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Flashcards in Biochemistry Deck (84)
1

Proton

● Subatomic particles inside an atom
● Relatively positive charge

2

Neutron

● Subatomic particles inside an atom
● Neutral in charge

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Electron

● Subatomic particles inside an atom
● Negative charge

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Ground state

When all the electrons in an atom are in the lowest available energy levels

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Excited state

When an atom absorbs energy, and its electrons move to a higher energy level

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Isotopes

● Atoms of one element that vary only in the number of neutrons in the nucleus
● Chemically, all isotopes of the same element are identical because they have the same number of electrons in the same configuration

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Half-life

Amount of time needed to convert 50% of the parent compound into daughter compound

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Radioisotopes

● Radioactive isotopes
● Used in medicine and dating

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Tracer

Can be incorporated into a molecule and used to trace the path of carbon dioxide in a metabolic pathway

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Ionic bonds

Result from the transfer of electrons

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Anion

A negative ion

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Cation

A positive ion

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Covalent bonds

Form when atoms share electrons

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Nonpolar

When electrons are shared equally between two atoms

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Diatomic molecules

Two identical atoms form a nonpolar covalent bond

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Polar

When electrons are shared unequally between two atoms

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Hydrophobic

● Water hating
● Nonpolar and lipid-soluble

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Hydrophilic

● Water loving
● Include substances that are polar or that carry a charge or that are ionic

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Hydrogen bonds

Bonds formed between two water molecules

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Specific heat

Amount of heat a substance must absorb to increase 1 gram of the substance by 1 degree

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Transpirational-pull cohesion tension

● As one molecule of water is lost from the leaf by transpiration, another molecule is drawn in at the roots
● One of the way to move water molecules up

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Capillary action

● Combined forces of cohesion and adhesion
● Water moves up a thin tube

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Surface tension

● Hydrogen bonds are slightly stronger on the surface of water
● Allows insects to walk on water without breaking the surface

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Spring overturn

● The cycling of the nutrients in the lake
● Oxygen from the surface is returned to the depths, and nutrients released by the activities of bottom-dwelling bacteria during winter are carried to the upper layers of the lake

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pH

● A measure of the acidity and alkalinity of a solution
● Ranges from 1 - 14
- 7 is neutral
● pH = - log [H+]

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Buffer

● Substances that resist changes in pH
● It works by either absorbing excess hydrogen ions or donating hydrogen ions when there are too few
● The most important buffer in human blood is the bicarbonate ion

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Isomers

Organic compounds that have the same molecular formula but different structures

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Structural isomers

Differ in the arrangement of their atoms

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Cis-trans isomers

Differ onl in spatial arrangement around double bonds, which are not flexible like single bonds are

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Enantiomers

● Molecules that are mirror images of each other
● L- (left-handed) D- (right-handed)

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Organic compounds

Compounds that contain carbon

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Carbohydrates

● The body uses them for fuel and as building materials
● Consist of three elements -- carbon, hydrogen, oxygen

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Lipids

● Hydrophobic organic compounds that include fats, oils, waxes, and steroids
● Most lipids consist of 1 glycerol and 3 fatty acids
Functions
● Energy storage -- 1 gram lipid = 9 calories
● Structural -- phospholipids, cholesterol
● Endocrine

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Proteins

● Complex, unbranhced macromolecules
Functions
● Growth and repair
● Signaling from one cell to another
● Regulation -- hormones such as insulin lower blood sugar
● Enzymatic acivity -- catalyzing chemical reactions
● Movement -- actin and myosin are protein fibers responsible for muscle contractions

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Nucleic Acids

● Encode all hereditary information
● Include ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)

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Dehydration synthesis

Release of one molecule of water to form polymers

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Hydroalysis

Breakdown of a compound by adding water

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Monosaccharides

● Monomer of carbohydrates
● Have a chemical formula of C6H12O6
● Three examples are glucose, galactose, and fructose

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Disaccharides

● Consist of two monosaccharides joined together
● Have the chemical formula C12H22O11

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Polysaccharides

● Polymer of carbohydrates
● Macromolecules
● Formed as many monosaccharides joined together
● Cellulose and starch are found in plants
● Chitin and glycogen are found in animals

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Glycerol

An alcohol that makes up the "head" of lipids

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Fatty acid

● Hydrocarbon chain with a carboxyl group at one end
● Exist in two varieties, saturated and unsaturated

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Saturated fatty acid

● Come from animals
● Solid at room temperature
● Linked to heart disease when ingested in large quantities
● Butter
● Contain only single bonds between carbon atoms

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Unsaturated fatty acid

● Extracted from plants
● Liquid at room temperature
● Considered to be healthy dietary fats
● Have at least one double bond formed by the removal of hydrogen atoms in the carbon skeleton
● They hold fewer hydrogen atoms than saturated fatty acids

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Steroids

● Lipid that do not have the same general structure as other lipids
● Consist of four fused rings
● Cholesterol, testosterone, estradiol

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Phospholipids

● Modified lipids
● Consist of only two fatty acids attached to the glycerol backbone, forming two hydrophobic "tails"
● The thrid hydroxyl group of the glycerol attaches to a phosphate group, which is charged and therefore hydrophilic
● Phospholipid bilayer is the structural basis of all plasma membranes

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Amino acids

● Monomer of proteins
● Consist of a carboxyl group, an amine group, and a variable (R) all attached to a central asymmetric carbon atom
- The R group differs with each amino acid

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Peptide bonds

Bonds that join amino acids together to form polymers of proteins

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Primary structure of proteins

The unique linear sequence of amino acids

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Secondary structure of proteins

● Results from hydrogen bonding with the polypeptide molecule
● Refers to how the polypeptide coils or folds into two distinct shapes -- an alpha helix or a beta pleated sheet
- Peptide bond and hydrogen bond

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Tertiary structure of proteins

● Intricate 3-D shape of a protein that is superimposed on its secondary structure
● Determines the protein's specificity

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Quaternary structure of proteins

Proteins that consist of more than one polypeptide chain

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Fibrous proteins

Proteins that exhibit either alpha helix or beta pleated sheet or both

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Denaturation

Lost of a protein's characteristic shape as well as its function

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Conformation

Unique shape of each protein that determines what job it performs and how it functions

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Chaperone protiens/Chaperonins

Molecules that assist in folding other proteins

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Prions

Misfolded proteins

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Nucleotides

● Monomer of nucleic acids
● Consists of a phosphate (P), a 5-carbon sugar (deoxyribose/ribose), and a nitrogen base

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Function groups

● The components of organic molecules that are most often involved in chemical reactions
● These groups are attached to the carbon skeleton, replacing one or more hydrogen atoms that would be presnet in hydrocarbon

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First law of thermodynamics

● States that energy cannot be created or destroyed, only transformed from one form to another
● Often known as the law of conservation of energy

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Second law of thermodynamics

States that during energy conversions, the universe becomes more disordered

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Gibb's free energy

Free energy, represented by the letter G

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Exergonic

If energy is released during the course of a reaction, the reaction is exergonic or exothermid and change is G is negative

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Endergonic

If in a chemical reaction energy is absorbed, the reaction is endergonia or endotehrmic and change in G is positive

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Metabolism

The sum of all the chemical reactions that take place in cells

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Catabolism

Reactions that break down molecules and release energy

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Anabolism

Reations that build up molecules and absorb energy

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Enzymes

● Serve as catalytic proteins that speed up reactions by lowering the energy of activation
● Made up of protein
● Substrate specific
● Can be reused after a reaction
● Catalyze reactions in both directions

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Energy of activation

The amount of energy needed to begin a reaction

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Transition state

The reactive (unstable) condition of the substrate after sufficient energy has been absorbed to initiate the reaction

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Induced-fit model

● Describes how enzymes work
● As the substrate enters the active site, it induces the enzyme to alter its shape slightly so the substrate fits better

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Cofactors

Inorganic molecules that help enzyme's functions

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Coenzymes

Organic molecules that help enzyme's functions

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Competitve inhibitors

● Compounds that resemble the substrate molecules and compete for the same active site on the enzyme
● They reduce the amount of product by preventing or limiting the substrate from binding to the enzyme
● Can be overcome by increasing the concentration of substarte

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Allosteric regulators/noncompetitve inhibitors

● Bind to a site distinct and separate from the active site of the enzyme
● This binding of the inhibitor to the alternate site causes the enzyme to change shape in a way that inhibits the enzme from catalyzing substrate into product

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Feedback inhibition

The end product of the pathway is the allosteric inhibitor for an enzyme that catalyzes an early step in the pathway

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Cooperativity

● A type of allosteric activation
● The binding of one substrate molecule to one active site of one subunit of hte enzyme causes a change in the entire molecule and locks all subunits in an active position
● This mechanism amplifies the response of an enzume to its substrates

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What happened to the energy when a bond is formed? Why?

● Energy is released
● Atoms acquire a more stable configuration by completing their outer shell

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What is required to break a bond?

Energy must be supplied

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What are the five intramolecular factors that contribute to the tertiary structure?

● Hydrogen bonding between R groups of amino acids
● Ionic bonding between R groups
● Hydrophobic interactions
● Van der Waals interactions
● Disulfide bonds between cysteine amino acids

81

What does protein structure depend on?

● The primary structure of a protein
● Physical and chemical consditions in the environment
- pH
- Salt concentration
- Temperature

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What are the three complementary techiniques that are used to reveal the 3D shape of proteins?

● X-ray crystallography
● Nuclear magnetic resonance (NMR) spectroscopy
● Bioinformatics

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What are the four nitrogen bases?

● Adenine (A)
● Cytosine (C)
● Guanine (G)
● Thymine (T) / Uracil (U)

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What are the four ways to regurate enzymes?

● Competitive inhibitors
● Allosteric inhibitors
● Feedback inhibition
● Cooperativity