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BIOCHEM STUDY GUIDEBIOCHEM STUDY GUIDE, Study Guides, Projects, Research of Biochemistry

Virginia State University (VSU)Biochemistry

BIOCHEM STUDY GUIDEBIOCHEM STUDY GUIDE

Typology: Study Guides, Projects, Research

2023/2024

Available from 05/31/2024

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BIOCHEM STUDY GUIDE
1. Unit 2 Amino acids, peptide bonds, and protein structures
2. Amino Acids: The building blocks of proteins
3. Chemical elements, atoms and bonds—Optional Review
a. Electrons-only subatomic particle involved in chemical reactions
b. Energy- compacity to cause change (doing work)
c. Covalent bonds- sharing a pair of valance electrons by two atoms ex: H—H
d. Ionic bonds- chemical bond resulting from attraction of atoms of opposite charge
(salt bridge)
e. Hydrogen bonds- weak chemical bond formed when slightly + hydrogen atom and a
polar covalent bond in one molecule is attracted to the slightly negative atom of a polar
covalent bond in another molecule or in another region of the same molecule ex: H20
& NH3 (ammonia)
4. Amino Acid Structure and Chemical Properties
a. Amino- tends to pick up a proton- giving it a positive charge ex: NH2
b. Carboxyl- group tends to have negative charge- because it tends to lose a proton
ex: COOH
c. Hydrophobic (nonpolar)- water hating
i. makes hydrophobic interactions
ii. Only has carbon and hydrogen ex: CH2, CH3
iii. Heat breaks hydrophobic interactions
d. Hydrophilic (polar)- Water loving
i. makes hydrogen bonds
ii. In addition to C & H, R group has O, N, or S
iii. Change in pH or adding salt can break hydrogen bonds, reducing agents
break the disulfide bonds.
e. Charged- positive (basic) or negative (acidic)
i. Makes ionic bonds
ii. Change in pH or adding of salt can break ionic bonds
f. Disulfide bonds
i. Strongest bond
ii. A double bond btw two Sulphur atoms in cysteine side chains
iii. What type of amino acids participate in disulfide bonds? Cysteine
iv. Disrupted by reducing agents
g. Zwitterions- a molecule or ion having separate positively and negatively charged groups.
h. What is the basic structure of amino acid?
i. Carboxyl group- tends to have a neg charge (COOH-)
ii. Amino group- tends to pick up a proton- giving it a positive charge (NH2)
iii. Carbon- alpha carbon, can form 4 covalent bonds
iv. R- where amino acids differ from one another (side chair/variable)
5. Polypeptides and Functional Proteins
a. Polypeptides- A single protein chain consisting of several amino acids bonded by
peptide bonds
b. Peptide bonds- amino acids are linked together by a specific type of bond called a
peptide bond.
6. Levels of protein structure
a. Dehydration- associated with water loss in the body
b. Hydrolysis- chemical breakdown of a compound due to reaction with water
c. Alpha helix- delicate coil held together by hydrogen bonds btw 4th amino acid ex: a-
keratin, hair (chain twists)
pf3
pf4
pf5
pf8
pf9
pfa
pfd
pfe
pff
pf12
pf13
pf14
pf15
pf16
pf17
pf18
pf19
pf1a
pf1b
pf1c

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BIOCHEM STUDY GUIDE

  1. Unit 2 Amino acids, peptide bonds, and protein structures
  2. Amino Acids: The building blocks of proteins
  3. Chemical elements, atoms and bonds—Optional Review a. Electrons-only subatomic particle involved in chemical reactions b. Energy- compacity to cause change (doing work) c. Covalent bonds- sharing a pair of valance electrons by two atoms ex: H—H d. Ionic bonds- chemical bond resulting from attraction of atoms of opposite charge (salt bridge) e. Hydrogen bonds- weak chemical bond formed when slightly + hydrogen atom and a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule or in another region of the same molecule ex: H & NH3 (ammonia)
  4. Amino Acid Structure and Chemical Properties a. Amino- tends to pick up a proton- giving it a positive charge ex: NH b. Carboxyl- group tends to have negative charge- because it tends to lose a proton ex: COOH c. Hydrophobic (nonpolar)- water hating i. makes hydrophobic interactions ii. Only has carbon and hydrogen ex: CH2, CH iii. Heat breaks hydrophobic interactions d. Hydrophilic (polar)- Water loving i. makes hydrogen bonds ii. In addition to C & H, R group has O, N, or S iii. Change in pH or adding salt can break hydrogen bonds, reducing agents break the disulfide bonds. e. Charged- positive (basic) or negative (acidic) i. Makes ionic bonds ii. Change in pH or adding of salt can break ionic bonds f. Disulfide bonds i. Strongest bond ii. A double bond btw two Sulphur atoms in cysteine side chains iii. What type of amino acids participate in disulfide bonds? Cysteine iv. Disrupted by reducing agents g. Zwitterions- a molecule or ion having separate positively and negatively charged groups. h. What is the basic structure of amino acid? i. Carboxyl group- tends to have a neg charge (COOH-) ii. Amino group- tends to pick up a proton- giving it a positive charge (NH2) iii. Carbon- alpha carbon, can form 4 covalent bonds iv. R- where amino acids differ from one another (side chair/variable)
  5. Polypeptides and Functional Proteins a. Polypeptides- A single protein chain consisting of several amino acids bonded by peptide bonds b. Peptide bonds- amino acids are linked together by a specific type of bond called a peptide bond.
  6. Levels of protein structure a. Dehydration- associated with water loss in the body b. Hydrolysis- chemical breakdown of a compound due to reaction with water c. Alpha helix- delicate coil held together by hydrogen bonds btw 4 th^ amino acid ex: a- keratin, hair (chain twists)

d. Beta sheet- 2 or more segments of polypeptide chains lying side/side ex: spider web, silk fibers parallel to one another e. Denaturation-Process of ruining the functional structure of a molecule. It will no longer be able to carry out its intended function. A process by which the native functional structure of a molecule has been disrupted f. What are the 4 level of protein structure? List distinguishing features of each i. Primary sequence of amino acids forming a protein or polypeptide chain, the most basic element of its structure (peptide bonds) ii. Secondary three-dimensional structure of sheets, helices, or other forms taken on by polypeptide chain, due to electrostatic attractions between neighboring resides (stabilized by hydrogen bonds) iii. Tertiary three-dimensional structure resulting from folding and covalent cross- linking of a protein (hydrogen bonds, ionic bonds-positive or negative charges, and disulfide bridges) iv. Quaternary overall protein structure consisting of two/more polypeptide chains aggregated into one functional macromolecule ex: hem + iron= hemoglobin, connective tissues (hydrophobic and hydrophilic interactions, & disulfide bridges)

  1. A Protein’s Structure Depends on its Environment a. Aggregation- clustering b. What environmental change breaks each type of bond? i. hydrophobic bond, weak strength, heat disrupts the interaction (fever, frying an egg) ii. ionic bonds, change in pH and adding salt disrupts the interaction iii. hydrogen bonds, change in pH or adding salt can break these bonds iv. disulfide bonds- reducing agents disrupts this process c. What type of amino acid side chain leads to protein aggregation? i. Hydrophobic interaction ii. Ex: sickle-cell hemoglobin in proteins lead to their aggregation into a fiber; capacity to carry oxygen is greatly reduced iii. Ex: Alzheimer’s disease, accumulation of proteins inside and around neurons leads to neuronal cell death and brain atrophy (jelly doughnut protein aggregation)
  2. Protein Function and Disease a. How do environmental changes affect protein folding? i. High temp, pH and salt concentration or other aspects of its environment are altered, the weak chemical bonds and interactions within a protein may be destroyed causing the protein to unravel and lose its native shape. b. How do mutations affect protein structure? i. Changes in DNA lead to changes in mRNA, and the code mRNA determines the sequence of amino acids, which are the basis of protein structure. (changes amino acids which changes the overall structure) ii. Mutations cause misfolding- neurodegenerative diseases
  3. Enzymology and Catalytic Mechanism
  4. Enzyme Action a. Substrates- molecule that an enzyme will specifically bind to b. Products- released from the enzyme active site
  1. Enzyme Regulation a. Allosteric site- site that allows molecules to either active or inhibit enzyme activity, away from active site on enzyme b. Competitive inhibitor- inhibitor binds to the active site and prevent substrate from binding c. Non-competitive inhibitor- binds to the enzyme away from the active site (allosteric site) altering enzyme shape so that even if substrate binds- the active site functions less effectively, if at all. d. Feedback inhibition- prevents over production of product- method of metabolic control in which the product of metabolic pathways acts as an inhibitor of an enzyme within that pathway e. What are the differences between competitive and non-competitive inhibitors? Competitive inhibition, the inhibitor binds directly to the active site of an enzyme. In non-competitive inhibition, the inhibitor binds to a site on the enzyme that is NOT the active site. f. When given an enzyme pathway, be able to analyze the pathway under normal conditions and under inhibition. What molecules increase/build-up or decrease given a specific inhibitor?
  2. DNA & RNA Structure a. Gene expression-

process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNA’s that are not translated into proteins and instead function as RNAs. (Recruitment of RNA polymerase and subsequent production of a new RNA transcription of a gene) (DNA > RNA > Protien) b. Nucleotides- building block of a nucleic acid, consisting of a five-carbon sugar (a pentose) covalently bonded to a nitrogenous base and one to three phosphate groups. Pyrimidine- one of two types of nitrogenous bases found in nucleotides; (cytosine C, thymine T, and uracil U) Purines- found in nucleotides, characterized by a six-membered ring fused to a five-member ring; (Adenine A, and Guanine G) c. Antiparallel- refers to the arrangement of the sugar-phosphate backbones in a DNA double helix (they run in opposite 5’ S 3’ directions); somewhat like a divided highway; the sugar-phosphate backbones are on the outside of the helix and the nitrogenous bases are paired in the interior of the helix. (held together by hydrogen bonds)

g. Which nucleotides base-pair together to form DNA? (A-T) (C-G) h. To form RNA? (A-U) (C-G)

  1. DNA & RNA Work together to Make Proteins
  2. Transcription & Translation a. Template DNA- DNA template is a single strand of DNA that is used by DNA polymerase enzyme as a basis of copying the DNA. b. Coding DNA Sequence of DNA that codes for proteins, coding DNA is also known as an exon. Coding DNA sequences are separated by long regions of DNA called introns that have no apparent function. c. Replication Process by which DNA makes a copy of itself during cell division >unzip double helix

    helicase breaks hydrogen bonds, holds the complementary bases of DNA together separation of 2 DNA strands (Y shape, replication fork)-templates for new DNA one strand orientated in the 3’ to 5’ direction (towards replication fork-leading strand) and 5’ to 3’ direction (away from the replication fork-lagging strand) d. Transcription Process of changing DNA to RNA; happens in the nucleus ; involves the DNA, mRNA, and RNA polymerase e. RNA polymerase Action house- primary enzyme involved in transcription that reads the DNA sequence of a gene and produces a complementary f. Promoter Region of DNA where transcription of a gene is initiated. Located upstream of a gene and is the binding site for transcription factors that recruit the RNA polymerase; during initiation of transcription, RNA polymerase binds to the “promoter” g. Transcription factors Specific proteins that recognize and bind to the promoter sequence of gene. The binging of transcription factors helps to recruit RNA polymerase to the transcription start site to begin gene expression. (helps start the transcription process) h. mRNA

DNA- MRNA= PROTIENS

q. What is the relationship between mRNA and tRNA? tRNA is a type of RNA that helps decode a messenger RNA (mRNA) sequence into a protein.

  1. Control of Gene Expression a. Splicing Portions of an mRNA sequence called introns (intervening sequences) are removed and the remaining portions of the gene (expressed sequences, or exons) are joined. “cut-and-paste job” b. Introns Intervening sequences in a newly made mRNA molecule that are removed by splicing before the mRNA is released into the cytoplasm for protein synthesis (translation). c. Exons The expressed sequences from a new mRNA strand that remain in the mRNA after splicing. The exons will be the part of the mRNA translated into protein; Protein coding sequences along a stretch of DNA The terms intron and exon are used for both RNA sequences and the DNA sequences that specify them. In primary transcription from a gene, RRNA

polymerase II transcribes both introns and exons from the DNA, but the mRNA that enters the cytoplasm is abridged version. RNA splicing, the introns are cut out from the molecule- exons join, forming an mRNA molecule with a continuous coding sequence. d. Histones promote coiling of the nucleosomes into a larger chromatin fiber (nucleosome)/ group of basic proteins that hold DNA in supercoils / They are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation; prevent tangling e. Nucleosomes DNA + histone = nucleosome f. Methylation Process by which methyl groups are added to histones can lead to condensation of chromatin and reduced transcription; decreasing transcription (removal of extra methyl groups can “turn on” genes) g. Acetylation Additionofacetylgrouptoanaminoac idinahistonetail-appearsto promotetranscriptionbyopeningup thechromatinstructure;increasi ng transcription h. How does mRNA splicing allow us to create multiple proteins from a single gene/mRNA? In splicing, some sections of the RNA transcript (introns) are removed, and the remaining sections (exons) are stuck back together. Some genes can be alternatively spliced, leading to the production of different mature mRNA molecules from the same initial transcript—multiple proteins. i. What factors increase gene expression? What factors decrease gene expression? How do these factors work together to control transcription? Transcription factors are proteins that help turn specific genes “on” or “off” by binding to nearby DNA.

  • Activators boost a gene’s transcription; for instance, they may help the general transcription factors and/or RNA polymerase bind to the promoter
  • repressors decrease transcription; for example they may block/get in the way of RNA polymerase, so they cant bind to the promoter or begin transcription

Process that corrects mismatched nucleotides in the otherwise complementary paired DNA stands, arising from DNA replication errors and recombination, as well as from some types of base modifications (occurs before replication) d. Homologous Recombination Repair for double strand breaks- uses undamaged section of similar DNA as a template. Type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of double-stranded or single stranded nucleic acids; damage d/t gamma rays/x-rays e. Non-homologous End-joining Repair for double stand breaks- serious of proteins trims off a few nucleotides and fuses the ends back together f. What type of DNA damage does each repair pathway fix? g. What are the steps each repair pathway takes to fix the damage DNA? Damage to a single nucleotide- base excision repair

  1. DNA repair enzymes
  2. DNA pol adds a new nucleotide
  3. Ligase seals the remaining nick Damage to a small number of bases- nucleotide excision repair
  4. DNA repair enzymes recognize the damaged bases and remove a small section of DNA surrounding the damage
  5. DNA pol fills the gap
  6. Ligase seals the nick Mistakes in replication- proofreading, mismatch repair
  7. DNA polymerase removes the incorrect base
  8. DNA polymerase inserts the correct base (almost like a delete key)
  9. DNA repair enzymes recognize a mistake made during replication and remove several bases surrounding the mismatched base
  10. DNA polymerase inserts the correct bases
  11. Ligase seals the remaining nick Double-strand breaks-non-homologous end joining, homologous recombination repair
  12. Homologous recombination
  • Double stranded breaks are aligned with homologous DNA
  • Undamaged DNA provides the needed sequence to repair the damage
  1. Non-homologous end joining
  • The broken ends of the DNA are glued together without regard for sequence (last resort)
  1. PCR and Genetic Testing a. PCR Technique for amplifying DNA in vitro by incubating it with specific primers, a heat-resistant DNA polymerase, and nucleotides

b. Primers Short DNA sequences, bind or anneal to complementary matches on the target DNA sequence c. Denaturation Heat briefly to separate DNA strands d. Annealing cool to allow primers to form hydrogen bonds with ends of target sequence e. Elongation/extension DNA polymerase adds nucleotides to the 3’ end of each primer f. What are the steps of PCR, including definitions of each step?

j. How does PCR compare to normal DNA replication in the cell? Both involves a template strand and polymerase chain reactions, differences:

  • Machinery involved- extreme temps, denaturation/annealing vs body temperature to sustain replication
  • Type of polymerase- DNA polymerase in eukaryotes vs PCR thermostable DNA polymerase derived from bacteria or archaea
  • Length of DNA- who genomic DNA is routinely replicate in the body; PCR reaction, the polymerase used has short half- life, only effective for small fragments of DNA
  • Features of polymerase used- DNA requires high fidelity, speed, proofreading, and repair; PCR reactions use simpler polymerase that are not as “feature-rich”
  1. Myoglobin and Hemoglobin: Structure and Function a. Heme – iron containing compound b. Affinity- stickiness for oxygen c. What are the structural differences between myoglobin and hemoglobin? i. Myoglobin- single subunit, one polypeptide chain that combine to one oxygen molecule (monomer); tertiary structures, but no quaternary structure ii. Hemoglobin- has four subunits that could each bind to one oxygen molecule (polymer); has tertiary structure, but not quaternary structure; of the subunits or subunit binds oxygen via the iron
  2. T state- deoxygenated (purple), heme is bent, subunits are farther apart; acidic, low pH, binds oxygen
  3. R state- oxygenated (bright red), heme is planar, subunits are closer together; basic, high pH, releases oxygen
  4. Change in light absorption is what we are measuring when using a pulse oximeter to monitor the oxygen levels in blood BOTH- bind to oxygen the same way; they both have iron molecule in the center of their structure, and will bind directly to the oxygen molecule d. What are the functional differences between myoglobin and hemoglobin? i. Myoglobin- oxygen storage molecule that stores oxygen in the muscle cells for when needed ii. Hemoglobin- oxygen delivery protein picks up oxygen in the lungs and delivers it throughout the body to the tissues e. Given the concentrations of oxygen (mmHg or torr), what is the saturation of myoglobin? What is the saturation of hemoglobin?
  1. Dynamic Structure of Hemoglobin
  2. Oxygenated versus Deoxygenated Hemoglobin a. Cooperativity Structural changes that increase the affinity for oxygen in hemoglobin b. What are the structural properties of the tense state of hemoglobin? The relaxed state? T-state- deoxygenated, deep purple, heme group bent R-state- oxygenated, bright red, heme group planer/flat c. What causes hemoglobin to change from the tense state to the relaxed state? When oxygen binds to one monomer of hemoglobin, the tetramer’s conformation shifts from T state to R state- the shift promotes binding of oxygen to the remaining monomer’s heme groups, thus saturating the hemoglobin molecule with oxygen
  3. Modulators of Hemoglobin Function a. How does carbon monoxide (CO) affect the structure of hemoglobin? How does it cause poisoning? CO binds to hemoglobin at the same sites as O2, but binds 200x more tightly- because of CO high affinity for hemoglobin it occupies the “spot” for longer periods of time, with less oxygen available to bind and deliver O2-leading to carbon monoxide poisoning b. (5.2) How does 2,3-BPG (2,3-DPG) affect the structure of hemoglobin? What is the natural function 2,3-BPG? DPG- produced during glycolysis, reversibly binds with hemoglobin, allosterically causing it to have a lower affinity for oxygen
  4. The Bohr Effect hemoglobin is induced to release more oxygen to supply cells than it needs. his is a phenomenon in which hemoglobin responds to changes in pH to deliver oxygen where it is needed most. For example, in an active muscle, an abundance of CO2 is produced during aerobic metabolism. The increased CO2 creates an acidic environment that prompts effective oxygen delivery.
  5. pH and Hemoglobin Structure a. pH pH is determined by the concentration of H+ ions in a solution; ranges from 0-14. b. Protons subatomic particle found in the nuclei; positively charged c. Acid Increases the hydrogen ion concentration of a solution, low pH d. Base Reduces the hydrogen ion concentration of a solution, high Ph (**pH increases= hydrogen ions decrease) e. What are we measuring when we measure pH? What level of pH is considered acidic? Basic? molar concentration of hydrogen ions in the solution and as such is measuring acidity or basicity; Acidic < 7 > Basic f. What factors change the pH of the blood? The lower the pH, the more acidic the blood. g. How do changes in pH affect hemoglobin’s structure? When pH rises, hemoglobin loses hydrogen ions from specific amino acids in its structure and enhances ability to bind

the breakdown of complex molecules in living organisms to form simpler ones, together with the release of energy; destructive metabolism. (i.e. glycolysis= ATP is used) c. Anabolism the synthesis of complex molecules in living organisms from simpler ones together with the storage of energy; constructive metabolism. (i.e. assembly of a protein chain from individual amino acids= ATP is produced) d. Carbohydrates A sugar (monosaccharide) or one of its dimers (disaccharides) or polymers (polysaccharides) e. Monosaccharides Simple sugars (i.e. ribose, glucose, fructose) f. Disaccharides. Double sugars-two monosaccharides joined by a covalent bond (i.e. sucrose, lactose, maltose) g. Polysaccharides Composed of many sugar buildings blocks (i.e. starch, glycogen, cellulose) h. Apha linkages In starch all the glucose monomers are in alpha configuration i. Beta linkages In cellulose all the glucose monomers are in beta configuration, making every glucose monomer “upside down” with respect to its neighbors j. How do the different linkages between the monomers of polysaccharides affect how they are digested? Starch is a polysaccharide, consisting of many molecules of glucose linked together by alpha linkages. The human body digests the starch, leading to an increase in blood glucose. The breakdown of starch is a catabolic process k. What is the structure and function of ATP? i. Adenine + Ribose + 3 Phosphates = Adenosine Triphosphate ii. Energy carrying molecule found in the cells of all living things; ATP captures chemical energy obtained from the breakdown of food molecules and releases it to fuel other cellular processes iii. Molecule that carries energy within cells; end product of a processes of photophosphorylation (adding a phosphate group to a molecule using energy from light), cellular respiration, and fermentation

  1. Glucose Storage a. Insulin Hormone made by the pancreas that allows your body to use sugar (glucose) from carbs in the food that you eat for energy or to store glucose for future use; helps keep blood sugar from getting to high/low b. Glycogen a substance deposited in bodily tissues as a store of carbohydrates. It is a polysaccharide which forms glucose on hydrolysis. c. Glycogenesis the formation of glycogen from sugar d. Glut Insulin-regulated glucose transporter found primarily in adipose tissues and striated muscle (skeletal and cardiac). e. What are some real-life scenarios that would lead to insulin release from the pancreas?

Insulin is released from the beta cells in your pancreas in response to rising glucose in your bloodstream. After you eat a meal, any carbohydrates you've eaten are broken down into glucose and passed into the bloodstream. The pancreas detects this rise in blood glucose and starts to secrete insulin. f. How does insulin help reduce blood glucose levels? How does Glut4 aid in this process? Insulin helps cells absorb glucose, reducing BS and providing the cells with glucose for energy. Glut4 is insulin dependent and is responsible for most of the glucose transport into muscle and tissues

  1. Tapping into glucose stores a. Glucagon Role is to prevent blood glucose levels from dropping too low; stimulates the conversion of stored glycogen (stored in the liver) to glucose and released in the blood stream b. Glycogenolysis Breakdown of glycogen (n) to glucose-1-phosphate and glycogen (n-1). c. What are some real-life scenarios that would lead to glucagon release from the pancreas? When the amount of glucose in the bloodstream is too low; Glucagon causes the liver to convert stored glycogen into glucose, which is released into the bloodstream. d. How does glucagon help increase blood glucose levels? Glucagon works to counterbalance the actions of insulin. 4-6 hours after you eat your blood sugar decreases, triggering your pancreas to produce glucagon-this hormone signals your liver and muscle cells to change the stored glycogen back into glucose.
  2. Aerobic Metabolism a. Aerobic metabolism (when oxygen is present) A way the body creates energy through the combustion of carbohydrates, amino acids, and fats in the presence of oxygen. (combustion=burning) b. Cellular respiration Catabolic pathways of aerobic and anerobic respiration, which break down organic molecules and use an electron transport chain to produce ATP.