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Biochemistry Note-Taking Guide2023////
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.
*****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. 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.
2.1 Amino Acids: The Building Blocks of Proteins (^14) Subtopic: Chemical Elements, Atoms, and Bonds—Optional Review Electrons Energy Covalent bonds
Biochemistry Note-Taking
Guide2023////
Ionic bonds Hydrogen bonds (^15) Subtopic: Amino Acid Structure and Chemical Properties Amino Carboxyl Hydrophobic Hydrophilic Disulfide bonds Zwitterions
- 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 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
*****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 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 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
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. 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
*****Unit 4: DNA and RNA*** Page Section Vocabulary Key Questions** - You should be able to answer these upon completion of the Unit/Section. 36 DNA and RNA 37 4.1 DNA and RNA Structure Gene expression Nucleotides Antiparallel Complementar y
- 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 Bases are paired by hydrogen bonds 39 4.2 DNA and RNA Work Together to Make Proteins (^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.
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 47 4.4 PCR and Genetic Testing
PCR
Primers Denaturati on Annealing Elongation
- What are the components of a PCR reaction? Target DNA Heat stable DNA polymerase Nucleotides (dNTP) Primers
- How are primers used to assist in a PCR reaction?
- How do you calculate the number of copies of DNA produced by a specific number of PCR cycles? Every cycle doubles the amount of DNA
- How does PCR compare to normal DNA replication in the cell? RNA primers are used during DNA replication, while DNA primers are used in PCR. PCR uses heat to separate DNA strands. PCR uses heat stable DNA polymerase from bacteria, as normal human polymerase would disintegrate in high heat.
*****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
*****Unit 6: Carbohydrate Metabolism and Adenosine Triphosphate (ATP)*** Page Section Vocabulary Key Questions** - You should be able to answer these upon completion of the Unit/Section. 66 Carbohydrate Metabolism and Adenosine Triphosphate (ATP) 67 6.1 Food as Fuel
- What are some examples of monosaccharides? Disaccharides? Polysaccharides? Mono - glucose disa - sucrose poly - glycogen 68 Subtopic: Introduction to Metabolism
ATP
Catabolism Anabolism Carbohydrates Monosaccharid es Disaccharides Polysaccharide s Alpha linkages Beta linkages
- How do the different linkages between the monomers of polysaccharides affect how they are digested? All polysaccharides are connected by glycosidic linkages (covalent bonds) Glycogen is a polysaccharide that has Alpha linkages in 1- configuration Starch is a polysaccharide that has Alpha linkages in 1- 6 configuration Cellulose is a polysaccharide that has Beta linkages (indigestible by humas)
- What is the structure and function of ATP? ATP is a nucleotide that consists of three main structures: the nitrogenous base, (adenine), the sugar (ribose), and a chain of three phosphate groups bound to ribose. 69 Subtopic: Glucose Storage Insulin Glycogen (stored glucose) Glycogenesis Glut Insulin = promotes synthesis of glycogen when glucose is abundant Glycogen = stored glucose in the form of polymer Glycogenesis = the process of glycogen synthesis, in which glucose molecules are added to chains of glycogen for storage Glycolysis = the breakdown of glucose by enzymes, releasing energy and pyruvic acid.
- What are some real-life scenarios that would lead to insulin release from the pancreas? Insulin is released after a meal, or in other words after ingestion of glucose.
- How does insulin help reduce blood glucose levels? How does Glut4 aid in this process? It stimulates body to transport glucose to the cells, as well as glycogenesis. Glut4 is a glucose transporter protein. (^70) Subtopic: Tapping Into Glucose Stores Glucagon Glycogenolys is Glucagon = pancreatic hormone that tell the liver to release glycogen Glycogenolysis = breakdown of glycogen into glucose Gluconeogenesis = creation of new glucose by the liver
- What are some real-life scenarios that would lead to glucagon release from the pancreas? Running a marathon, once glucose is needed from the storage
- How does glucagon help increase blood glucose levels? It tells the liver to release glycogen 72 6.2^ Making^ ATP 73 Subtopic: Aerobic Metabolism Aerobic metabolism Cellular respiration Glycolysis Citric Acid Cycle Electron Transport Chain (ETC) NAD+/ NADH FAD/FADH Substrate- level phosphorylati on Oxidative phosphorylation Aerobic metabolism = metabolic reaction that requires O2 presence in ATP production.
- What are the three pathways of aerobic metabolism? Where in the cell does each pathway take place? Glycolysis – in cytoplasm The Citric Acid Cycle – in mitochondrial matrix ETC with Oxidative Phosphorylation – in mitochondrial inner membrane
- What molecules are the substrates for each pathway (“ins”)? What molecules are the products for each pathway (“outs”)? How do the products of one pathway become substrates for the next pathway? Look at the picture
- How is ATP generated in glycolysis? How is it generated in the ETC? How many ATP are generated in each pathway? Aerobic respiration generates around 30-32 ATP per glucose molecule (2+2+26/28 per cycle).
Most of the energy of a fat is stored in the fatty acids. A metabolic sequence called beta oxidation breaks the fatty acids down to two- carbon fragments, which enter the citric acid cycle as acetyl CoA. Fats make excellent fuels, in large part due to their chemical structure and the high energy level of their electrons. A gram of fat oxidized by respiration produces more than twice as much ATP as a gram of carbohydrate. 74 Subtopic: Anaerobic Metabolism Anaerobic metabolism Fermentation Gluconeogenesis The Cori Cycle Anaerobic metabolism = metabolic reaction that doesn’t require O2 in ATP production.
- What are the two different fates of pyruvate? What factors affect the use of pyruvate by the cell? Pyruvate Acetyl-CoA if O2 is present Pyruvate Lactic acid if O2 is not present (fermentation)
- What are the three pathways of anaerobic metabolism/the Cori Cycle? Where in the cell does each pathway take place? In which organ or cell type does each pathway take place? Fermentation happens in cytosol. Cori Cycle happens in overworked muscles or RBCs (these cells lack mitochondria) Cori Cycle
- What molecules are the substrates for each pathway (“ins”)? What molecules are the products for each pathway (“outs”)?
- What is the role of fermentation in regard to NAD+/NADH? During process of fermentation NAD+ is regenerated, and pyruvate is converted to lactate.
- What are at least 3 different molecules that can be used as substrates of gluconeogenesis? The major substrates of gluconeogenesis are lactate, glycerol, and glucogenic amino acids.
- How much ATP is used in gluconeogenesis? What is the net outcome of ATP in The Cori Cycle? Net outcome in the Cori Cycle is -4 ATP. Glycolysis is where 2 ATP and 2 NADH are created, and it is considered a substrate- level phosphorylation. Gluconeogenesis happens in the liver where 6 ATP are lost. Gluconeogenesis has 2 key roles:
- It prevents acidosis since it consumes lactic acid.
- It produces glucose that can be used by the peripheral muscle cells.
- How are aerobic and anaerobic metabolism the same? How are they different? Which aerobic and anaerobic pathways are controlled by insulin? Controlled by glucagon? There are two general mechanisms by which certain cells can oxidize organic fuel and generate ATP: aerobic respiration and fermentation. The distinction between these two is that an electron transport chain is used in aerobic respiration but not in fermentation. Fermentation is a way of harvesting chemical energy without using either oxygen or any electron transport chain. Glycolysis oxidizes glucose to two molecules of pyruvate. Glycolysis generates 2 ATP whether oxygen is present or not. The oxidizing agent of glycolysis is NAD+. In aerobic respiration NAD+ is recycled from NADH by the transfer of electrons to the electron transport chain. During lactic acid fermentation, pyruvate (the end product of glycolysis) gets processed into lactate, and NADH is utilized in the reaction. As a result, NADH breaks down to produce NAD+
- How can diabetes lead to glycation and AGEs? When the blood contains too much glucose, some of the glucose molecules attach to proteins, a process known as glycation. Glycated proteins can accumulate in capillaries, disrupting blood flow to a variety of tissues. For example, glycated Hgb is also known as Hgb A1c. Advanced glycation end products (AGE) are glucose molecules linked to lipids and proteins. They can cause apoptosis or pathogenic behavior of cells. Glycation
*****Unit 7: Lipids*** Page Section Vocabulary Key Questions** - You should be able to answer these upon completion of the Unit/Section. 81 Lipids Lipids are hydrophobic molecules, particularly its hydrocarbon chain. Fatty acids are the simplest lipids 82 7.1 Triglycerides Function in Energy Storage 83 Subtopic: Triglyceride Structure Saturated fatty acid Unsaturated fatty acid Triglycerides Cholesterol Phospholipids Micelle
- How does the length of a fatty acid affect its melting point and physical state at room temperature? The longer they are, the higher melting point. The longer they are, the more solid they are on room temp (solid > 13C atoms).
- How do we label the different carbons and bonds in a fatty acid? Alpha, Beta, Omega carbon Alpha, Beta, Omega bond Beta bond is broken up in beta-oxidation Essential fatty acids also have Omega 3/Omega 6 double bonds
- How do we count the carbons in a full structure of a fatty acid? A structure formula? A zig-zag structure? Look at the chart There are twice as many H then C atoms, and 2 O2 atoms: C 8 H 16 O 2 Formula changes for unsaturated fatty acids
