Chapter 2 - Cell Chemistry Flashcards
(162 cards)
0
Q
Electrostatic forces occurring between positively charged protons of one atom and negatively charged electrons of another atom that hold these atoms together within a molecule or between molecules.
A
Chemical Bonds
1
Q
Bond that holds atoms in the same molecule together
A
Intramolecular bonds
2
Q
Four types of intramolecular bonds
A
- Ionic bonds
- Covalent bonds
- Hydrogen bonds
- Hydrophobic interactions
3
Q
Bonds that form between two different molecules
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Intermolecular bonds
4
Q
Four types of intermolecular bonds
A
- Hydrogen bonds
- Hydrophobic interactions
- Electrostatic (ionic) forces
- Van der Waals forces
5
Q
Why do bonds form?
A
- To become more stable
6
Q
Atoms are stable when ……
A
- Electrons are in lowest possible energy levels
2. Outermost energy level is filled to the maximum
7
Q
Bond formed by the attraction of oppositely charged ions
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Ionic Bonds
8
Q
How are ions formed?
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When electrons are lost or gained
9
Q
What disrupts forces holding ions together?
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Electrical attraction of water molecules
10
Q
Strong bond between where electrons are shared between atoms to fill valence shell
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Covalent bond
11
Q
In some compounds, _________ are formed; these increase with number of bonds
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Single, double, and triple covalent bonds form
12
Q
What kinds of bonds are found in biological systems?
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Only single and double covalent bonds
13
Q
The force of attraction of a nucleus on the electrons moving around it or for the electrons in a chemical bond
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Electronegativity
14
Q
Two types of covalent bonds
A
- Non-polar
2. Polar
15
Q
Electrons are shared equally and there is no polarity; occurs between atoms of similar or identical electronegativity
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Non-polar
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Electrons are shared unequally between two atoms so there is a positive and negative pole (but the net charge is zero; not an ion); occurs between atoms with different electronegativities
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Polar
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Composed of all/mostly ionic bonds; generally water soluble to point of saturation
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Ionic
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Composed of all/mostly polar covalent bonds; generally water soluble
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Polar
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Composed of all/mostly non polar covalent bonds; not water soluble
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Nonpolar
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Composed of part hydrophilic and part hydrophobic regions; one part water soluble, other part not
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Amphipathic
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Q
Composed of solute and solvent
A
Solutions
22
Q
“Weak” bonds that forms due to electrostatic interactions between Hydrogen atoms (positive polarity) and more electron attracting (electronegative) atom (negative polarity)
A
Hydrogen Bond
23
Q
What can a hydrogen atom be bonded with to make a hydrogen bond?
A
Nitrogen and Oxygen
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What is the strongest type of Hydrogen bonds?
Multiple hydrogen bonds
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Hydrogen bonds play a major role in the biological properties of _____ and plays a major role in the _____ and other properties of water.
- Proteins
| - Solubility
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Weak bonds that occur when nonpolar molecules, or nonpolar regions of molecules, associate tightly in a polar solvent. Non polar molecules disrupt hydrogen bonding among water molecules so they are squeezed together or pushed by water molecules to minimize their volume (therefore disrupting minimum number of hydrogen bonds).
Hydrophobic interactions
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Hydrophobic interactionsn play important roles in three things
1. Enzymes binding substrates
2. Protein conformation
3. Stabilization of RNA and cell membranes
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Weak attractive forces that occur between atoms when they become closer than 2-4 A.
Van der Waals
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Van der Waals bonds form due to what?
Temporary polarities in atoms and molecules
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Van der Waals forces play important roles in what three things?
1. Enzymes binding substrates
2. Protein-nucleic acid interactions
3. Membrane fluidity
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Groups of atoms that when bonded to organic compounds impart unique chemical properties to those compounds
Functional groups
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This is a major component of al macromolecules
Carbon
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Three single bonded oxygens bonded to a phosphate. One double bonded oxygen to a phosphate. One carbon single bonded to a single bonded oxygen.
- Found in what?
Phosphate Ester
| - Nucleic acids
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A carbon single bounded to a sulfur and doubly bonded to an oxygen.
- Biological relevance?
Thioester
| - Energy metabolism; biosynethesis of fatty acids
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Two carbons that have a single bond to an oxygen
| - Biological relevance?
Ether
| - Certain types of lipids
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An oxygen doubly bonded to a carbon. And a hydroxyl group bonded singly to the carbon.
- Biological relevance?
-Carboxylic acid
| Organic, amino, fatty acids, lipids, proteins
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Double bonded oxygen to a carbon. Single bonded hydrogen to the carbon.
- Biological relevance?
Aldehyde
| - Functional group of reducing sugars such as glucose; aldehydes
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An OH group and two hydrogens bonded to a C.
| - Biological relevance?
Alcohol
| - Lipids, carbohydrates
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Two C bonded singly to an O. One O doubly bonded to a C. Two H bonded singly to the other C.
- Biological relevance?
- Ester
| Triglycerides
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Functional group that can act as an acid; make molecules more polar and more water soluble
Carboxyl group
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Makes molecule an alcohol; makes molecule more polar and more water soluble
Hydroxyl group
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Makes molecule an organic base; makes molecule more polar and water soluble
Amino group (NH2)
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Three types of molecules
1. Monomers
2. Macromolecules
3. Polymers
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Small molecules that are the building blocks of larger molecules
Monomers
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Large molecules
Macromolecules
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Largest molecules composed of covalently bonded similar or identical monomers
Polymers
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When a molecule has less than or equal to one carbon
Inorganic
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When a molecule has greater or equal to two carbons
Organic
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Three inorganic molecules
1. Water
2. Salts
3. Acids/bases/buffers
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Four organic molecules
1. Carbohydrates
2. Lipids
3. Polypeptide/proteins
4. Nucleic Acids
5. There are others as well
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_____ are the most abundant material besides water
Proteins
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______ is the major constituent of all microbial cells (90-92%)
Water
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Four major reasons why water is a good polar molecules that carries its properties
1. Can form hydrogen and other bonds
2. Good solvent for polar and ionic molecules
3. High specific heat
4. Exhibits cohesion and adhesion
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Ionic compounds consisting of a cation and an anion held together by an ionic bond
Salts
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____ often dissociate in water into their respective ions
Salts
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Proton donors; increase concentration of H+ ions in a solution
Acids
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Proton acceptors; decrease the concentration of H+ ions in a solution
Bases
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Compounds that resist changes in pH by sometimes behaving like an acid, and sometimes like a base; found in all cells
Buffers
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Fats, oils, sterols, other
Lipids
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Three facts about lipids
1. Nonpolar compounds
2. Hydrophobic
3. Play crucial roles in most membrane and as energy storage molecules
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Monosaccharides, polysaccharides
Carbohydrates
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What are carbohydrates and what role do they play?
- Polymers of sugar units bonded together by glycosidic bonds
- Play important roles in cell walls and as energy storage molecules
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Polymers of amino acids
Proteins
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Three facts about proteins
1. Most abundant macromolecules in cells
2. Found throughout cell
3. Have important structural and enzymatic roles
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Polymers of nucleotides
Nucleic acids
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What are nucleic acids composed of? Which is more abundant?
RNA and DNA
| - RNA
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Monosaccharides and disaccharides (sugars)
Monomers
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Monomers are organic compounds that contain ___, ____, and _____ at a ration of ______
- Polar molecules
- Hydrophilic
Carbon, hydrogen, and oxygen
| 1,2,1
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Most biologically important carbohydrates have ________
5 or 6 carbon atoms
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Structural backbones of nucleic acids
Pentoses (C5 sugars)
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Monomeric constituents of cell wall polymers and energy reserves
Hexoses (C6 sugars)
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Functions of carbohydrates
- Energy storage
| - Building blocks for polysaccharides and nucleotides
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- Sugar
| - Backbone of RNA
Ribose
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- Sugars
| - Backbone of DNA
Deoxyribose
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- Sugar
| - Energy source; cell walls
Glucose
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- Sugar
| - Energy source; fruit sugar
Fructose
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When other chemicals replace one or more of the hydroxyl groups on the sugar
Derivatives of simple carbohydrates
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Carbohydrates containing two monosaccharides
Disaccharides
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Carbohydrates containing three monosaccharides
Trisaccharides
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Carbohydrates containing several monosaccharides
Oligosaccharides
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Carbohydrates containing monomeric units (monosaccharides) connected by glycosidic bonds
Polysaccharides
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The covalent bonds linking adjacent sugars together
Glycosidic bonds
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Two possible geometric orientations of glycosidic bonds
1. Alpha
| 2. Beta
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Configuration of bond does what?
Imparts different functional properties to macromolecules composed of the same building blocks
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When two monomers are joined, what is removed?
Water
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Polysaccharide composed of glucose monomers joined to each other by alpha glycosidic bonds
Starch
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What is the function of starch?
Energy storage
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Polysaccharide composed of glucose monomers joined to each other by beta glycosidic bonds
Structural polysaccharide ( cellulose, chitin)
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When polysaccharides are combined with other classes of macrmolecules
Complex polysaccharides
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Polysaccharides + proteins
Glycoproteins
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Polysaccharides + lipids
Glycolipids
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Why are glycoproteins important?
- Include eukaryotic cell surface receptor molecules
| - Typically reside on external surfaces of the membrane
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Important in cell walls of gram-negative bacteria
Glycolipids
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Simple fats, oils, sterols, and phospholipids
Lipids
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Three characteristics about lipids
1. Non polar and hydrophobic
2. Composed of C, H, and O but NOT in a 1;2;1 ratio
3. Fatty acids are major constituents of biological lipids
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Simple fats
Triglycerides
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What is a triglyceride composed of?
- Three fatty acids
- Three carbon alcohol
- Glycerol
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What is the function of a triglyceride?
Energy storage
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In a triglyceride, what links the glycerol and fatty acids?
Ester bonds
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What do fatty acids consist of?
- Carboxyl group
| - Hydrocarbon chain
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No double bonds between carbons, straight linear molecule
Saturated fatty acid
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One or more double bonds between carbons in a triglyceride; bent or kinked molecule
Unsaturated fatty acid
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Simple lipids that contain additional elements such as phosphorous, nitrogen, sulfur, or small hydrophilic organic compounds
Complex lipids
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What are phospholipids composed of?
- Complex lipids containing 2 fatty acids
- Glycerol
- Phosphate group and something attached to the phosphate
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What do phospholipids do?
Play a major structural role in cytoplasmic membranes; amphipathic
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Two structural lipids found in cell membranes
1. Sterol
| 2. Hopanoid
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Found in all eukaryotes, and a very few prokaryotes
Sterols
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Found in many prokaryotes, but not in any eukaryotes
Hopanoids
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Polymer of nucleotides
Nucelic acids
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Polymer of deoxribonucleotides; genetic material in all cells and some viruses
DNA
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Polymer of ribonucleotides; plays role in protein synthesis in all cells; genetic material of most viruses
RNA
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What are nucleotides composed of?
1. C5 sugar (pentose), either RNA or DNA
2. Nitrogen Base
3. Phosphate
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Nitrogen bases are attached to C5 sugars by ______ and bonded to a phosphate
N-glycosidic linkage
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Major components of nucleic acids
Nucleotides
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Three jobs of nucleotides
1. Key forms of chemical energy
2. Carriers of sugars in biosynthesis of polysaccharides
3. Regulatory molecules for certain enzymes or metabolic events
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Two chemical classes of nitrogen bases of nucleic acids
1. Purine bases
| 2. Pyrimidine bases
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Contain two fused heterocyclic rings
Purine bases
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Contain a single six membered heterocyclic ring
Pyrimidine bases
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Parts of purine bases
Adenine and guanine
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Parts of pyrimidine bases
Thymine
Cytosine
Uracil
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Covalent bond that connects two adjacent nucleotides on the SAME strand
Phosphodiester Bond
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Sequence of nucleotides in a DNA or RNA molecule
Primary Structure
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Nucleic acids are what kind of molecules?
Amphipathic molecules
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- Double stranded in cells, complementary strands
| - Strands held together by hydrogen bonds
DNA
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- Typically single stranded
| - Demonstrates secondary structure (folding back upon itself)
RNA
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Four classes of RNA
- mRNA
- tRNA
- rRNA
- small RNA
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Two major types of proteins
1. Enzymes
| 2. Structural proteins
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Catalytic proteins; catalysts for chemical reactions
Enzymes
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Integral parts of cellular structures (such as eukaryotic chromosomes)
Structural proteins
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Monomers for proteins
Amino Acids
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What do most Amino Acids consist of?
- Carbon
- Hydrogen
- Oxygen
- Nitrogen
- 2 of 22 contain Sulfur
- 1 contains Selenium
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Amino Acids contain two important functional groups
1. Carboxylic acid group
| 2. Amino group
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Adjacent amino acid monomers are held together by covalent bonds called _____
Peptide bonds
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Amino acids differ why?
Because of different side chains (R)
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Impart chemical properties
Side chains of amino acids
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Amino acids with ______ are grouped into families
Similar chemical properties
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Four classifications of amino acids
1. Ionizable: acidic
2. Ionizable: basic
3. Nonionizable polar
4. Nonpolar (hydrophobic)
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Related, but nonidentical molecules
Isomers
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Enantiomers (mirror image isomer); have same chemical properties but often have different physical properties
Optical isomers
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Enzymes capable of interconverting specific enantiomers
Racemases
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What is the function of structural polysaccharides?
Structural strength of cell walls
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Structural term meaning a series of amino acids (10s, 100s, 1000s, and 10,000s amino acids long) joined to eachother by a peptide bond
Polypeptide
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What bond holds a polypeptide together?
Peptide bond
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Each polypeptide has an amino end and a ____ end
Carboxyl
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A given polypeptide could be a ____ or only a ____
- A whole protein
| - Subunit of a protein
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A functional unit consisting of one or more polypeptides having one or more functions
Protein
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Linear array of amino acids in a polypeptide
Primary structure
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Localized folds or twists in parts of polypeptide that form a more stable structure; held together by hydrogen bonding between amino group Hydrogen and carbonyl Oxygen
Secondary structure
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Another name for the secondary structure of polypeptides
Helix
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What are secondary structures held together by?
Hydrogen bonding betwen amino group Hydrogen and Carbonyl Oxygen
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Overall, three dimensional shape of a polypeptide
Tertiary structure
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What does tertiary structure form?
Exposed regions or grooves in the molecules that are important for binding to other molecules
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What are tertiary structures made of?
1. Hydrogen bonds
2. Electrostatic interactions
3. Hydrophobic interactions with water
4. Disulfide bonds
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Covalent bonds between -SH groups from two different amino acids
Disulfide bonds
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Overall arrangement of polypeptides in a protein; only found in proteins composed of two or more polypeptides
Quaternary structures
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Each polypeptide in the protein, held together by either/both covalent and noncovalent linkages
Subunit
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Unfolding of polypeptide chains
Denaturation
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Denaturation occurs because of
1. Extremes of Ph
2. High temperatures
3. Certain chemicals
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What does protein denaturation do?
1. Causes loss of biological functions
| 2. Can be reversible and irreversible
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Two different kinds of denaturation
1. Gentle
| 2. Harsh
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Denaturation that occurs at 100 degrees
Harsh denaturation
