Download Biochemistry Note-Taking Guide Latest Update and more Exams Nursing in PDF only on Docsity!
Biochemistry Note-Taking Guide Latest Update
Read This First - This Note-Taking Guide is meant to be used as you go through each of the Units in
Biochemistry. It is only effective when used with course materials, including all of the Essential Reading
material in Campbell Biology (), the course videos () and podcasts (), the Learning Check questions, and
the Unit Quizzes. We highly recommend that you print out this guide and use it to make your own notes
on the course by writing the vocabulary definitions and answering the questions in your own words. We
also recommend that you review your notes every day for all Units to keep the course material fresh in
your mind even as you learn new material in the course.
If there are definitions or questions you are unable to answer on your own, please click here to discover multiple options
for working with a Course Instructor. We would love to help you succeed in Biochemistry! {{click here if
you’d like a PDF version}}
*****Unit 2: Amino Acids, Peptide Bonds, and Protein Structure*** Page Section Vocabulary Key Questions** - You should be able to answer these upon completion of the Unit/Section. Please add your own notes as necessary. Amino Acids, Peptide Bonds,
Proteins are all constructed from the same set of 20 amino
acids, linked in unbranched polymers. The bond between
amino acids is called
a peptide bond , so a polymer of amino acids is called a
12 and Protein Structure
polypeptide. A protein is a biologically functional molecule
made up of one or more polypeptides, each folded and coiled
into a specific three-dimensional structure.
2.1 Amino Acids: The Building Blocks of Proteins 14 Subtopic: Chemical Elements, Atoms, and Bonds—Optional Review Electrons Energy Covalent bonds
2.2 Levels of Protein Structure To become functional proteins, polymers of amino acids ( polypeptides ) must fold and take on a particular shape. Primary – backbone of peptide chain formed by peptide bonds during dehydration reaction Secondary – backbone atoms of peptide chain connected by hydrogen bonds forming Alpha helix or Beta sheets Tertiary – R group interactions via: hydrophobic interactions (weakest), hydrogen bonds, ionic bonds or disulfide bonds (strongest) Quaternary – R group interactions (like above), but with other polypeptide chains 18 Subtopic: Polypeptides and Functional Proteins Polypeptide s Peptide bonds When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration reaction, with the removal of a water molecule. The resulting covalent bond is called a peptide
bond. This happens during the formation of primary structur e in the peptide chain. (^19) Subtopic: Levels of Protein Structure Dehydratio n Hydrolysis Alpha helix Beta sheet Denaturati on
- Protein Folding: What are the 4 levels of protein structure? List distinguishing features of each.
- What bonds make up each level of protein structure and how are they formed? Primary – peptide bonds (a type of strong covalent bond) between monomer amino acids Secondary – hydrogen bonds between polypeptide backbone Tertiary – bonds between R groups (hydrogen/ionic/disulfide bonds, hydrophobic/van der Wals interactions) Quaternary – same as tertiary, but between different polypeptide chains (^20) Subtopic: A Protein's Structure Depends on Its Environment Aggregation
- What environmental change breaks each type of bond? Heat – 2 nd,3rd,4th^ protein structure and its bonds pH – hydrogen and ionic bonds (2nd, 3 rd^ and 4 th structure) chemicals – hydrogen bonds (2nd, 3rd and 4th^ structure) enzymes – peptide bonds (1st structure)
- What type of amino acid side chain leads to protein aggregation???? Hydrophobic acids tend to aggregate better
*****Unit 3: Enzymology and Catalytic Mechanism*** Page Section Vocabulary Key Questions** - You should be able to answer these upon completion of the Unit/Section. 26 Enzymology and Catalytic Mechanism 27 3.1 Enzyme Action Substrates Products Intermediates Active site Enzyme specificity Induced fit Kinase Phosphatas e
- How do enzymes catalyze reactions? Enzymes are specific to one substrate and can catalyze only one type of reaction. In most enzymatic reactions, the substrate is held in the active site by so- called weak interactions, such as hydrogen bonds and ionic bonds. Enzymes are unchanged by the reaction.
- How do enzymes affect reaction rate and activation energy? They increase the reaction rate and decrease the activation energy
- What are the 4 steps of the enzymatic cycle?
- Substrate binding
- Formation of enzyme-substrate complex
- Product formation and dissociation
- Enzyme recovery
3.2 Factors that Influence Enzyme Activity Many enzymes require nonprotein helpers for catalytic activity, often for chemical processes like electron transfers that cannot easily be carried out by the amino acids in proteins. These adjuncts, called cofactors , may be bound tightly to the enzyme as permanent residents, or they may bind loosely and reversibly along with the substrate. The cofactors of some enzymes are inorganic, such as the metal atoms zinc, iron, and copper in ionic form. If the cofactor is an organic molecule, it is referred to, more specifically, as a coenzyme. Most vitamins are important in nutrition because they act as coenzymes or raw materials from which coenzymes are made. (^30) Subtopic: Enzymes Are Affected by Their Environment
- How do environmental changes affect enzymes? Enzyme activity is impacted by change in heat, pH, and enzyme inhibitors. Temperature and pH are environmental factors important in the activity of an enzyme. Up to a point, the rate of an enzymatic reaction increases with increasing temperature. Above that temperature, however, the speed of the enzymatic reaction drops sharply. The thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic
decrease given a specific inhibitor? Allosteric regulation is the term used to describe any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site. It may result in either inhibition or stimulation of an enzyme’s activity. The binding of an activator to a regulatory site stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme. In another kind of allosteric activation, a substrate molecule binding to one active site in a multi-subunit enzyme triggers a shape change in all of the subunits, thereby
increasing catalytic activity at the other active sites. Called cooperativity , this mechanism amplifies the response of enzymes to substrates: One substrate molecule primes an enzyme to act on additional substrate molecules more readily. Cooperativity is considered allosteric regulation because, even though substrate is binding to an active site, its binding affects catalysis in another active site.
40 Subtopic: Transcription and Translation Template DNA Coding DNA Replication Transcription RNA polymerase Promoter Transcription factors mRNA Translatio n tRNA Ribosome s Codons Anticodo ns
- How do we make complementary DNA (ie coding to template, or template to coding)? Complementary DNA is created codingtemplate strand. DNA exists as a double helix.
- How do we make mRNA? Which strand of DNA is complementary to the mRNA? mRNA is created out of template DNA strand only. RNA molecules exist as single strands and are more variable in shape Transcription is the synthesis of RNA using information in the DNA. The two nucleic acids are written in different forms of the same language, and the information is simply transcribed, or “rewritten,” from DNA to RNA. For a protein-coding gene, the resulting RNA molecule is a faithful transcript of the gene’s protein-building instructions. This type of RNA molecule is called messenger RNA (mRNA) because it carries a genetic message from the DNA to the protein-synthesizing machinery of the cell. An enzyme called an RNA polymerase pries the two strands of DNA apart and joins together RNA
nucleotides complementary to the DNA template strand. The stages of transcription: initiation, elongation, and termination. The DNA sequence where RNA polymerase attaches and initiates transcription is known as the promoter ; the sequence that signals the end of transcription is called the terminator. The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule is called a transcription unit.
- How do we make proteins? Which type of nucleotide sequence is used and in which direction? How do we read the codon table? Translation is the synthesis of a polypeptide using the information in the mRNA. During this stage, there is a change in language: The cell must translate the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide. The sites of translation are ribosomes.
- What is the relationship between mRNA and tRNA? mRNA carries a genetic message from DNA out of the cell and into the cytoplasm where Ribosome attaches. Here is where tRNA comes and transfers a specific amino acid in order to create a polypeptide chain in the translation process. Anticodon on tRNA attaches to codon on mRNA.
(^43) 4.3 DNA Damage and Repair 44 Subtopic: Mutations Point mutations Nonsense mutations Missense mutations Silent mutations Frameshift mutations Insertion mutations Deletion mutations
- You are given a normal and mutated DNA or RNA sequence. What steps will you take to determine the type of mutation that has occurred? Point mutations: (changes to a single letter) Silent mutation is a mutation that doesn’t exert any effect on the protein. Changes a codon w/o changing a protein Missense mutation is a mistake mutation that changes a codon, w/ changes to amino acid Nonsense mutation is a mutation in which no amino acid is produced, only stop codon
Frameshift mutations: (change the reading frame/multiple codons) Insertion mutation adds an extra letter to the sequence Deletion mutation deletes a letter from the sequence (^45) Subtopic: DNA Repair Pathways Base Excision Repair (BER) Nucleotide Excision Repair (NER) Mismatch Repair Homologous Recombination Non- homologous End-joining What type of DNA damage does each repair pathway fix? BER – single nucleotide NER – several nucleotides MMR – mistakes in DNA replication HR/NHEJ – double stranded breaks
- What are the steps each repair pathway takes to fix the damaged DNA? Look at the slides PCR is a procedure used to synthesize copies of DNA.
- What are the steps of PCR, including the definitions of each step? Denature – DNA strand separation with heat Anneal – DNA primers base pair to target DNA strands Elongation/Extension – DNA polymerase binds to primers and synthesize new DNA PCR
- What are the components of a PCR reaction? Target DNA Heat stable DNA polymerase Nucleotides (dNTP)
*****Unit 5: Myoglobin and Hemoglobin*** Page Section Vocabulary Key Questions** - You should be able to answer these upon completion of the Unit/Section. 52 Myoglobin and Hemoglobin (^53) 5.1 Hemoglobin and Myoglobin: Structure and Function Heme Affinit y
- What are the structural differences between myoglobin and hemoglobin? Myoglobin – single subunit protein w/ primary/secondary/tertiary structure contains one heme/iron/can bind one O Hemoglobin – it is a 4 subunit protein (2 alpha, 2 beta) w/ prim/sec/tert/quat structure contains 4 heme/iron/can bind 4 O
- What are the functional differences between myoglobin and hemoglobin? Myoglobin – found in muscle tissue, stores O2 in muscle, has high O affinity Hemoglobin – found in the blood, delivers O2 to body, has lower O affinity
- Given the concentration of oxygen (mmHg or torr), what is the
saturation of myoglobin? What is the saturation of hemoglobin? Look at the O2 binding curve. 55 5.2 The Dynamic Structure of Hemoglobin 56 Subtopic: Oxygenated versus Deoxygenated Hemoglobin Cooperativity Cooperativity makes other O2 molecules more likely to bind to Hemoglobin if another O2 is already bound to it. It also works in the opposite direction when Hemoglobin reaches tissue that needs to be oxygenated. Myoglobin doesn’t have cooperativity.
- What are the structural properties of the tense state of hemoglobin? The relaxed state? Relaxed (R) state has higher affinity for O2 Tense (T) state has lower affinity for O
