Week 6

Enzymes ppt

All chemical bonds contain stored energy

During a chemical reaction stored energy is released due to the breaking of these bonds

The amount of energy released during a chemical reaction is related to the number of bonds Broken during the event

  • the left over components are used in some way

Activation Energy (EA):

  • in order to break a chemical bond, energy has to be added to the system

  • The amount of energy required depends on the type of bond being broken

  • The amount of energy released from a broken bond is more than what was needed to cause the bond to break.

  • Every chemical reaction has a specific EA

  • ATP → ADP → Pi

  • When EA is added to reactants, the energy contained by these molecules is elevated above that of their resting state

  • The higher state of energy is called the transition state

  • We break the outer Phosphoanhydride bond when we need energy

Metastable state:

  • at normal cellular temps the number of biologically important chemical reaction is optimally low

    • This is because reactants are very stable

Overcoming the activation energy barrier:

  • the EA requirement is a barrier that must be overcome for the desired reactions to proceed at reasonable rates

  • The only way a reaction involving metastable reactants would proceed at an appropriate rate would be to increase the energy, or lower the EA

  • A fever will increase the amount of energy in the reactants of biological reactions

  • A chemical catalyst lowers the activation energy requirement of reactants, and will increase the rate at which reactions occur

  • Catalysts can be inorganic (metals), or organic (proteins)

    • Organic is more common in biological systems

Catalysts: 3 basic properties

  • increase the rate of reaction by lowering the EA requirement

  • Act by forming Transient reversible complexes substrate molecules (not permanently changed or consumed)

  • Change the rate at which equilibrium is achieved, but have no effect on the position of equilibrium

Enzymes: biological catalysts

  • have a specific shape, due to being organic molecules

    • Inorganic catalysts are less specific in their shape

    • The shape is a compliment of a substrate

  • Organic and inorganic catalysts increase reaction rates by 10^7-10^17, and 10³-10^4, respectively

  • Most catalysts are proteins called enzymes

  • Some are RNA molecules called ribozymes

Active Site:

  • every enzyme has a set of amino acids that for an active site when the protein is folded into higher order structures

  • The active site is a groove or pocket with a specific shape (baseball and glove)

  • Substrate binds to the active site

  • The amino acids responsible for creating the active site aren’t necessarily adjacent to one another in the primary sequence

  • Of the 20 different Amino acids, only a few are involved in forming active sites:

    • Cysteine

    • Histidine

    • Serine

    • Aspartame

    • Glutamate

    • Lysine

Enzyme Cofactors:

  • specific non protein cofactors (prosthetic groups) tightly bound at an active site.

  • Derived form vitamins and the metallic ions are minerals

  • Required for some reactions

  • Cofactors can be metallic ions or small organic molecules (coenzymes)

  • Need of these lead to the RDA (recommended daily amount) of vitamins and minerals in our diets

Enzyme Specificity:

  • Due to the structure of the active site, enzymes are capable of discriminating between very similar molecules

  • Some are less specific, and can bond to a number of closely related substrates

  • Inorganic catalyst are nonspecific

  • Due to the specificity of most enzymes, a cell must possess thousands of different kinds of enzymes to carry out all its metabolic functions

6 classes of Enzymes: all end in “ase”

  • Oxidoreductase

    • oxidation-reduction reactions

    • Example: alcohol dehydrogenase

  • Transferases

    • transfer functional groups from one molecule to another

    • Example: Glycerokinase

  • Hydrolases

    • Hydrologic cleavage of one molecule into two molecules

    • Example: Carboxypeptidase A

  • Lyases

    • Removal of a romp from, or addition of a group to a molecule with rearrangement of electrons

    • Example: Pyruvate Decarboxylase

  • Isomerases

    • Movement of a functional group within a molecule

    • Example: Maleate isomerase

  • Ligases

    • Joining of Two molecules to form a single molecule

    • Example: Pyruvate carboxylase

Sensitivity to Temp:

  • Enzymes only work in a narrow range of temps

  • Optimal at 37*C for human enzymes

  • High fevers (40*C+) will denature protein enzymes causing them to become inactive

Sensitivity to pH

  • optimal is ~7.4 in human tissues

  • Changes in pH will affect the net charge of amino acids at the active site or on the substrate itself

  • Some enzymes are active in acidic environments (the stomach) while others are active in basic environments (the bowel)

Bio action of enzymes

  • 3 steps:

    • Substrate binding

    • Substrate activation

    • The catalytic event

Substrate binding:

  • substrate collides with the active site of an enzyme and becomes bound to it by weak hydrogen and/or ionic bonds

  • Weak at of the bonding makes this action readily reversible

  • Causes a slight distortion in the 3D shape of both the substrate and enzyme (called induced fit model)

  • Bonding makes the substrate more susceptible to catalytic attack

Substrate activation:

  • the process of subjecting the substrate to a chemical environment that’s conducive for catalysis

  • 3 methods of activation:

    • Bond distortion

      • Chemical bonds become distorted and therefore weakened after 3D enzyme-substrate binding

    • Proton transfer

      • Enzymes receive protons which increases their chemical reactivity

    • Electron transfer

      • Enzymes receive electrons which increases their chemical reactivity by forming temporary, but highly reactive bonds

Catalytic Event:

  • The actual chemical reaction that allows a desired chemical reaction to take place

Failure of an enzyme:

  • failure to carry out its intended reaction can lead to human disease

    • Phenylketonuria (PKU)

      • Caused by mutation in the PAH gene that codes for the liver enzyme: phenylalanine hydroxylase, which normally converts the amino acid phenylalanine into the amino acid Tyrosine

      • Babies born to mother who have PKU and uncontrolled phenylalanine diets, have a significant risk of intellectual disability

RNA enzymes:

  • ribozymes

  • Ribosomal RNA:

    • A large ribosomal unit is the site of the peptide transferase activity that catalyzes peptide bond formation

  • Tetrahymena RNA

  • Ribonuclease P.

Enzyme Regulation:

  • not usually beneficial often cell to allow an enzyme to function at an indiscriminately high rate

  • Have to be highly controlled to meet the needs of the cell

Enzyme inhibitors:

  • Alternative substrates, drugs, toxins all have an inhibitory effect on enzyme activity

  • Allosteric effectors bond to an enzyme casing a conformational change

  • The change in shape prevents the enzyme from attaching to its intended substrate

    • Called: Conformational change

  • Can either reduce reaction rates or block the reaction completely

  • They controlled the mechanisms in the cell

    • Controlling reactions can be beneficial for the cell, but They can also kill a cell

  • Noncompetitive inhibitors are allosteric

    • Bonds to a different active site than the specified site for a normal substrate

    • Blocks enzymatic activity by changing the shape of the enzyme, which inhibits binging of the normal substrate

  • Substrate analogues: similar in shape to a normal substrate, therefore binding to the same active site

    • Important for fighting disease

      • Inhibit specific enzymes synthesized by pathogenic bacteria and viruses

    • A competitive inhibitor

    • Cannot be converted to a functional product

    • Sulfa drugs resemble the folic acid precursor PABA

  • Competitive inhibitors directly bond to an active site specified for a normal substrate

  • Can be reversible or irreversible

    • Irreversible cause permanent loss of catalytic activity

      • includes heavy metals, nerve gas, pesticides and penicillin

        • Penicillin inhibits an enzyme needed in the synthesis of bacterial cell walls

    • Reversible is weakly bond and will let go when equilibrium is reached


The Cell and its Organelles ppt.

How life began:

  • formation of small organic molecules

  • Polymerization of small organic molecules into large organic molecules

  • Large molecules developed ability to self-replicate

  • Self-replicating molecules became encapsulated by a simple membrane (the first living cell)

Living organisms have 2 groups:

  • Prokaryotes: no membrane bound nucleus, instead has nucleoid (bacteria, archaea)

  • Eukaryotes: membrane-bound nucleus containing DNA (Plants, animals)

Parts of the Eukaryotic Cell:

  • plasma membrane: outer boundary

  • Nucleus: houses DNA

  • Cytoplasm: region between the plasma membrane and the nucleus

  • Cytosol: semifluid solution of the cytoplasm

  • Cytoskeleton: protein structure that help maintain the cell’s shape

Plasma Membrane:

  • surrounds cell

  • Defines the cells boundary

  • Comprised of:

    • phospholipid bilayer

      • Has an internal hydrophobic Region which creates a permeability barrier for water-soluble substances

    • membrane proteins

      • Act as enzymes

      • Anchor the cell

      • Transports proteins allow some substances to cross the membrane

      • Act as receptor to cause a reaction inside the cell

    • cholesterol

    • glycoproteins

  • Exocytosis:

    • Allows large substances to each a cell be creating a secretory vesicle from the cell’s phospholipid membrane

  • Endocytosis:

    • Allows substances to enter a cell by creating a vesicle around, then through invagination of, part of the cell’s plasma membrane

    • Phagocytosis is a version of this

  • Limitations on cell size

    • Surface to volume ratio

      • A greater surface area creates more places for Mel clues to enter or leave the cell

        • Microvilli in intestines is the cell membrane that allows for the cell to increase surface area

    • Rate of Diffusion:

      • Large molecules diffuse slower than small ones

    • Need to maintain adequate local concentrations of substances

      • Molecules need to collide with one another for a chemical reaction to occur, therefor reactants must remain close to one another for efficiency

    • A cell can increase the rate at which it absorbs nutrients in the gut by having a greater plasma membrane surface area

DNA:

  • consists as multiple linear molecules linked to a large amount of proteins (histones)

  • The DNA-histone complex is called chromatin

Compartmentalization of Activies:

  • Specific cellular activities take place in certain regions of the cell

  • An organelle is a membrane bound structure within an Eukaryotic cell

  • Membrane bound organelles are grouped into the internal membrane system

Organelles: each bound by its own membrane which may be single or paired

  • ER (endoplasmic reticulum)

  • Golgi Apparatus

  • Mitochondria

  • Nucleus

  • Lysosomes

  • Peroxisomes

  • Vacuoles

  • Vesicles

Nucleus:

  • Most prominent organelle

  • cell info center

  • Double-layered membrane (Nuclear envelope)

  • Small pores or openings allowing molecules to travel in and out

    • Each is lined with a pore complex that regulates the movement of macromolecules, such as:

      • Ribosome proteins

      • MRNA

      • Chromosome proteins

      • Enzymes

  • Contains chromosomes

  • Contains Nucleolus

    • Responsible for synthesizing ribosomes

Ribosomes:

  • synthesizes proteins

  • Formed by uniting 2 ribosomal subunits

Mitochondria:

  • powerhouse of the cell

  • Double-layered membrane

    • Inner layer encloses the mitochondrial matrix

      • DNA, RNA, Ribosomes

      • This tells us that Mitochondria use to be it’s own cell. Through Evolution, it became a part of the Eukaryotic cell (Endosymbiont Theory)

      • Mitochondria DNA only comes from your mother, because only the Ovum contains mitochondria; Sperm doesn’t

  • Can reproduce itself

  • Site of aerobic respiration (Oxidation of sugars to produce ATP)

  • Cristae (infolding) create more surface area

  • Cells with a higher energy demand has more mitochondria

Endoplasmic Reticulum (ER)

  • 2 kinds: rough and smooth

    • Rough is studded with ribosomes

    • Smooth isn’t

  • Continuous with the outer membrane of the nuclear envelope

  • Comprised of tubular membranes

  • ROUGH ER:

    • Appears rough under electron microscope

    • Synthesize proteins for use in membrane structure or secretion form the cell

    • Free ribosomes are not attached to the RER, and synthesize proteins for the cytosol or for import into organelles

  • SMOOTH ER

    • No ribosomes, doesn’t synthesize proteins

    • Synthesizes lipids and steroids

    • Can detoxify harmful chemicals

Golgi Apparatus:

  • similar to ER

  • Received proteins from the ER and modifies them for secretion from the cell via exocytosis

Lysosomes;

  • single membrane organelle

  • Stores hydrolases capable of digesting proteins, carbs, fat, etc

  • Enzymes kept sequestered in lysosomes so they not digest the cell in which they reside

Peroxisomes:

  • Also single membrane

  • Contain catalase which degrades H2O2 into H2O and O2.

  • Detoxifies methanol, ethanol, formaldehyde, etc

  • Involved in the oxidative breakdown of fatty acids

  • Prominent in the liver and kidneys

  • Found in animal cells, fungi, Protozoa

  • ALD (adrenoleukodystrophy)

    • Genetic peroxisomal disorder

    • Results in profound neurological debilitation and eventual death

    • Speeds up nerve cell stimulation due to myelin sheath degradation/damage

    • Your body can’t breakdown very long chain fatty acids, causing VLCFAs to build up in your brain, nervous system and adrenal glands

    • Effects more men than women because it is found on the X chromosome

Cytoskeleton:

  • 3D interconnected framework of proteins

  • Maintains unique shape of cells

  • Highly dynamic and constantly changing

  • Also responsible for cell movement, cytokinesis, organelle placement

  • Comprised of:

    • Microtubles

      • Hollow tube with a wall consisting of 13 protofilaments

      • Organization and maintenance of animal cell shape and polarity

      • Chromosome movement

      • Can be singlet, doublet, or triplet

      • 2 types:

        • Cytoplasmic: pervade the cytology and are responsible for a caring of functions, maintain cell shape

        • Axonemal: include organized and stable microtubules found in structures such as cilia and flagella

          • Flagella has a 9+2 arrangement (9 fused pairs surrounded 2 unfused MTs)

    • Microfilamtents

      • Two intertwined chains of F-actin

      • Muscle contraction

      • Cell locomotion

      • Cytokinesis

      • Smallest of the cytoskeletal filaments

      • Best known for their role in muscle contraction

      • Structural core of microvilli

        • At the base of microvilli the MF bundles into a network of filaments called the terminal web

      • Actin is a very abundant protein in all eukaryotic cells

        • Once synthesized, it folds into a globular-shaped molecule that can bind ATP or ADP (G-actin)

          • G-actin molecules polymerize to form microfilaments, F-actin

    • Intermediate filaments

      • Eight protofilaments joined end to end with staggered overlaps

      • Strengthening of nerve cell axons

      • Keeping muscle fibers in register

      • Most stable and least soluble of cytoskeletal components

      • Found in abundance in Keratin

    • There are drugs that perturb the cytoskeleton so that cancer cells (and often other cells) stop dividing

OUR MIDTERM WILL BE ON EVERYTHING WE HAVE COVERED IN THIS CLASS UP TO HERE!!!!