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****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}}
Biochemistry Note-Taking Guide
*****Unit 2: Amino Acids, Peptide Bonds, and Protein Structure*** Pa ge Secti on Vocabulary Key**^ Questions^ -^ You^ should^ be^ able^ to^ answer^ these upon completion of the Unit/Section. Please add your own notes as necessary. 12 Amino Acids, Peptide Bonds, and Protein Structure 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 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. 13 2.1 Amino Acids: The Building Blocks of Proteins (^14) Subtopic: Chemical Elements, Atoms, and Bonds— Optional Electrons Energy Covalent bonds
Ionic bonds Hydrogen bonds (^15) Subtopic: Amino Acid Structure and Chemical Properties Amino Carboxyl Hydroph obic Hydrophil ic Disulfide bonds Zwitterio ns
- What is the basic structure of an amino acid? List the 4 groups and describe what they look like. An amino acid is an organic molecule with both an amino group and a carboxyl group. At the center of the amino acid is an asymmetric carbon atom called the alpha carbon. The R group, also called the side chain, differs with each amino acid
- How do you identify the 3 different types of side chains: non-polar/hydrophobic, polar, and charged? Hydrophobic has C atom and is not charged (found in protein interior) Polar has S, N, or O atom and is not charged (found in protein exterior) Charged are positively or negatively charged (found in protein exterior)
- What kind of bonds do each of the 3 different types of side chains make? Hydrophobic have Hydrophobic bonds (weakest kind of bonds) Polar have Disulfide (S-strongest kind of bonds) or Hydrogen (N, O) bonds Charged have Ionic bonds 17 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 Polypept ides When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group
bond. This happens during the formation of primary structur e in the peptide chain. (^19) Subtopic: Levels of Protein Structure Dehydr ation Hydroly sis Alpha helix Beta sheet Denatur ation
- 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 ( nd , 3 rd and 4 th structure) enzymes – peptide bonds ( st structure)
- What type of amino acid side chain leads to protein aggregation???? Hydrophobic acids tend to aggregate better then hydrophilic Proteins that denature, tend to aggregate. These aggregated clumps can’t be broken down and will continue to accumulate until disease occurs
- How do environmental changes affect protein folding?
*****Unit 3: Enzymology and Catalytic Mechanism*** Pa ge 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 Intermediat es Active site Enzyme specificity Induced fit Kinase Phosph atase
- 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 29 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
- How do environmental changes affect enzymes?
bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures. Each enzyme has an optimal temperature at which its reaction rate is greatest. Most human enzymes have optimal temperatures of about 35–40°C. The optimal pH values for most enzymes fall in the range of pH 6–8. Certain chemicals selectively inhibit the action of specific enzymes. Sometimes the inhibitor attaches to the enzyme by covalent bonds, in which case the inhibition is usually irreversible. Many enzyme inhibitors, however, bind to the enzyme by weak interactions, and when this occurs the inhibition is reversible. Toxins and poisons are often irreversible enzyme inhibitors. (^31) Subtopic: Enzyme Regulation Allosteric site Competitive inhibitor Non- competitive inhibitor Feedback inhibition
- What are the differences between competitive and noncompetitive inhibitors? Some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active site. These mimics, called competitive inhibitors , reduce the productivity of enzymes by
blocking substrates from entering active sites. This kind of inhibition can be overcome by increasing the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to the sites. Noncompetitive inhibitors do not directly compete with the substrate to bind to the enzyme at the active site. Instead, they impede enzymatic reactions by binding to another part of the enzyme (allosteric site). This interaction causes the enzyme molecule to change its shape in such a way that the active site becomes much less effective at catalyzing the conversion of substrate to product.
- When given an enzyme pathway, be able to analyze that pathway under normal conditions and under inhibition. What molecules increase/build-up or 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.
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.
*****Unit 4: DNA and RNA*** Pa ge Section Vocabulary Key Questions** - You should be able to answer these upon completion of the Unit/Section. 3 6 DNA and RNA 37 4.1 DNA and RNA Structure Gene expressio n Nucleotide s Antiparall el Compleme ntary
- Which nucleotides/bases are used in DNA? Which are used in RNA? Know their abbreviations and their full names. (Example: A is adenine.) DNA: Adenine, Thymine, Cytosine, Guanine Purines: A and G RNA: Adenine, Uracil, Cytosine, Guanine Pyrimidines: T, U and C
- Which nucleotides base-pair together to form DNA? To form RNA? DNA: A-T, C-G RNA: A-U, C-G
s Antico dons 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.
