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BIOCHEMISTRY MODULE ONE 
 
ABOUT DNA AND RNA 
 

Key Concepts: 
 
● F 
 
About DNA: 
 

 
 

●

Nucleic acids: ​building blocks for genes; membrane-enclosed organelle that contains DNA and protein
...
 
○
Are essential to life
...
 
○
Function to ​encode​ ​heritable information ​and pass it on from generation to generation
...
  
○
Characterized by their interactions among themselves
...
 
■
2) a pentose sugar [either deoxyribose or ribose]
...
  

●

Nucleus:​ houses DNA and exercises strict control over what ​can ​and ​cannot ​access the DNA
...
  
○
Transcription:​ when information in a particular section of DNA is needed, the cell makes an RNA copy of that DNA section and 
carries the information ​out​ of the nucleus to the rest of the cell; the role of ​mRNA​
...
  
●
At the ​start​, a gene, which is a small segment along the long DNA strand that codes for a specific function, 
is copied or “transcribed” within the nucleus into a new form of nucleic acid called messenger RNA 
(mRNA)
...
  
■
There, it attaches to a ribosome, which begins the process of translating the RNA message into protein language
...
  
○
Contains a ​ribose​ sugar, and the same bases, with the exception of ​uracil​ in place of thymine
...
  
mRNA:​ leaves the nucleus and its information is used to make proteins in a process known as ​translation​
...
  

●

DNA: 

●
 

○
DNA nucleotides contain a deoxyribose sugar, and any of the four bases ​adenine, guanine, cytosine, ​and ​thymine​
...
 
○
Stores and transmits both chemical and information about how to replicate itself and information about traits
...
  
○
Encoded with information for specific cellular functions
...
  
○
Consecutively linked by a phosphodiester bonds form a polymer in which the bases project out from a backbone of repeating 
sugar-phosphate groups
...
 
○

Structure: 
■
Each has a nitrogenous base, a pentose sugar, and a phosphate
...
  
■
Nucleic acids are a​ lways​ made in the 5​ ’ -> 3’​ direction, which means the ​5’ end​ represents the ​beginning​ of a nucleic 
acid strand and ​nucleotides​ are added to the ​3’ end​
...
  
The same DNA strand can be shown in different directions
...
Turning it doesn’t change the identity of the molecule
...
  
■
This constant distance for correct base pairs is often illustrated by showing the DNA in a ladder-like structure (below, 
left​) with the two sugar-phosphate backbones as the vertical supports and the base pairs as the rungs
...
  

 

DNA Replication 一 The Structure of DNA Allows it to be Copied: 
 

 

●

DNA replication allows each cell (and each person) to pass on a complete set of DNA to the next generation
...
Thus, the resulting double-stranded molecules are identical
...
 
■
This creates a replication “fork” where the two original strands separate
...
 
■
DNA polymerase makes a polymer of DNA nucleotides
...
  
●
If the pairing is correct, DNA polymerase binds the nucleotide to the growing strand of DNA
...
  
●
To get around this, it uses ​RNA primers​
...
 

○

 
RNA primers are used at several places along the two strands of DNA - new DNA is created in fragments (​Okazaki fragments​)
...
  
■
As each Okazaki fragment is finished, the RNA primer is removed by RNase H and replaced with DNA by DNA 
polymerase
...
 
○
DNA ligase seals the nicks to create a continuous strand of new DNA
...
 
3’ → 5’ exonuclease:​ removal of erroneous nucleotides at the 3’ end of the new DNA strand
...
  
○
Can fold back on itself, forming base pairs between the complementary segments of the same strand
...
 

○
 
 
 
 

 
Formation of a stem-loop structure
...
 

FROM GENES TO PROTEINS 
 

Key Concepts: 
 
● F 

 
Biology Basics: 
 
●
Kinds of RNA: 
○
1) ​Ribosomal RNA (rRNA):​ a component, along with proteins, of a complex molecular machine known as a ribosome
...
  
○
2) ​Transfer RNA (tRNA):​ cloverleaf-shaped molecule that carries an amino acid on one end and an anti-codon on the other end
...
  
○
3) ​Messenger RNA (mRNA):​ single-stranded copy of the template strand of DNA
...
  
 
Transcription: 
 
●
The process by which enzymes use one of the strands of DNA within a gene as a template to produce an mRNA
...
  
○
This strand is called the ​coding strand​, and the ​template strand​ is called the ​noncoding strand​
...
 
■
Template strand:​ is the DNA strand used to make the RNA
...
  
○
Eukaryotes:​ any organism whose cells have a nucleus and other organelles
...
  
○
RNA polymerase: 
■
Function:​ to “read” the template strand of DNA and create the new RNA transcript by bonding together individual 
RNA nucleotides that are complementary to the DNA template
...
  
○
Transcription factors:​ recruit RNA polymerase to the transcription start site
...
 
○
Transcription bubble:​ RNA polymerase separates the two DNA strands in a small portion of the DNA molecule creating a 
transcription bubble, allowing it to access the template strand & begin RNA synthesis
...
  

○
○

○

 
 

Once RNA is finished being made, the newly synthesized RNA is released as a single-stranded molecule
...
  
■
This includes putting a “cap” on the 5’ end and a polyadenylated (poly-A) “tail” at the 3’ end
...
  
Splicing: 
■
Allows cells to increase variation in gene expression through alternative splicing
...
  
○
Causes: 
■
A given gene to generate more than one protein product
...
  

DNA DAMAGE AND REPAIR 
 

Key Concepts: 
 
● F 
 
●
●

DNA damage: 
○
Can block essential processes including ​DNA replication​ and ​transcription​ and can lead to mutations
...
  
■
They can result from ​replication errors​, from ​damage to the DNA​, or from ​errors introduced during repair of damage
...
(a) A missense mutation changes a single amino acid in the encoded polypeptide
...
Insertion/deletion 
mutations
...
(d) Deletion of a single nucleotide changes the reading frame 
of all codons beyond the point of insertion; this usually leads to formation of a new stop codon that terminates synthesis
...
Therefore, whereas addition (or 
deletion) of a multiple of three base pairs in a coding region would add (or subtract) amino acids to (or from) a 
protein, the addition of other numbers of base pairs shifts the reading frame from that point onward
...
  

 

 

 

 

 
 
 
 
 
 
 
 

●

DNA Repair: 
○
Base Excision Repair: 

 
A
...
B
...
Repair enzymes remove the 
altered/damaged nucleotide in a stepwise fashion
...
The single nucleotide gap is filled by a DNA 
polymerase
...
The remaining nick is sealed by a DNA ligase (ligase = to tie or join)
...
 
●
UV radiation can cause two thymines (Ts) that are adjacent to one another to fuse together to form a 
thymine dimer
...
  
Nucleotide Excision Repair: 
●

○

 

A
...
B
...
Repair enzymes remove a section of DNA that contains the damaged nucleotide
...
The gap is 
filled by a DNA polymerase
...
The remaining nick is sealed by a DNA ligase (ligase = to tie or join)
...
 
■
Patients are photosensitive and highly susceptible to skin cancers in sun-exposed areas of the body; rates of skin 
cancer are 2000-5000 times higher than for the average person
...
  
●

○

 
The left image shows the formation of thymine dimers as a result of UV damage
...
However, the defective NER pathway in XP means that UV damage, 
especially thymine dimers, cannot be effectively repaired and the damage accumulates in the DNA
...
 
This increased rate of mutation accumulation results in a higher probability of developing skin cancer
...
  
■
These breaks, and other types of severe damage, can be re-joined through homologous recombination
...
  
●
The process results in some of the sequence from the broken strand being incorporated into the intact 
strand, and vice versa
...
  
■

○

 
A
...
B
...
C
...
 
■
Also occurs in the absence of DNA damage as a mechanism to “shuffle” genes between a pair of homologous 
chromosomes that carry the same genes (i
...
, each member of the chromosome 15 pair will shuffle with one another, 
but not with other chromosomes from a different pair)
...
Thus, two parents with various 
characteristics will likely see those “mixed up” in their children
...
 
■
Is a rather extreme and problematic repair pathway
...
  
■
Usually used under circumstances of extreme DNA damage as a last resort by the cell to save the DNA
...
 

Single damaged base 
Thymine dimers 

Mutated DNA repair enzymes in nucleotide excision repair do not 
recognized damaged regions of DNA
...
 

Mismatch repair 

Mutation in the recombination machinery involved in DNA repair
...
 

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●
●
●
●

Histones:​ proteins that DNA wraps around to ​prevent tangling​ as well as ​promote coiling​ of the nucleosomes that it creates once combining 
the DNA and itself together into turning into a larger ​chromatin​ fiber
...
  
Genome:​ whole set of genes that a person has
...
  
Phenotype:​ all the observable characteristics or traits of an individual, including ones that are not easily seen
...
 
■
Differences emerge from subtle differences in genotype as well as environmental factors such as the ​quality of our 
food​, ​type of shelter we live in​, and ​financial security​
...
  
●
Somatic cell:​ any cell that ​isn’t​ a gamete
...
  
 
Representing the Inheritance of Alleles: 
 

●

 
This Punnett square shows the likely inheritance patterns of two parents who are heterozygous for PKU
...
 
The four square show the different possible combinations of the egg and sperm
...
The two homozygous possibilities have a probability of 25% 
each
...
 
 

●

●

 

 
This image shows the chromosomes of four biological siblings
...
The normal P allele is inherited from the father in A and B and from the mother in A and C
...
Both alleles appear on both the red and blue chromosomes, which indicates that 
the parents must both be heterozygous for the trait
...
 
Pedigree Charts: 
○
Assume that an ​unaffected, unrelated​ mate does ​not​ carry the trait
...
  

●
 
 
Degrees of Dominance: 
 

●

 
Complete dominance is a relatively simple inheritance pattern to determine from family pedigrees, as shown in the pedigrees below
...
For dominant traits, two affected parents can have an unaffected 
child
...
For joined eyebrows, a completely recessive trait, two unaffected parents can have an affected child
...
  

 
Incomplete Dominance and Codominance Complicate the Picture: 
 
●
Several traits result not from one gene dominating another but from several genes affecting the phenotype simultaneously
...
 
■
Example:​ height and body type
...
  
○
Incomplete dominance traits have a distinct phenotype for the heterozygous genotype
...
There are two different alleles for this trait: H for curly and H' for straight
...
 
●
Codominance:​ a case in which there are only ​two​ possible phenotypes (the dominant and the recessive)
...
 
Codominance is especially common with traits that are polygenic (controlled by multiple alleles)
...
There are three alleles of the gene for blood type: the A 
allele, the B allele, and the O allele
...
Similarly, the B allele codes for modifications that produce the marker protein "B"
...
If one of your alleles is A and the other is A or O, you have type A blood
...
If you have an A allele and a B allele, you have type AB blood
...
Notice that both A and B are inherited as dominant alleles, and O is inherited as a 
recessive allele
...
Often this third phenotype is a blending of the 
two homozygous phenotypes
...
The heterozygous 
genotype is wavy--a blend of both curly and straight
...
Notice the "blended" 
outcomes for heterozygotes
...
Actual families may differ somewhat because allele inheritance doesn't always follow the predicted probabilities
...
The 
possible blood types of the child are shown in blue
...
The bottom image shows a possible pedigree for blood type 
based on codominance inheritance patterns
...
  
○
This produces pattern of heredity called ​X-linked inheritance​ - the most common type of sex-linked inheritance
...
  
■
One example of sex-linked inheritance is red-green color blindness, the most common type of color blindness
...
As a result, red and green are seen as the same color (either red or green, depending on which cone is present)
...
Normal color vision, designated X​C​, 
dominates
...
The possible combinations are as follows: 

 
○

Only females who have two Xc genes are red–green color-blind
...
Because males do not have a second X chromosome that could mask the 
trait, all males with an Xc gene will be red–green color-blind
...
 

○

Both a Punnett square and a pedigree for the sex-linked trait of colorblindness are shown
...
Female carriers will pass the recessive trait to 50% of her 
sons, on average
...
Observing mixed traits in offspring indicate incomplete dominance, while observing both traits in a single 
individual indicates codominance
...
 
■
In the first step, the reaction mixture is heated to separate the DNA strands
...
 
■
In the third step, DNA polymerase extends the DNA primers to create a copy of the target DNA sequence
...
  
In each cycle, the two strands of the duplex DNA are separated by heating, then the reaction mixture is cooled to allow the 
primers to anneal (or pair) to their complementary segments on the DNA
...
  
■
The use of a heat-stable DNA polymerase eliminates the need to add fresh enzyme after each round of heating (heat 
inactivates most enzymes)
...
  
■

○

 

 

Components 

Needed for PCR? 

Needed for replication? 

Function 

DNA Polymerase 

Yes 

Yes 

Synthesizes the new strand of DNA 

Thermocycler 

Yes 

No 

Machine that cycles through the different 
temperatures needed for PCR 

DNA Ligase 

No 

Yes 

Ligates Okazaki fragments 

RNA Primer 

No 

Yes 

Initiates DNA replication 

dNTPs 

Yes 

Yes 

Building blocks of DNA, needed for DNA 
synthesis 

DNA Primer 

Yes 

No 

Initiates DNA synthesis in PCR  



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