Genetics and Cell Biology Exam 1 Study Guide

Organic Compounds-Four most common elements are H, C, O, N

Types of Bonds-Covalent Bonds

-shared electrons in valence shell-Polar covalent bonds have an unequal attraction for electrons due to the difference in

electronegativity-Non-polar covalent bonds have an equal attraction or electronegativity for electrons-ALL COVALENT BONDS ARE STRONG (about 90 kcal/mol to disrupt or create)-double bonds are stronger and shorter than single bonds

-Noncovalent Bonds-no shared electrons-weak bonds, but sum of non-covalent bonds can be strong-4 non-covalent bonds important in cells:

1. ionic bonds (strongest)2. hydrogen bonds 3. hydrophobic interactions4. van der Waals forces (dispersion, London) (weakest)

-ionic bonds-Ionization:

-Cation donates electron, + charge-Anion accepts electron, - charge

-Electrostatic attraction can also occur between partially charged atoms (VERY STRONG IN ABSENCE OF WATER)

-Opposite charged ionized atoms attracted to each other-Strong absence of H2O

-Hydrogen bonds-2 atoms share one hydrogen-Occurs between polar atoms

-Any atoms with polar covalent bonds can form H-bonds with water-Very weak bond, 1-5 kcal/mol

-Hydrophobic interactions-fear of water-nonpolar molecules in water associate with each other

-van der Waals attractions-between any two atoms-As two atoms get closer fluctuations in electric charges increase attractions, too

close and they repel-IMPORTANT IN PROTEIN STRUCTURE WHEN PROTEINS FIT CLOSELY TOGETHER,

SUM OF ALL VAN DER WAALS CAN BE STRONG

Water-polar-forms hydrogen bonds (cohesive)-effects solubility of other molecules

Hydrophilic – soluble in waterHydrophobic – insoluble in water

-Acids and Bases-highly polar molecules dissolved in water-Acids donate H+-Bases accept H+-pH measures concentration of H+ in solutions in mol/L (pH=-log[H+])-weak acids and bases only partially ionized in water

Carbon-almost all molecules in cell are based on carbon=organic molecules-carbon can form covalent bonds with 5 different atoms (C,O,H,P,N)-saturated and unsaturated bonds

-each carbon atom can form a total of 4 covalent bonds-single C-C bond

-single pair of electrons shared -each C bound to three other atoms=saturated-free rotation

-double C=C bond-2 pairs of electrons shared-each C bound to two other atoms=unsaturated-fixed = no rotation

Organic Macromolecules in Cell-Monomers = subunits-polymers = macromolecules-monosaccharides – polysaccharides-fatty acids – lipids/fats-amino acids – proteins-nucleotides – nucleic acids-covalent bonds between subunits formed by condensation or dehydration synthesis reaction-

molecule of water expelled-covalent bonds broken by hydrolysis reaction – molecule of water consumed-both reactions require energy and enzymes-macromolecules formed by adding subunits to one end of growing polymer in a specific order-covalent bonds between subunits form macromolecules-noncovalent bonds cause many macromolecules to fold-non-covalent bonds allow interactions between macromolecules-high energy molecules

-supply energy for biological work

-ATP-special nucleotide used to produce macromolecules-contains high energy bonds, breaking of these bonds releases energy

-NADH-redox reactions-movement of high energy electrons between molecules

Protein Structure and Function

-Protein structure-orders of protein structure type of bonding-denaturing proteins

-how proteins work-antibodies-enzymes

-regulation of protein and enzyme activity-competitive and non-competitive inhibition-allosteric regulation

Functions of Proteins-50% of dry cell weight-enzyme – lysosome-structural – actin-transport – hemoglobin-motor – myosin-storage – ferritin-signaling – signal protein-receptor – insulin receptor-gene regulation

Structure of Proteins-subunit (monomer) = amino acid

-alpha carbon attached to carboxyl group (weak acid), amino group (weak base), and an R-group

-only L isomer found-ionized at pH7-20 used to form all proteins

-polymer=polypeptides (proteins)-amino acids linked by peptide bonds-dehydration synthesis (condensation) reaction

-peptide bonds are rigid and there is no rotation around C-N bond-R-groups

-20 total amino acids differ by R-group-3 types: charged (acidic or basic), polar, and nonpolar

-types of R group effect solubility and non-covalent interactions that protein can participate in

Properties of R-groups-charged: ionic, soluble-polar: H+ bonds, soluble-nonpolar: hydrophobic, insoluble

-Special Amino Acids-Glycine: R group – H+, small, tends to be in bends of proteins-Cysteine: R group – H2C-SH, two Cysteines can form a disulfide bond (the only covalent

bond formed between R groups)-Levels of Protein Structure

-primary structure: order of amino acids along polypeptide backbone-held together by peptide bonds-order determined by DNA-Folded structures of the polypeptide chain determined by non-covalent

interactions-ionic (electrostatic)-hydrogen bonds-hydrophobic-van der Waals

-secondary structure: H bonds between carbonyl and amide groups of peptide bonds-alpha helix-beta pleated sheets

-tertiary structure: folded structure of lowest free energy-hydrophobic will be on the inside; polar side chains on the outside-formed by non-covalent interaction between R-groups-can also have a disulfide bond (exception)

-factors that influence where amino acid end up in a folded protein-charge of R group-polar vs nonpolar-size of R-group-bonds R group can form with other R groups

-domains: independently folded parts of the protein; subsets of the tertiary structure-quaternary structure: two or more polypeptide chains held together by non-covalent

bonds; sometimes disulfide bonds-each polypeptide chain is a subunit-ionic H+ bonding, hydrophobic, van der Waals-only works if all 4 subunits are connected-just like tertiary, R-groups are interacting

-mutations can effect protein folding and function-a mutation in DNA causes incorrect folding of the proteins

-sickle cell anemia due to single mutation in DNA sequence leads to single amino acid change

-prions are misfolded proteins that cause additional proteins to misfold and aggregate

-“Mad Cow” disease (infectious)-Creuztfeldt-Jakob disease (inherited)

-denaturing Proteins-native: folded protein-denature: disrupt all folding by disrupting all non-covalent bonds

-heat: H+ bonding breaking-pH change: ionic interactions-organic solvent or detergent: hydrophobic interactions

-SDS has a neg charged head, makes a neg charged protein-reducing agent

How Proteins Work-Proteins work by binding to other molecules-characteristics of protein binding

-specificity: limited type of molecule protein can bind-ligand: molecule protein binds to (chemical, protein, hormone, DNA)-binding site: region of protein that associates with ligand; distinct 3D shape creates

specificity-not exactly “lock and key”, more like “lock and key and password”-there can be competition-enzymes catalyze reactions by lowering the activation energy

Regulation of Protein Activity-feedback inhibition of enzymes

-reversible negative inhibition-competitive vs non-competitive

-allosteric regulation-If there is enough of an amino acid, that amino acid will bind to an enzyme early on to prevent

more from being made-reversible inhibition

-feedback inhibition is ALWAYS REVERSIBLE-other molecules can also inhibit reversibly-competitive inhibition

-inhibitor binds to enzyme at active site-non-competitive inhibition

-inhibitor binds outside active site (allosteric site)-enzymes can also be positively regulatedALLOSTERIC REGULATION: AN ALLOSTERIC EFFECTOR BINDS TO THE ENZYME,

CHANGING THE SHAPE IF THE ACTIVE SITE, THEREBY CHANGING ITS ACTIVITY

THE POINT – -The three dimensional structure of proteins is a result of interactions at many levels-These interactions can be chemically disrupted (knowing what sorts of reactions helps overall

understanding)

-Mutations can also disrupt protein structure by altering these interactions-Enzymes, as proteins, are subject to all the rules of protein structure as we’ve discussed.-Regulation of protein and enzyme activity ultimately controls what reactions occur in the cell

DNA and Chromosomal Structure-genotypic function: replication – information must be stored and transmitted-phenotypic function: gene expression – must control the phenotype of the organism-evolutionary function: mutation – changes must lead to variation; this variation is essential for

adaptation-chromosomes

-genes are located on chromosomes-chromosomes contain proteins and nucleic acids-the nucleic acids are deoxyribonucleic acid and ribonucleic acid-scientist initially questioned whether DNA or protein was the genetic material

The Genetic Material of Bacteriophage T2 is DNA: Hershey and Chase, 1952Hershey Chase used bacteriophage to infect bacteria. The phage were either radioactively

labeled with sulfur (S35) to label proteins or phosphorous (P32) to label DNA. Labeled phage was used to infect bacteria. After infection, the material was subjected to treatment in a blender to remove any phage still attached to the outside of the bacteria. The bacteria were then centrifuged to pellet the bacteria. The pellet and the liquid supernatant were assayed for the presence of radioactivity. It was found that P32 was mostly found in the pellet with the bacteria, while S35 was located mostly in the liquid supernatant. This result definitively showed that only DNA and not protein from bacteriophage entered the bacteria upon infection. Thus the DNA was directing the production of new phage inside the infected bacteria. This experiment was definitive proof that DNA, not protein, was the genetic material.

Central Dogma of Molecular Biology – DNA – transcript – RNA – translate – Protein

Key Points – -eukaryotic chromosomes are linear and are composed of DNA plus histone proteins-During mitosis/meiosis, chromosomes condense-Two essential structures that are the centromeres required for chromosome movement during

mitosis/meiosis and telomeres, which protect the ends of the linear chromosomes.

Summary of Replication – -DNA replicates by a semiconservative mechanism; as the two complementary strands of a

parental double helix unwind and separate, each serves as a template for the synthesis of a new complementary strand.

-The H-bonding of the bases in the template strands specify the complementary base sequences in the nascent DNA strands.

-Replication is initiated at unique origins and usually proceeds bidirectionally from each origin.

DNA polymerase summary – -DNA synthesis is catalyzed by enzymes called DNA polymerases.-All DNA polymerases require a primer strand, which is extended, and a template strand, which

is copied.-All DNA polymerases have an absolute requirement for a free 3’-OH on the primer strand, and

all DNA synthesis occurs in a 5’ to 3’ direction.-The 3’ to 5’ exonuclease activities of DNA polymerases proofread new strands as they are

synthesized, removing any misspelled nucleotides at the 3’ termini of primer strands.