Biochemistry: Mod 1 

 DNA = phosphate + deoxyribose sugar + A/T/C/G 

o Contains two strands. The strands are antiparallel (opposite each other). 

o 5’ → 3’  

3’ ← 5’ 

 RNA = phosphate + ribose sugar + A/U/C/G 

o Single strand, can fold back onto itself and form pairs between itself (stem‐loop). 

 Each nucleic acid is made up of polymers (many monomers) that are called nucleotides. 

o Nucleotides contain one or more phosphates, a five‐carbon sugar, and a nitrogen base. 

o Nucleotides are always made in the 5’ to 3’ direction. 

o 5 is always the beginning of the strand, 3 is the end where nucleotides are added. 

 DNA organization: DNA is wrapped around proteins called histones → nucleosome → chromaƟn fiber→ 

chromosomes 

 Steps to the central dogma: 

o Coding DNA → template DNA → mRNA → tRNA (amino acid) 

o DNA → transcribed to mRNA → translated to protein 

o Each step is complementary (opposite) to the previous step, but if you skip a step it will be identical to 

the previous step.  

o Example 

 1. Coding DNA strand       5’ AAA TTT GGG CCC 3’  

 2. Template DNA strand  3’ TTT AAA CCC GGG 5’ 

 3. mRNA                                 5’ AAA UUU GGG CCC 3’ 

 4. tRNA                    Lys     Phe    Gly   Pro 

 Pairing:   

o DNA: A → T 

o RNA: A → U 

 DNA replication: 

o Because DNA is a double helix, one strand can be separated and serve as a template for synthesis of a 

new strand. 

o Semi‐conservative: each copy of DNA contains a template strand and a new strand.

o Steps of replication: 

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o 1. The DNA must be separated, creating a replication fork. This is done by helicase. 

o 2. Primase attaches an RNA primer, where the replication is to start. 

o 3. DNA polymerase adds bases to the remaining of the strand until it reaches a stop codon. This 

is done in fragments, called okazaki fragments. 

 If an error is detected, it removes the nucleotides and replaces them with correct ones, 

known as exonuclease. 

o Exonuclease removes all of the RNA primers, and DNA polymerase fills in those gaps. 

o DNA ligase seals the two strands forming a double helix. 

 DNA → transcribed → mRNA → translated → protein  

 Transcription occurs in the nucleus: 

o Initiation: RNA polymerase binds to a sequence of DNA called the promoter, found near the beginning 

of a gene. Each gene has its own promoter. Once bound, RNA polymerase separates the DNA strands, 

providing the single‐stranded template needed for transcription.

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o Elongation: One strand of DNA, the template strand, acts as a template for RNA polymerase. As it 

"reads" this template one base at a time, the polymerase builds an RNA molecule out of complementary 

nucleotides, making a chain that grows from 5' to 3'. The RNA transcript carries the same information as 

the non‐template (coding) strand of DNA, but it contains the base uracil (U) instead of thymine (T).  

o Termination. Sequences called terminators signal that the RNA transcript is complete. Once they are 

transcribed, they cause the transcript to be released from the RNA polymerase. 

o Pre‐mRNA must go through extra processing before it can direct translation. 

 They must have their ends modified, by addition of a 5' cap (at the beginning) and 3' 

poly‐A tail (at the end). 

 Pre‐mRNAs must also undergo splicing. In this process, parts of the pre‐mRNA 

(called introns) are chopped out, and the remaining pieces (called exons) are stuck back 

together