Chemical Bonds & Biological Molecules

Chemical Bonds and Electronegativity

• Covalent bonds involve the sharing of electrons between atoms.
• A single bond shares one pair of electrons.
• A double bond shares two pairs of electrons.
• Electronegative atoms pull electrons more strongly than other atoms.
• Oxygen and nitrogen are electronegative atoms commonly found in biological molecules.
• Covalent bonds between oxygen/nitrogen and hydrogen are polar, resulting in partial electrical charges near the atoms.
• Covalent bonds between carbon and hydrogen are non-polar because carbon and hydrogen pull electrons equally.
• Weak bonds are important for creating and maintaining the shape of macromolecules
  • Hydrogen bonds and Van der Waals forces are examples of weak bonds.
  • A molecule's shape is related to its function, especially with proteins.

Structure and Function of Large Biological Molecules

• Structure and function are always linked in biological systems.
• Lipids, carbohydrates, proteins, and nucleic acids are the four classes of macromolecules important to cells.
• Carbohydrates, proteins, and nucleic acids are polymers.
• Unique arrangements of monomers can produce diverse polymers, creating cellular and species diversity.
• Polymers are formed by dehydration reactions.
• Polymers are broken down by hydrolysis.

Polysaccharides and Proteins

• Polysaccharides are polymers of sugars.
• Monosaccharides are simple sugars that contain multiples of CH2O and are also called carbohydrates.
• Glucose (C6H12O6) is a key monosaccharide in cells.
• Monosaccharides can be used directly for fuel, or converted into polymers.
• Two monosaccharides are linked via dehydration to form disaccharides; sucrose (table sugar) contains glucose and fructose.
• Polysaccharides are longer polymers of monosaccharides.
• Storage polysaccharides are glucose polymers like starch in plants and glycogen in animals.
• Storage polysaccharides differ in the types of bonds that link glucose molecules, resulting in different structures.
• Animals have enzymes that digest both back down to simple glucose.
• Structural polysaccharides include cellulose, a glucose polymer that forms fibrous cell walls.
• Cellulose differs from starch in terms of how glucose molecules are connected.
• Animals lack the enzymes to hydrolyze cellulose, so some utilize symbiotic microbes to gain energy.
• Proteins are the most abundant macromolecules and perform a variety of functions for cells.
• Proteins are polypeptides, which are polymers of amino acids.
• There are 20 different naturally occurring R groups, classified as nonpolar or polar (including electrically charged acidic and basic).
• Peptide bonds connect two amino acids.
• Proteins have an N terminus (free amine group) and a C terminus (free carboxyl group).
• New amino acids are always added to the C terminus.

Protein Conformation and Structure

• Protein conformation is key to function.
• Proteins have four levels of structure:
• Primary: the sequence of amino acids.
• Secondary: folding into repeating structures (alpha helix, beta-pleated sheet) stabilized by hydrogen bonds along the peptide backbone.
• Tertiary: the entire 3D shape of a polypeptide, stabilized by weak bonds between R groups.
• Quaternary: some proteins are assembled from multiple polypeptide subunits (e.g., collagen, hemoglobin).
• Weak forces collectively hold proteins together, for example, hydrogen bonds, ionic bonds, hydrophobic interactions, and Van der Waals forces.
• Nonpolar amino acids are typically on the protein interior as they cannot hydrogen bond with water on the outside.
• Alternations in protein structure can cause illness.
• Sickle cell disease provides a classic example of the importance of protein structure.
• A single amino acid difference in the primary structure (a non-polar amino acid substituted at position 6) alters the secondary and tertiary structure.
• Non-polar segments cause hemoglobin molecules to aggregate and crystallize into long fibers.
• Red blood cell shape is deformed, cells clog in capillaries, and are easily lysed, creation disease symptoms.
• Protein unfolding is denaturation, caused by breaking of the weak bonds holding protein structure in place due to changes in the protein's environment (pH, temperature, etc.).
• Cells use protein-based chambers called chaperonins to provide the correct environment for folding.
• Nucleic acids store and transmit hereditary information:
• They are polymers of nucleotides.
• Nucleotides have three key components: a pentose sugar (ribose or deoxyribose), a phosphate group (attached to the 5' carbon of the sugar), and a nitrogenous base (attached to the 1' carbon of the sugar).
• Polymerization creates phosphodiester bonds between sugars and phosphates, resulting in a "sugar-phosphate backbone."
• The phosphate of a new nucleotide is attached to the 3' OH of the previous nucleotide.
• Bases are not involved in polymerization.
• DNA strands have a free phosphate at the 5' end and a free C-OH at the 3' end.
• New nucleotides can only be added to the 3' end. DNA Structure
• DNA structure is a double helix:
• Two strands of polynucleotides wind around each other.
• Sugar-phosphate backbone is on the outside of the helix.
• Complementary base pairs in the center hold the helix together.
• Adenine hydrogen bonds with thymine (A-T).
• Guanine hydrogen bonds with cytosine (G-C).
• Strands run in an antiparallel direction.
• Chromosomes are the basic unit of inheritance.
• Chromosomes are made of protein and DNA
• Initial bias was towards proteins as the genetic material.
• Griffith demonstrated bacterial transformation in 1928 using R and S bacteria.
• Avery demonstrated in 1944 that destroying DNA with enzymes (but not protein or RNA) would block transformation.
• Hershey and Chase showed in 1952 that DNA, not protein, entered bacterial cells during viral infection, proving that DNA is the genetic material.
• Watson and Crick developed the model for the antiparallel double helix of DNA in 1953 using models built to fit data from Franklin and Wilkins’ X-ray crystallography and Chargaff’s Rule (A=T, C=G)
• The structure suggested a mechanism for replication
• DNA's basic structure includes a sugar-phosphate backbone, hydrogen-bonded base pairs interior, and anti-parallel ends (3' and 5').
• DNA replication occurs in a semi-conservative manner:
• Existing strands separate.
• Each strand serves as a template for synthesizing a complementary strand.

DNA Replication

• DNA replication requires multiple proteins.
• Initiation requires the following things:
• Specialized sequences called origins of replication.
• Hundreds or thousands per chromosome in eukaryotes
• Helicase, which opens and unwinds DNA, creating a bubble with two replication forks.
• DNA synthesis moves in opposite directions from the bubble.
• Single-stranded binding proteins to keep strands separated.
• Topoisomerase to relieve overwinding stress by breaking and rejoining DNA ahead of the fork.
• Synthesis of DNA is performed by DNA polymerase.
• DNA polymerase needs a primer and can only add nucleotides to the 3' end of an existing strand and new DNA is synthesized by DNA polymerase III, always to the 3' end of primers (5'-3' direction)
• At each fork, the process starts with primase, which makes RNA primers.
• This process creates leading and lagging strands:
• The leading strand primer has an available 3' end, so elongation continues until the strand hits the next fork coming in the opposite direction.
• For the lagging strand, Okazaki fragments are synthesized, RNA primers are added downstream, and DNA polymerase III fills them in moving in the 5'-3' direction (opposite to the overall direction of synthesis, or "back stitching").
• Multiple primers are required on the lagging strand.
• DNA polymerase I removes RNA primers and replaces them with DNA on both leading and lagging strands.
• DNA ligase anneals fragments.
• Be able to draw a replication fork, label the two ends (5' and 3'), and explain how replication occurs on both the leading and lagging strands, including the functions of all the involved proteins/enzymes.
• DNA replication is highly accurate because mismatched bases distort the shape of the helix, and DNA polymerases proofread and replace mismatched bases.
• Other DNA repair enzymes repair DNA after damage, such as from UV radiation.
• Telomeres, located at the ends of chromosomes, are repetitive sequences that do not contain essential genes.
• Telomere length decreases with each round of division due to the inability to add to the 5' end of DNA, which prevents erosion of real genes.
• Telomere shortening is believed to be correlated with aging, limiting cells to a finite number of divisions.
• Germ cells restore telomeres with telomerase, which is also activated in cancer cells, presenting a potential trade-off between aging and cancer..
• In cells, DNA is complexed with proteins (chromatin) for packaging, with histone proteins assembling into nucleosomes, DNA winding around them to form a "beads on a string" structure, and additional levels of winding compacting it into chromosome structure.

Cell Structure and Function

• The cell is the basic unit of life:
• All organisms are made of cells.
• All cells come from pre-existing cells.
• All cells are related through common ancestry and share common properties, with some differences based on cell type.
• There are two types of cells:
• Prokaryotes include bacteria and archaea, and are generally smaller.
• Eukaryotes include protists, animals, fungi, and plants, and are generally larger.
• Both cell types have common features:
• Surrounded by a cell membrane made of phospholipids and proteins.
• Contain DNA as their genetic material, found in chromosomes complexed with proteins (prokaryotic chromosomes are single and circular, while eukaryotic chromosomes are numerous and linear).
• All cells have ribosomes and cytoplasm (cytosol).
• Eukaryotic cells use membranes to establish compartments called organelles.
• Prokaryotic cells are smaller and structurally simple (but biochemically and metabolically complex).
• Eukaryotic cells are larger and structurally more complex, but biochemically more uniform.
• The nucleus is the largest organelle and acts as the information center. It is surrounded by a double membrane (inner and outer), and the outer membrane is continuous with the ER.
• Membranes contain protein-lined pores that create molecular channels for the passage of molecules in and out of the nucleus.
• Ribosomes outside the nucleus are used to translate mRNA into protein.
• Free ribosomes make proteins in the cytoplasm.
• Bound ribosomes direct newly made proteins into the ER.
• The endomembrane system creates an internal linked system of compartments for protein trafficking and secretion.
• This pathway includes the ER, Golgi apparatus, lysosomes, and plasma membrane.
• Proteins move from compartments via transport vesicles.
• Lysosomes, which bud off of the Golgi apparatus, function in intracellular digestion including food vacuoles and organelle autophagy.
• Secreted proteins bud off the Golgi apparatus in vesicles and are released from the plasma membrane.
• Mitochondria and chloroplasts are used in energy pathways in cells and are believed to have developed through endosymbiosis with an ancestral eukaryotic cell engulfing a prokaryotic cell, with a symbiotic relationship occurring instead of digestion.
• Mitochondria and chloroplasts have key similarities to prokaryotic cells, including having a double membrane, DNA in a circular chromosome, and a more prokaryotic-like ribosome structure.
• The cytoskeleton, consisting of microfilaments (actin filaments) which are the smallest in diameter, microtubules which are the largest in diameter, hollow, polymers of tubulin, and and intermediate filaments is a network of protein fibers used for support, maintenance of cell shape, and movement.
• Cells secrete materials that are external to the plasma membrane.
• Plant cells have cell walls, complex components with cellulose.
• Animal cells have an extracellular matrix (ECM): collagen fibers, fibronectin, proteoglycans, and integrin receptors that link to the cytoskeleton inside the cell.
• Cells have emergent properties that are greater than the sum of their parts.

Gene Expression and Protein Synthesis

• DNA has two functions as genetic material, the first be accurately replicated and passed on to the next generation.
• (already covered)
• The second is to provide information to direct the synthesis of proteins for individual cells-
• Protein synthesis occurs in two stages:
• Transcription occurs in the nucleus with DNA transcribed into pre-mRNA.
• RNA processing converts pre-mRNA into mRNA in the nucleus.
• Translation occurs in the cytoplasm where ribosomes translate the mRNA into an amino acid sequence.
• Transcription, which is highly selective is a closer look.
• Much of DNA sequences are not genes.
• Actual genes are transcribed selectively by different cell types.
• During transcription, only one of the two DNA strands (the template strand) is transcribed for a given gene.
• Initiation occurs through the following steps.
• Initiation sequences in the promoter include the TATA box.
• The promoter sequence recruits and binds proteins called transcription factors.
• RNA polymerase then recognizes the promoter and transcription factor complex, binds, unwinds the helix, and prepares to synthesize RNA from the template strand.
• Elongation occurs when the RNA polymerase reads the template and base pairs DNA with ribonucleotide (A, C, G, or U).
• A new nucleotide is always added to the 3' end, and no primer is required.
• RNA and DNA stay base-paired only briefly, then the DNA helix recloses as the polymerase moves down the template.
• In prokaryotes, an mRNA is released and polymerase detaches when the termination sequence in the DNA is reached.
• In eukaryotes, once the RNA polymerase has transcribed the polyadenylation sequence, proteins bind the RNA, causing it to be released and the RNA polymerase to detach.
• In eukaryotes only, RNA processing must occur before pre-mRNA leaves the nucleus:
• The primary transcript undergoes processing in the following ways:
• A 5' cap (modified G) is added post-transcriptionally.
• A 3' poly A tail is added post-transcriptionally.
• Introns are spliced out and connected by spliceosomes (made of proteins and snRNPs).
• Alternative splicing can occur, which may explain how multiple forms of a protein can be made from the same gene.
• The mature mRNA then enters the cytoplasm.
• Translation of mRNA occurs in the cytoplasm and requires the following things.
• mRNAs
• tRNAs
• Relatively small (80 nucleotides).
• Amino acid attached to one end.
• Contain an anticodon at the base.
• Charged with the appropriate amino acid by aminoacyl tRNA synthetases.
• The following is also required:
• Ribosomes (two subunits with large and small), contain rRNA and multiple proteins.
• Initiation occurs through.
• A small subunit binding to mRNA.
• The initiator tRNA (anticodon UAC is complementary to the starter codon AUG) carrying methionine (Met) and binds to the P site.
• The small subunit then moves down the mRNA until AUG is under the P site.
• The large subunit then binds.
• Therefore, all proteins start with methionine at the N terminus since AUG specifies Met as the amino acid.
• Elongation occurs when the second tRNA binds to the A site (based on codon-anticodon base pairing).
• A peptide bond is catalyzed between amino acids, leaving the growing protein remains attached to tRNA in the A site.
• During translocation, the ribosome moves along the mRNA by 3 nucleotides towards the 3' end, opening the A site with a new codon underneath.
• The empty tRNA moves into the E site and is ejected.
• The cycle then repeats.
• Termination happens when the stop codon is under the A site.
• Release factor protein binds, cutting the peptide's attachment to tRNA by adding water, and releasing the new protein, and dissociating complex.
• A major decision point happens when determining how proteins are targeted to their correct destination within the cell. Specifically, you have to decide whether or not to remain in the cytoplasm or move through with the endomembrane system-that included the ER, Golgi, the plasma membrane, and lysosomes.
• All translation begins on free ribosomes in the cytoplasm.
• Proteins destined for the nucleus and mitochondria are directed via a localization sequence post-translationally as part of their structure.
• The nuclear localization sequence is a patch of positively charged amino acids on the surface of the protein.
• A signal peptide present at the N terminus of the newly synthesized peptide, which contains 5-30 non-polar amino acids, designates proteins that are destined for the endomembrane system.
• A signal-recognition particle (SRP) binds that signal peptide and thus, halts translation and binds to the ER membrane.
• The SRP is then released, translation resumes, and the protein is inserted into the ER lumen.
• Proteins become glycoproteins through glycosylation which occurs in the ER and Golgi.
• Different destinations get different sugars, which act as sorting signals.
• Transport vesicles carry proteins to the cis face of the Golgi (the side facing the ER).
• Vesicles bud off the trans face of the Golgi (the side facing the plasma membrane). Some proteins go into lysosomes, and some go into secretory vesicles to carry proteins to the plasma membrane.
• Sorting is based on the types of sugars they get while in the ER and Golgi.
• Mutations can alter proteins.
• Point mutations are small changes in the nucleotide sequence.
• Base pair substitutions can create the following.
• Silent mutations where there is no change in amino acids due to the redundancy of the genetic code.
• Missense mutations where the incorrect amino acid is substituted in the protein like in the disease, sickle cell.
• Nonsense stop mutations where a codon is created and a truncated version of a protein is made.
• Fameshift mutations are considered insertions and or deletions that can throw the codon sequence out of the frame.
• Frame shift mutations usually have more negative consequences such as, creating change in the amino acid that can stop codons.
• CRISPR Cas9 technology can be used for gene editing.
• Complementary guide RNAs are incorporated when you plan to edit a gene.
  • Guide RNAs cause the enzyme to find the cas9 to that the particular gene you plan to alter.
  • Cas9 then makes a double stranded cut.
  • Cells will try to repair the tissue but then usually leads to deletions and frameshift mutations.
• you can use "Knock out" of genes such as BCL114 can be used to help treat diseases such as sickle cell.
• You can also use mutations to repair providing you with a good copy of you gene to copy and will replace the cut region with the correct copy.
• Also, there are ethical and safety issues that relate to CRISPR.
  • FDA has approved treatment that are safe and can even cure sickle cell.