Double stranded
 SUGAR = deoxyribose
 Contains thymine base

RNA contains:
 Single stranded
 SUGAR = ribose
 Contains uracil base

DNA replication: 1. Must be separated
2. Synthesize by DNA polymerase (protein)
3. DNA polymerase matches nucleotides to parental sequence
4. If pairing is correct, then nucleotide is bonded to DNA.

,DNA
Template DNA (Non-Coding) -------- (pneumonic TP = PAIR)
 Runs in opposite direction and are complementary
Non-Template (Coding) --------------- (pneumonic NTR = REPLACE)
 Runs in same direction as mRNA
 Strands are identical, only difference is the replacement of T with U

DNA is antiparallel and has opposite 5’ and 3’ orientations

COMPLEMENTARY gets PAIRED
 A (adenine) pairs with T (thymine) if DNA
 A (adenine) pairs with U (uracil) if RNA
 C (cytosine) pairs with G (guanine)
 5’ pairs to 3’
Match numbers and letters in exact same order!!
Examples: 1. Template and Non-Template
2. mRNA and tRNA
3. Non-Coding and mRNA
Amino Acid Sequence
(read 5’ to 3’ to plug
Complementary sequence Stays same, change T to U into codon table
Template (Non-Coding)  Coding (Non-Template)  mRNA 
tRNA
complementary,
RNA contains U
NON-COMPLEMENTARY - REPLACE
 Sequences are identical, just need to replace T with U

IDENTICAL
 Just match numbers and letters in exact order

Gene Expression – is the transcription of new RNA.

MUTATIONS
 Can result from damage to DNA or errors introduced during damage repair.
 Point Mutations – changes in a single base pair. Multiple kinds:
1. Silent Mutations – does not change amino acid sequence d/t redundancy in genetic code
2. Missense Mutations – codon now encodes a different amino acid
3. Nonsense Mutations – stop codon terminates translation
4. Frameshift Mutations – insertions or deletions disrupt the coding of a protein

Apoptosis – programmed cell death.

DNA REPAIR
1. Base Excision Repair (BER) – a single nucleotide is removed. Steps:
 Recognize damage
 Remove damage by excising part of one strand to leave a gap
 Resynthesize the sequence using genetic information from other strand to fill the gap
 Ligate to seal gap and restore continuity of DNA backbone
2. Nucleotide Excision Repair – about 30 nucleotides are removed

,  Thymine Dimer – when UV radiation causes two thymines that are adjacent to one another to fuse
together – can only be fixed by cutting away several nucleotides.
3. Mismatch Repair – removes replication errors
 Cell can distinguish newly synthesized DNA from parental DNA to remove only newly synthesized
DNA to preserve parental DNA.
 Proofreading:
1. DNA polymerase removes incorrect base
2. DNA polymerase inserts correct base
 Mismatch:
1. Recognizes mistakes made during replication and cuts out several bases surrounding
mismatched base
2. DNA polymerase inserts correct base
3. Ligase seals it off
4. Homologous Recombination – process of repairing double stranded breaks caused by exposure to xrays or
radioactivity.
 DNA sequence that is nearly identical is located and uses the sequence of the intact DNA strands to
fix the double strand break – this results in DNA from both strands being mixed.
 Can also occur in absence of damage just to shuffle genes to create diversity on each chromosome
5. Non-Homologous End Joining – extreme repair pathway – LAST RESORT!
 Removes damaged portions and glues remaining parts back together without repairing or inserting.

Enzymes  Helicase – separates DNA double helix
 Ligase – seals gaps to create continuous DNA strand

INHERITENCE
 Gene = segment of DNA that encodes the sequence instructions for a particular product.
 Humans have 46 chromosomes (23 pairs) – half are inherited from mom and other half from dad.
o Chromosomes 1 through 22 are autosomal, while 23 is sex-linked.
 Genotype (pair of genes) determines phenotype (characteristics)
 Allele – each member of the gene pair
 Pedigree Chart – family tree that highlights certain traits over multiple generations
o Female = circle, male = square, affected individuals are colored in
 Punnett Squares – paternal alleles are on the left and maternal are at the top
 Carriers are heterozygous dominant = recessive trait
 Male/female equally affected = autosomal

Sex-Linked Inheritance
o X-Linked  males (XY) have one copy of alleles found on X chromosome. Predominantly affects males.
o Can skip generations
o Female carriers can pass traits to 50% of their sons
o X-Linked recessive – only males are affected
o X-Linked dominant – daughters of affected male will have the trait
o Y-Linked  rare because Y chromosome is small and doesn’t carry many genes

o "Heterozygous" means it has two different alleles (Ff)
o "Homozygous dominant" means it has two copies of the dominant allele (FF)
o If an allele is dominant, the dominant phenotype MUST be expressed
o "Homozygous recessive" means it has two copies of the recessive allele (ff)