BIOChemistry Study Guide OA1
Hemophilia Pedigree-Father has hemophilia, mother does not. What is the outcome for their
children?mHis daughters would become carriers. It’s X-link recessive
Pedigree chart. Only one is autosomal Dominant.
Autosomal = males and females equally affected. Dominant = non-carrier parents.
Punnett Square 4 squares with drop down boxes, you must select the correct answer for each. They put
a dead puppy in one to throw you off, look at the remaining 3 puppies.
• Complete dominance - either 3 black 1 white.
• Codominance - black, white, 2 spotted with both.
• Incomplete Dominance - black, white 2 grey.
Know steps of PCR, one question asks about the first step. Ligase is not involved in PCR!
Polymerase Chain Reaction = the process of copying DNA in the lab. With PCR you need Template
DNA, Nucleotides (dNTPS), DNA Polymerase, and DNA primers.
Step One: Denaturation= DNA is heated to 95C to separate it.
Step Two: Annealing = reaction is cooled to 50C. primers stick to the DNA that you
want to copy and add DNA polymerase
Step Three: Elongation = reaction heated to 70C and DNA polymerase add nucleotides building
a new DNA strand.
Know about base excision repair. BER (base excision repair) removes a single nucleotide!
Base excision repair is used to repair damage (mutation) to a bases caused by harmful molecules.
DNA glycosylase sees the damaged DNA and removes it.
DNA polymerase puts the right one back in while DNA ligase seals it!
Mismatch repair occurs during replication. (MMR)
During replication, DNA polymerase proofreads if a mismatch pair gets through. MMR removes a large
section of the nucleotides from the newly formed DNA and DNA and polymerase tries again.
Know what DNA damage is corrected by mismatch repair.
When a base is mismatched but to errors in replication. Such as G - T instead of G - C. DNA polymerase
comes by and fixes it.
What happens when DNA polymerase binds to DNA to make RNA. Transcription!
DNA polymerase (needed for DNA replication) takes the individual nucleotides and matches the them to
the parental sequences to ensure a correct pair. It must bind with RNA primer to work.
Mutations.
Nonsense - Change in 1 nucleotide produces a STOP codon
Silent - Change in 1 nucleotide but codes for the same amino acid
Missense - Change in 1 nucleotide leads to a code for a different amino acid.
During RNA splicing, introns are cut out, and the remaining exons are joined together!
Know the processes of DNA-RNA-mRNA,
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, BIOChemistry Study Guide OA1
Know what ionized Alanine looks like.
It’s an Amino acid “R” group. Alanine is a hydrophobic amino acid that has CH3 it’s a weak interaction.
For ionized look for the one with the + or - charge
Misfolding of protein structure in Alzheimer’s
abnormal protein aggregation caused by intracellular tangles and extracellular plaques (senile)
Tau is fibrous material inside cells with this the connections are lost. This becomes defective and
form filaments in the neuron.
Amyloid-beta is a large precursor protein in the cell. Clearly linked to Alzheimer’s disease creating
senile plaques. Starts in the hippocampus and moves up.
Neurodegenerative protein aggregation
Alzheimer’s disease, the most common neurodegenerative disease. The formation of aggregated amyloid-
beta fibers is another characteristic of Alzheimer's disease, but neurodegeneration and memory loss can be
detected before amyloid fibers accumulate in the brain.
Molecules that help denatured proteins in folding. (ie. sickle cell)
molecular chaperones- and they bind to the newly made polypeptide and enable proper folding. Ensuring
proper protein folding is vital because proteins that do not fold properly often due to genetic mutations
that substitute one amino acid for another can lead to a variety of diseases.
Levels of protein structure (3-dimensional shape of polypeptide)
Primary = amino acid chain, Covalent bond (strong), does not denature.
Secondary = alpha helix & Beta sheet, H bond, denatured by salt and ph change, contain carboxyl
group and amino groups. Hydrogen bonds formed from 2 polar amino acids!
Tertiary = side chain interaction, (R-group) Changes seen with increased temp, salt, change in pH
and reducing agents. ex. sickle cell, arthritis, hemophilia.
Quaternary Subunit= more than one polypeptide, Changes seen with increased temp. Hbg
What structure would be unaffected by complete denaturation of multi-subunit
Tertiary structure is hydrophobic. Protein structure is stabilized primarily by the hydrophobic effect,
disruption of the hydrophobic effect is the simplest way to denature a protein this is done by heating it up.
Methotrexate treatment in cancer, possible affects enzyme activity. and APC gene decreased expression
because of Methyl group.
Methotrexate works by blocking an enzyme process in cancer cells so they cannot grow. APC is classified
as a tumor suppressor gene.
Substrate enzyme complex - like a lock and key
Substrate binds to an active site, producing an enzyme-substrate complex. The geometric and the
chemical complementarity between the enzyme and substrate depend on noncovalent forces.
Know substrates, enzymes, products and inhibitors.
substrate is a molecule that an enzyme will bind preferentially to any other molecule, and each enzyme is
specific for that substrate, it won't react with molecules that are not its substrate.
active site, which serves as the binding platform for its specific substrate(s) and acts as the site of the
chemical reaction.
Induced fit
Substrate and active site are somewhat complementary prior to substrate binding, enzymes will adjust
their active site conformation slightly as the substrate binds to improve the fit. When the molecule is
This study source was downloaded by 100000830214522 from CourseHero.com on 03-25-2022 02:49:01 GMT -05:00
https://www.coursehero.com/file/38352968/Updated-Study-Guidedocx/
Hemophilia Pedigree-Father has hemophilia, mother does not. What is the outcome for their
children?mHis daughters would become carriers. It’s X-link recessive
Pedigree chart. Only one is autosomal Dominant.
Autosomal = males and females equally affected. Dominant = non-carrier parents.
Punnett Square 4 squares with drop down boxes, you must select the correct answer for each. They put
a dead puppy in one to throw you off, look at the remaining 3 puppies.
• Complete dominance - either 3 black 1 white.
• Codominance - black, white, 2 spotted with both.
• Incomplete Dominance - black, white 2 grey.
Know steps of PCR, one question asks about the first step. Ligase is not involved in PCR!
Polymerase Chain Reaction = the process of copying DNA in the lab. With PCR you need Template
DNA, Nucleotides (dNTPS), DNA Polymerase, and DNA primers.
Step One: Denaturation= DNA is heated to 95C to separate it.
Step Two: Annealing = reaction is cooled to 50C. primers stick to the DNA that you
want to copy and add DNA polymerase
Step Three: Elongation = reaction heated to 70C and DNA polymerase add nucleotides building
a new DNA strand.
Know about base excision repair. BER (base excision repair) removes a single nucleotide!
Base excision repair is used to repair damage (mutation) to a bases caused by harmful molecules.
DNA glycosylase sees the damaged DNA and removes it.
DNA polymerase puts the right one back in while DNA ligase seals it!
Mismatch repair occurs during replication. (MMR)
During replication, DNA polymerase proofreads if a mismatch pair gets through. MMR removes a large
section of the nucleotides from the newly formed DNA and DNA and polymerase tries again.
Know what DNA damage is corrected by mismatch repair.
When a base is mismatched but to errors in replication. Such as G - T instead of G - C. DNA polymerase
comes by and fixes it.
What happens when DNA polymerase binds to DNA to make RNA. Transcription!
DNA polymerase (needed for DNA replication) takes the individual nucleotides and matches the them to
the parental sequences to ensure a correct pair. It must bind with RNA primer to work.
Mutations.
Nonsense - Change in 1 nucleotide produces a STOP codon
Silent - Change in 1 nucleotide but codes for the same amino acid
Missense - Change in 1 nucleotide leads to a code for a different amino acid.
During RNA splicing, introns are cut out, and the remaining exons are joined together!
Know the processes of DNA-RNA-mRNA,
This study source was downloaded by 100000830214522 from CourseHero.com on 03-25-2022 02:49:01 GMT -05:00
https://www.coursehero.com/file/38352968/Updated-Study-Guidedocx/
, BIOChemistry Study Guide OA1
Know what ionized Alanine looks like.
It’s an Amino acid “R” group. Alanine is a hydrophobic amino acid that has CH3 it’s a weak interaction.
For ionized look for the one with the + or - charge
Misfolding of protein structure in Alzheimer’s
abnormal protein aggregation caused by intracellular tangles and extracellular plaques (senile)
Tau is fibrous material inside cells with this the connections are lost. This becomes defective and
form filaments in the neuron.
Amyloid-beta is a large precursor protein in the cell. Clearly linked to Alzheimer’s disease creating
senile plaques. Starts in the hippocampus and moves up.
Neurodegenerative protein aggregation
Alzheimer’s disease, the most common neurodegenerative disease. The formation of aggregated amyloid-
beta fibers is another characteristic of Alzheimer's disease, but neurodegeneration and memory loss can be
detected before amyloid fibers accumulate in the brain.
Molecules that help denatured proteins in folding. (ie. sickle cell)
molecular chaperones- and they bind to the newly made polypeptide and enable proper folding. Ensuring
proper protein folding is vital because proteins that do not fold properly often due to genetic mutations
that substitute one amino acid for another can lead to a variety of diseases.
Levels of protein structure (3-dimensional shape of polypeptide)
Primary = amino acid chain, Covalent bond (strong), does not denature.
Secondary = alpha helix & Beta sheet, H bond, denatured by salt and ph change, contain carboxyl
group and amino groups. Hydrogen bonds formed from 2 polar amino acids!
Tertiary = side chain interaction, (R-group) Changes seen with increased temp, salt, change in pH
and reducing agents. ex. sickle cell, arthritis, hemophilia.
Quaternary Subunit= more than one polypeptide, Changes seen with increased temp. Hbg
What structure would be unaffected by complete denaturation of multi-subunit
Tertiary structure is hydrophobic. Protein structure is stabilized primarily by the hydrophobic effect,
disruption of the hydrophobic effect is the simplest way to denature a protein this is done by heating it up.
Methotrexate treatment in cancer, possible affects enzyme activity. and APC gene decreased expression
because of Methyl group.
Methotrexate works by blocking an enzyme process in cancer cells so they cannot grow. APC is classified
as a tumor suppressor gene.
Substrate enzyme complex - like a lock and key
Substrate binds to an active site, producing an enzyme-substrate complex. The geometric and the
chemical complementarity between the enzyme and substrate depend on noncovalent forces.
Know substrates, enzymes, products and inhibitors.
substrate is a molecule that an enzyme will bind preferentially to any other molecule, and each enzyme is
specific for that substrate, it won't react with molecules that are not its substrate.
active site, which serves as the binding platform for its specific substrate(s) and acts as the site of the
chemical reaction.
Induced fit
Substrate and active site are somewhat complementary prior to substrate binding, enzymes will adjust
their active site conformation slightly as the substrate binds to improve the fit. When the molecule is
This study source was downloaded by 100000830214522 from CourseHero.com on 03-25-2022 02:49:01 GMT -05:00
https://www.coursehero.com/file/38352968/Updated-Study-Guidedocx/
