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129 Cards in this Set
- Front
- Back
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Enantiomer/ Optical Isomer
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Mirror Images
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anabolism
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synthesis
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catabolism
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breakdown
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All cells are bordered by...
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phospholipid membrane
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two border membranes, no nucleus, limited internal membranes
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prokaryotic cells
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single outer membrane but extensive internal membrane- bordered organelles, with a nucleus
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eukaryotic cells
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What is the Value of a membrane bounded compartment in a cell?
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-Can concentrate interacting molecules making reactions more efficient
-Can separate molecules and reactions from those that are interfering or nonproductive |
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ATP stands for..
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Adenosine Triphosphate... and universally used as energy currency
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ATP consists of..
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Three phosphate groups, adenine and ribose
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What is the Central Dogma of information flow in all cells?
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DNA> RNA> Protein
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96% of elements in biology are..
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C, O, H, N........ rest mainly P, S, Cl, Ca, K.... 25 total
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1 proton + 2 neutrons, a beta emitter, 3H
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Tritium
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6 protons + 8 neutrons, a beta emitter, decays to 14N
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Carbon-14
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Radioisotopes used in research:
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Tritium, Carbon-14, Phosphorus- 32, Sulfur- 35
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Chemical properties of an element are determined by:
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the number and distribution of electrons in the outer shell
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Shared Valence electrons
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Covalent bond
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- .6-1 kcal/mole strength
- complementary electrostatic interaction -located in non-polar areas |
Van der Waals forces
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- 1.5-3 kcal/mole strength
- H attraction to electronegative atom -located mainly hydrophilic areas |
H bonds
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- 3-7 kcal/mole strength
-electrostatic interaction -mainly hydrophilic areas |
Ionic Bonds
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- 60-100 kcal/mole strength
- share valence electrons - located everywhere |
Covalent bonds (peptide bond)
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Shape and stability of molecule and its interaction with other molecules is determined by..
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the number and kind of molecular bonds formed
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Water is a ____ molecule.
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polar
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nonpolar molecules with non-polar C-H bonds are...
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hydrophobic (cannot form many H-bonds) eg. oil and grease
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Water dissociates at a low rate to..
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hydrogen H+ and hydroxide OH- ions
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pH=
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-log[H+]
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To find how much more acidic or basic a solution is...
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do 10^(negative of that pH)... increases tenfold
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Something that reversibly releases and accepts H+ ions
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Buffer
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What's special about Carbon?
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Has valence of four so can form 4 stable covalent bonds forming tetrahedron shaped molecule
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double bonds result in_____ shape
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planar
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Three types of isomers may be formed:
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structural, geometric, enantiomer
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cis isomer
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"X's" are on same side
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trans isomer
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"X's" are opposite sides
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If carbon hadn't been used here on Earth what would have taken it's place?
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Silicon
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For small molecules groups determine...
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the chemistry possible for that molecule
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Groups determine the chemistry possible and play a large role in the shape and stability, hyrdophilic or hydrophobic character and therefore function of a what kind of molecule
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macromolecule
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Which is not a funcional group?
a. COOH b. NH2 c. SH d. PO4 e. OH- |
e. OH-
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Why does adding phosphate to protein often change the activity of protein?
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-changes proteins charge and changes it's conformation or shape
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Hydroxyl (____)known as_______ are nonpolar or polar? Form what kind of bonds?
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(-OH) alcohols are polar and form h-bonds with water molecules
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Carbonyl (_____) known as ______ and ______ are found in ____and may be ______ isomers with different properties.
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(C=O) aldehydes and ketones are found in sugars and may be structural isomers w/ different properties
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What is the difference between an aldehyde and a ketone?
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Aldehydes have carbonyl at end
Ketone has it within |
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Carboxyl(______) known as_____or._______ are found in cells in the ________ form. Has ____ properties because the covalent bond between oxygen and hydrogen is so polar.
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(-COOH) known as carboxylic or organic acids and are found in cells in the ionized form with charge of 1-. Has acidic properties.
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Amino(____) known as ______ and _______ acts as a _____. Ionized with a charge of __ under cellular conditions.
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(-NH2) known as amines, possibly amino acids acts as a base. Ionized with a charge of +1.
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Sulfhydryl(______) known as _____ can react and form _____ bond with other sulhydryl group.
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(-SH) known as Thiols can react and form covalent bond with other sulfhydryl group.
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What is cross linking?
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The bonding of two sulfhydryl groups such as linking cysteines in hair proteins to maintain straightness or curliness.
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Phosphate(____) known as ___________ has the potential to react with ____, releasing energy. It also contributes negative charge to molecule which it is a part of.
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(PO4) known as organic phosphates or potentially ATP has the potential to react with water.
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Methyl(_____) known as ______. The arrangement in male and female__________ affects their shape and function. Addition of methyl group to DNA can affect expression of genes.
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(-CH3) known as methylated compounds... cytidine, testosterone.. arrangement in male and female sex hormones
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An unbranched polymer of amino acid
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Protein
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Bonding together of monomers
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polymerization
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____ adds a water molecule and
____ removes a water molecule |
Hydrolysis
Dehydration |
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A short chain of amino acids
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peptide
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a single long chain of amino acids
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polypeptide
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_____ is composed of one or more polypeptides held together as a functioning unit
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protein
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solubility, shape and function of protein is determined by
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20 different R groups
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first amino acid
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methionine
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chemical reason why these 2 amino acids differ in solubility:
Tyrosine= .196g/ 100ml Serine= 5g/ 100 ml |
serine lacks the 6 c ring
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monomer in, water out
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condensation reaction
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peptide bond formed between
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carboxyl and amino group
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the sequence of amino acids
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primary structure
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3D folding into a helix or sheet caused by H bonds between adjacent sheets
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secondary structure-
alpha helix beta pleated sheet |
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hydrogen bonds form between
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peptide chains
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folding caused by R group interactions
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tertiary structure- also gives rise to surface binding sites
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folding formed by interactions between polypeptides
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Quaternary structure
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some proteins have non-protein groups such as metal ions, sugars, lipids or heme groups which are called
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prosthetic groups
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How do we determine protein shape?
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x-ray crystallography
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These act as scaffold to aid correct folding
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chaperon proteins
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Proteins can denature(unfold) artificially because of:
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-heating
-exposure to non-polar solvents(ether, chloroform) -acids or bases |
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Function: Selective acceleration of chemical reactions
Example: Enzymes what kind of protein? |
enzymatic protein
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Function: Support
Example: silk fibers, collagen and elastin in animal connective tissue, keratin in hair, horns, feathers, etc. what kind of protein? |
structural protein
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Function: storage of amino acids
Example:Ovalbumin in egg white, casein. the protein of milk |
storage protein
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Function: transport of other substances
Example: Hemoglobin |
Transport protein
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Function:Coordination of an organism's activities
Example:Insulin.. secreted by pancreas what kind of protein? |
hormonal protein
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Function: response of cell to chemical stimuli
what kind of protein? |
receptor protein
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Function:Movement
Example: Actin and myosin in muscles, proteins in cilia and flagella |
contractile and motor protein
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Function: protection against disease
Example: Antibodies combat bacteria and viruses |
defensive protein
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These catalyze biochemical reactions
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enzymes
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Transcription factors that help RNA polymerase II, ribosome proteins help make protein
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Gene-expression protein
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define Energy
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the capacity to do work
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First Law of Thermodynamics:
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The energy in the universe is constant, but can be transformed or transferred
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Second Law of Thermodynamics:
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All changes occur to increase randomness or disorder (entropy or S) of the universe
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G=
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free energy
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Delta G < 0 ....
Delta G > 0.... |
spontaneous
requires energy input |
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Delta G =
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Delta H - TdeltaS
delta H is enthalpy change: change in chemical bond energy delta S is entropy change T is absolute Temp. in Kelvins |
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Negative Enthalpy Change means products are..
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more stable (more disordered)
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Positive Entropy change means products are
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more stable (more disordered)
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reaction rate of exergonic reaction is determined by..
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activation energy
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Delta G is _______ in std. condition
and ______ in cell. |
-7.3 kcal/mole
-13 kcal/mole |
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What to enzymes do?
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lower the activation energy and are biological catalysts
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the part whose shape allows it to bind to the substrate and creates the correct orientation to stress its bonds to make rearrangement for favorable
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active site
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Non-protein elements or compounds complexed with the polypeptide and essential for enzyme function
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co- factor ( these may be metals) eg. Mg+2 for DNA polymerase
if more complex.. called coenzymes |
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look like substrate, fit into active site and block substrate but go out again resulting in slow substrate reaction
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competitive inhibitor
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Don't look like substrate, bind elsewhere than active site but change enzyme conformation so active site is less apt to bind the substrate
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non-competitive inhibitor
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molecule differs in shape from substrate, is a natural regulator of enzymes shape and function can block or turn on enzyme action
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allosteric regulation
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an early enzyme is turned off using allosteric regulation by an end product
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feedback inhibition
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What do Nucleic Acid monomers play a role in?
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-Energy Currency (e.g ATP and GTP)
-Regulation of processes (e.g donate phosphate groups in phosphorylation) -Making up polynucleotides (the polymers of DNA & RNA which store, express and transmit genetic hereditary information) |
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Example of Purine
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Adenine and Guanine
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Example of Pyrimidine
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Cytosine, Thymine (DNA only), Uracil (RNA only)
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A base plus a deoxyribose (DNA) or oxyribose (RNA) sugar.
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Nucleoside (e.g deoxyadenosine or adenosine)
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A base plus sugar plus 1 to 3 phosphates
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Nucleotide (e.g adenosine triphospate)
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This functions in storing genetic info as a double stranded polynucleotide
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DNA
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Two H bonds with a ______ pair
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A-T
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Three H bonds with a ______ pair
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G-C
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Strongest DNA molecules are those with the most _______
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G-C's
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Three RNA forms are involved in genetic information transfer from DNA to protein. All have a DNA template for their sequence and are single stranded. Name the three.
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Messenger, Transfer, Ribosomal
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This type of RNA encodes information for amino acid sequence of proteins
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Messenger
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This type of RNA acts as an adapter molecule between mRNA and amino acids
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Transfer
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This type of RNA has 3 types making up part of the ribosome in which translation (protein synthesis) occurs.
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Ribosomal
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What is transcription?
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Making RNA from DNA template
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What is translation?
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Making polypeptide from mRNA template
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In _______ one strand is the template for another.
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DNA
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In ______ one strand of DNA is the template.
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RNA
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In _____ mRNA is the template
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Protein
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The group of compounds including simple sugars(monosaccharides), disaccharides and macromolecule polysaccharides (monosaccharide polymers)
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Carbohydrates
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What do carbohydrates play a major role in?
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-Energy use and storage (glucose, starch in respiration)
-Structure, especially in cell walls of bacteria, plants, fungi -Part of nucleic acid backbone -Often added to make glycoproteins or glycolipids on animal cell surfaces for cell-specific type recognition |
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Monosaccharides are polyhydroxylic aldehydes and ketones most commonly with... ___, ___ or ___ C's
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3(triose)
5(pentose) 6(hexose) |
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Animals use only ______ bonds
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alpha
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C1 to C4 alpha linkage straight chain broken down by alpha amylases type of polysaccharide
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Starch
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C1 to C4 beta linkage straight chain borken down by microbial enzymes type of polysaccaride
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Cellulose
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a mixture of C1 to C6, C1 to C4, and C1 to C3 making a branched chain form for energy storage in animals in liver and muscles. has alpha linkage
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Glycogen
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Insect exoskeleton
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Chitin
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In bacterial cell wall part peptide, part polysaccharide- target for antiobiotics (penicillin type)
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Peptidoglycan
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In structure these are a mixed bag of non-polymeric hydrophobic molecules of diverse structures
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Lipids
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What are the major functions of lipids?
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-Makes a large part of the cells membrane (e.g phospholipids and cholesterol)
-Store large amounts of energy (e.g fatty acid) -Steroids are used as hormones |
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What are fats (triglycerides) made up of?
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glycerol and three fatty acids which can vary in C number and presence of double bonds
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What links the glycerol to the fatty acid?
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ester bond
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Saturated fats (w/o C=C) have _____ temperature
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higher
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unsaturated fats (w/ C=C) have ____ temperature
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lower
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A trans fat has _______ and would have a ______ melting temperature than a cis fat of the same C length.
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fatty acids in trans isomer; Lower? ... has some C=C bonds
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In a phospholipid: Glycerol bonds to _________ plus a modified phosphate group
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two fatty acids
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Ampithetic molecules is....
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molecule with both hydrophobic and hydrophilic parts (e.g phospholipid
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