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WGU Biochemistry C 785 Study Guide
Page 10 Video Notes for Units 2-
Unit 2 – Amino Acids, Peptide Bonds, Protein Structure
- Amino Acid: building blocks of proteins
- Monomer: single amino acid
- Polymer: amino acid chain of linked monomers called polypeptides
- Amino Group: N with at least 1 H, can be NH2 or NH
- Hydrogen Hat: between amino group and carboxyl group, attached to alpha carbon
- Variable Group “side chain” “R”: unique portion of amino acid
- Carboxyl Group: C with 2 attached O’s, can be COOH, or COO
- Hydrophobic Amino Acid: consists only of carbons and hydrogens end in H, CH, CH2, CH3 – they are nonpolar – Hydrophobic interactions occurs between two nonpolar amino acids H, CH, CH2, CH4, are the weakest type of bond – but the most important type for protein structure – are broken with heat (increased temperature)
- Polar Amino Acid: end in OH, NH, SH, create hydrogen bonds, can be broken by changes in pH or changes in salt concentration. SH: Disulfide bond/bridge made by SH side chains, is strongest, fewest in number, and only broken with reducing agents
- Peptide Bonds: form at amino group and carboxyl group, “loss of H2O”
- Ionic Bonds: occurs between two amino acids with opposite charges (charged amino acids, -/+, negative is acidic positive is basic), are broken with pH changes or changes in salt concentration
- Dehydration Synthesis: when two molecules are covalently bonded with loss of a water molecule (H20) one provides hydroxyl group OH and the other provides hydrogen H. Amino group and carboxyl group both give up something and then they bind and form a new bond polymer chain
- Hydrolysis: addition of a water molecule H2O to break a bond, breaks polymers
- 4 Levels of Protein Structure: Primary linear chain of amino acids, Secondary alpha helix and beta sheet shapes, create by Hydrogen bonds of polypeptide backbones Tertiary 3D, stabilized by side chains Quaternary consists of two or more polypeptide chains, more than one subunit – tertiary and quaternary are mature structures that are properly folded.
- Denaturation: high temperatures and various chemical treatments will denature a protein, causing it to lose its shape and ability to function “form=function” it may renature when chemical and physical aspects of environment are restored to normal.
Unit 3 – Enzymology and Catalytic Mechanism
- Enzymes: are proteins, they catalyze reactions when properly folded, can be disrupted just like amino acids by heat, pH, etc., “enzymes are proteins that act as biological catalysts, Lactose isa substrate that can be converted to glucose and galactose which are products by lactase which is an enzyme (enzymes usually end in “ase”). Enzymes lower the activation energy of a reaction “makes it easier and quicker”. People who are lactose intolerant do not have lactase that breaks it down into usable products. Excessive internal heat can denature hydrophobic interactions thus causing important enzymes to lose their function.
carried out, once demand increases this will reverse and allows the cycle to continue, this is a type of noncompetitive inhibition, binds to allosteric site not active site.
- Uninhibited Reaction: the substrate binds to the active site on the enzyme and gets turned into products.
- Competitive Inhibition: an inhibitor binds to the enzyme in the place of a substrate, they will have similar shapes “lock and key” to the substrate. You can overcome competitive inhibition by increasing the amount of substrate present.
- Noncompetitive Inhibition: The noncompetitive inhibitor does not bind to the active site in the place of a substrate like competitive inhibitors, instead they bind to allosteric sites, which is a site other than the active site. When this occurs, this causes a change in the shape in the active site thus preventing binding of the substrate. Thus, preventing an enzyme from converting a substrate into product. Because they are noncompetitive, they cannot be outcompeted by adding more substrate. “Noncompetitive can always inhibit the enzyme”
Key Points: enzymes are specific to one substrate or family of substrates and catalyze one type of reaction – enzymes lower the activation energy of a reaction – enzymes increase the rate of a reaction – kinases kindly add a phosphate group – phosphatases remove a phosphate group – enzymes usually end in “ase” - enzymes function at an optimal temperature and pH, deviation from these optimal values will decrease enzyme function – competitive inhibitors bind to the active site when the substrate is suppose to bind, they have a similar shape as the substrate “lock and key”, and can be outcompeted by increasing the amount of substrate – non-competitive inhibitors bind to the allosteric site (any site other than the active site) – the end product of a pathway
can act as a feedback inhibitor and shut down the pathway by binding to one of the first enzymes in the pathway at an allosteric site.
Unit 4 - DNA and RNA Part 1
How is information transmitted in the cell from DNA to RNA to proteins?
How do DNA and RNA nucleic acids control the functions of our cells?
DNA Sequencing
*DNA replication (making template DNA), Transcription (mRNA) Translation (mRNA into amino acids)
Central Dogma of Biology = flow of information in the cell
DNA stores all the information our body needs to function, and each cell in our body has the exact same DNA, DNA is stored in nucleus of cell.
Nucleus = library, DNA = book, mRNA = photocopy of DNA book
DNA is not allowed to leave nucleus, so DNA is copied into new molecules, mRNA or messenger RNA by transcription, mRNA is allowed to leave nucleus and travel to cytosol the main part of the cell. Transcription = the process of making mRNA or messenger RNA from the DNA inside the nucleus.
Ribosomes “the machine in the cell that make proteins by translation”
Ribosomes pick up and use the mRNA and another molecule called tRNA to make a protein. “Translation”
*Transcription is when DNA is converted to mRNA
*Translation is when ribosomes use mRNA and tRNA to make proteins
the coding DNA must be paired with its appropriate base pair to make
the template DNA. Coding and template DNA are COMPLEMENTARY!
5’ 3’
A T T
A C
G T A
3’ 5’
The complimentary rules “antiparallel and base pairing” also apply when the cell performs transcription to use the template DNA to make mRNA.
Transcription: Complementary mRNA from template DNA. Template DNA is the complementary (opposite) of coding DNA mRNA is the complementary form of template DNA. mRNA will look the same as coding DNA with the exception of the T in the coding DNA strand being replaced with U in the mRNA strand.
*A T for DNA – A U for mRNA so A is always with T or U * C Galways.
How mRNA is used to make protein sequences through TRANSLATION: mRNA is the messenger that carries the genetic code into the cytosol from the nucleus in order to make proteins. mRNA is read by ribosome. Ribosome always reads from 5’ to 3’ in three nucleotide codons. Each codon can be translated into an amino acid.
*Decoding table is always read from 5’ to 3’ and read in 3 codon groups “5’-AUC UGC-3”. Take the first letter of the mRNA sequence and find on
left-hand side of table. Next find the second letter in the mRNA sequence on the top of the table. Lastly find where the left-hand side and top intersect. Then you can find the last letter in the sequence to determine the amino acid if forms. (a three-codon group is 3 letters/ bases).
mRNA translation by the ribosome inside of the cell happens when the ribosome reads the mRNA from 5’ to 3” and it always reads 3 bases at a time [5’-AUC UGG-3’]. The ribosome needs a translator to read an amino acid. This is where tRNA comes into play. tRNA is complementary to the mRNA and it has the amino acid that matches the mRNA. *tRNA has an anticodon to mRNA meaning it would be anti-parallel and it would base-pair; anticodon is on one end of the tRNA and on the other end is the amino acid that matched the mRNA. Next a second tRNA will come in that is anti-parallel and base-pair with the second 3 letter codon, one we have at least two amino acids available in the ribosome the ribosome will catalyze the chemical reaction that forms a peptide bond between the two amino acids (Peptide Bonds: form at amino group and carboxyl group, “loss of H2O” lose an OH from carboxyl group and a H from amino group). This is how an amino acid chain is created to form a protein--> Remember both mRNA and tRNA both use uracil U and not thymine T because it is specific for DNA only!
*When looking at sequencing problems make sure you recognize what kind of sequence you are given and what kind of sequence you need to find. So if you are asked to find the template DNA you can immediately eliminate any answer choice with U because U is specific for RNA and vice versa RNA can eliminate any choices with a T! Genetic code table is always mRNA! always write down your 4 sequences in order so you can remember the complementary relationships 1) coding DNA 2) template DNA 3)mRNA 4)tRNA coding DNA is complementary to template DNA, template DNA is
- methylation tighten and 2) acetylation loosen write this on your write board!
*Promoters, transcription factors, and RNA polymerase work together
to turn transcription on. “high” gene expression = transcription “on” mRNA is made.
A template DNA strand will include a promoter DNA sequence that indicates the start of a gene (a start line in 5K) must have start line to know where to begin making the mRNA, transcription factors must mark the start line, they are small proteins (like foot stop for the runners at start line), next the RNA polymerase (runner) comes into the picture. RNA polymerase is the enzyme that is actually going to make the mRNA. These are all needed to increase gene expression to make mRNA. the promoter (start line) must be visible and available to perform the transcription. The nucleosomes and the chemical markers associated with them that can either allow this promoter (start line) to be exposed or hide it away so that we turn off the transcription. Nucleosomes are quaternary structures made up of proteins called histones (each nucleosome has 8 histone subunits) they are used to keep our DNA organized and confined. The DNA wraps around the nucleosome, when it is wrapped tightly the promoter start line is hidden away from the transcription factors and RNA polymerase meaning that gene expression is low or no, transcription is off mRNA in
not made. There are factors that can cause the nucleosomes to become more widely spaced, the DNA will loosen around them, and the promoters will become exposed. This allows transcription factors and RNA polymerase to attach, so nucleosomes that are widely spaced gene
expression is high, transcription is on mRNA is made. Chemical markers signal the nucleosomes to move. Methylation = a chemical marker that is put on the histone proteins to cause the nucleosomes to
pack tightly together. So high methylation leads to low gene
expression. Acetylation = a chemical marker put on the histone proteins that cause the nucleosomes to spread allowing the promoter (start line) to be exposed for transcription factors and RNA polymerase allowing for the making of mRNA meaning there is high gene expression.
Histones make up nucleosomes, each nucleosome has 8 histone subunits. They are used to keep our DNA organized and confined. Histones promote coiling of DNA and prevent DNA strands from tangling.
*High Gene Expression: Transcription is ON – mRNA is being made decreased methylation (methylation causes tightly packed DNA), increased acetylation (acetylation causes DNA to loosen), widely spaced nucleosomes, exposed promoter (start line), use transcription factors (foot blocks), use RNA polymerase (runner).
*Low Gene Expression: Transcription is OFF – mRNA not made. increased methylation (caused tightly packed DNA), decreased acetylation (causes DNA to loosen), tight nucleosome packing, hidden promoter (no start line), no transcription factors (foot blocks), no RNA polymerase (runner).
Write on white board during test!
*Splicing (RNA splicing): Different proteins from the same gene.
Our genetic code is protected through the mRNA and the introns we have in that mRNA. Introns are sequences of nucleotides that do not code for protein. So, when we initially transcribe a gene into mRNA, it’s actually going to contain the sequences that both code for protein, which are called exons and also the sequences that do not code for proteins that are between the exons that are the introns. Since introns do not code for protein, we have to get rid of them before we exit the nucleus to perform translation (mRNA to amino acids in ribosome
(allows us to make hundreds of thousands of proteins using only 30K genes in our DNA. Throw out all introns, and some exons.
- High Gene Expression transcription is on, mRNA is made
- Low/No Gene Expression transcription is off, mRNA no made
*DNA/RNA Part 1 Words to know:
- Gene expression – Nucleotides – Antiparallel – Complementary – Template DNA – Coding DNA -Replication – Transcription – RNA polymerase – Promoter – Transcription factors - mRNA – Translation
- tRNA – Ribosomes – Codons – Anticodons (on one end of tRNA) – Splicing – Introns – Exons – Histones – Nucleosomes – Methylation – Acetylation
Unit 4 - DNA and RNA Part 2
Goal for part 2:
- Identify the different types of DNA mutations and how they change DNA, RNA, and proteins
- Know the different types of DNA repair, what type of damage they fix, and how they fix damage
- Understand how “PCR” polymerase chain reaction is used in genetic testing, including the steps for PCR, components, and number of DNA molecules produced
DNA Damage and Repair
Mutations: changes to DNA sequence, can be very large and affect
entire chromosome or can be a single letter change. a single letter change in the coding DNA will be carried over throughout the
template DNA, mRNA, and tRNA resulting in a different amino acid being produced via translation.
Point Mutations single letter changes: occurs we replace one DNA letter for another at one point within the DNA strand. The following three are all “point mutations”:
*Silent Mutation: occurs when there is a single letter change in the letter sequence of a 3 letter codon in the DNA coding strand that does not result in a change in the amino acid or protein produced.
*Missense Mutation: occurs where there is a single letter change in the letter sequence of a 3 letter codon that results in a different amino acid and protein being produced. “missense=mistake”
*Nonsense Mutation: occurs where there is a single letter change in the letter sequence of a 3 letter codon that results in a stop codon. When a stop codon occurs no amino acid is produced so when our amino acid sequence is being translated, there is nothing to continue the amino acid strand or polypeptide. This is the end of our protein. “nonsense=no”
Frameshif t Mutations occurs when either a letter is added (insertion mutation) or deleted (deletion mutation) thus changing the reading frame or 3 letter codon of our DNA sequence that determine our amino acid. By adding or taking away a letter we canpotentially change multiple amino acids.
*Insertion Mutation: occurs when an extra letter is added to the second codon (3 letter set) that results in changes in the 3 rd^ and 4 th codon with an extra stand-alone letter at the end.
*Deletion Mutation: occurs when one letter is deleted from a codon (3 letter set) that results in there being one less amino acid in the chain.
that will recognize mismatches and remove them so that DNA polymerase can try again.
*Double stranded breaks 1) homologous recombination (HR) or 2) non-homologous end joining (NHEJ)
-High energy or ionizing radiation can cause a double stranded break to both our coding and out template DNA strands. There are two repair mechanisms that fix double stranded breaks.
-Humans have pairs of chromosomes. The two chromosomes are very similar of homologous. When there is a double stranded break, the homologous chromosome to the one that was damaged can be used as a blueprint to repair the damaged area. A section of DNA from the damaged chromosome is removed and then a section from the homologous chromosome is placed in the missing section. Then the homologous chromosome and the repaired chromosome each have their corresponding missing sections filled in. This process is called homologous recombination (HR) because it uses the homologous chromosome to recombine DNA from one strand into another. If the double stranded breaks within a chromosome are too severe for HR to correct, then the broken ends of the double stranded DNA is shortened and connected together without using the homologous chromosome. Because the broken pieces are connected, there is a good chance that not all of the DNA will be corrected and that there will be missing pieces. This makes this a major error prone process. This is called non-homologous end joining.
Epigenetics: Changes to DNA that do not modify the coding sequence of the DNA but do affect its winding and unwinding from nucleosomes. These changes can increase and decrease the availability of DNA and hence, the transcription of a gene.
*Active Gene Transcription:
- Epigenetic modifications to nucleosomes – Promoters – RNA Polymerase – Transcription Factors
Find more information of this!
PCR and Genetic Testing
PCR= a tool used to amplify a specific segment of DNA, (not used to detect epigenetic changes because they do not affect the sequence
of the DNA. PCR looks at DNA sequence!
PCR Primer: DNA polymerase needs a primer to begin DNA synthesis
primers will direct the DNA polymerase to synthesize complementary strands of the target DNA.
DNA polymerase can synthesize new DNA strands from 5’ to 3’ direction. DNA needs a free 3’ end to bind to and initiate synthesis of a DNA.
Polymerase Chain Reaction or PCR makes copies of sample DNA in a machine called a Thermocycler.
PCR allows us to identify genetic diseases or identify individuals who may carry mutated genes.
PCR is used to make copies of DNA not RNA so you must start off with DNA. You must also have DNA polymerase to copy DNA, DNA primers must be used for high temperature, and also the letters of DNA or DNA nucleotides.
*If you start with only one copy you will start with 1 strand.
Cycle 1, 1 cycle 2, 2 cycle 3, 4 cycle 4, 8
Key Words:
point mutations – nonsense mutations – missense mutations
silent mutations – frameshift mutations – base excision repair BER –
nucleotide excision repair NER – mismatch repair – homologous
recombination HR – nonhomologous end joining NHEJ – PCR –
primers – denaturation – annealing – elongation
Unit 5: Myoglobin and Hemoglobin
Myoglobin: protein, has only one strand or polypeptide, has one heme, one oxygen, and one iron in the center of the heme that is responsible for binding to oxygen. Since there is only one polypeptide strand, we can say it has its own primary, secondary, and tertiary structure. Is
found in the muscle muscle is an active tissue thus requiring lots of energy – ATP. It requires oxygen to generate energy for the muscle. Myoglobin binds to oxygen, storing it in the muscle, because of this we say that myoglobin has a high affinity (stickiness for oxygen). If you have a high affinity for something you hold onto it. Non cooperative, hyperbolic curve on graph.
Hemoglobin: protein, has four separate subunits (2 alpha and 2 beta), each subunit has its own heme and iron, and each subunit can bind to
one oxygen this means one hemoglobin contains 4 heme, 4 iron, and can bind 4 oxygens. Hemoglobin has primary, secondary, tertiary, and quaternary structure. Quaternary is when proteins have more than one
subunit. Hemoglobin is found in the blood, and it delivers oxygen to every tissue in the body. All tissues require energy – ATP to perform their daily functions. Energy can be generated very efficiently when oxygen is present. Hemoglobin delivers oxygen to tissues in need. Hemoglobin has lower affinity (stickiness) for oxygen. It is a delivery protein. Cooperative, will sit at table if others are already there, just like will exit if someone else exits first. Sigmoidal curve on graph, slight S shape.
*Key points Myoglobin is in the muscle; hemoglobin is in the blood. Myoglobin stores oxygen, hemoglobin delivery oxygen to tissues. Myoglobin is primary, secondary, tertiary, hemoglobin is also quaternary. Myoglobin has 1 subunit with 1 heme, 1 iron, and 1 oxygen, hemoglobin has 4 subunits with 4 heme, 4 iron, and 4 oxygens. Myoglobin has a high affinity for oxygen, hemoglobin has a low affinity for oxygen.
Primary: one amino acid sequence
Secondary: alpha helices, beta sheets H-bonds in backbone
Tertiary: 3D, R group bonds, H-bonds, ionic bonds, hydrophobic
interactions, disulfide bonds.
Quaternary: multiple subunits.
Hemoglobin is dynamic: What causes hemoglobin to change its shape?
Hemoglobin changes its shape due to oxygen binding. This sensitivity is what allows hemoglobin to efficiently deliver oxygen to tissues within
the body. Hemoglobin has cooperativity. other molecules are more likely to bind to hemoglobin when one oxygen is already bound. The first oxygen is the hardest to bind, the following bond easier. The same goes for delivery. Once one oxygen leaves the other will too.
