Honors Bio chapter 3

Organic Compounds

Carbon-based molecules

Hydrocarbons

compounds composed of only hydrogen and carbon

Carbon Skeleton

the chain of carbon atoms in an organic molecule

Isomers

Compounds with the same formula but different structural arrangements

Functional groups

affect molecule's function by being a part of chemical reactions and a determining factor for the outcome

Hydrophilic

water-loving

Hydroxyl group

hydrogen atom bonded to oxygen atom; compounds with it are called alcohols; OH

Carbonyl group

carbon atom linked by a double bond to an oxygen atom; if it's on the end, it is called a aldehyde. if it's in the middle, it is called a ketone

Carboxyl group

carbon double-bonded to an oxygen atom and also bonded to a hydroxyl group; compounds with it are called carboxylic acids; acts as an acid(gives H+)

Amino group

nitrogen atom bonded to two hydrogen atoms; compounds with it are called amines; acts as a base(takes H+)

Phosphate group

phosphorus atom bonded to 4 oxygen atoms; compounds with it are called organic phosphates

Methyl group

carbon atom bonded to three hydrogen atoms; compounds with it are called methylated compounds; not a functional group but still affects outcome because it affects shape of the molecule

Macromolecule

big molecule

Polymers

large molecule consisting of many identical or similar building blocks strung together

Monomers

the building blocks that make up polymers

Dehydration reaction/synthesis

releases H2O to connect monomers

Hydrolysis

adding H2O to break apart a polymer

Enzymes

biological catalysts that speed up chemical reactions in cells; generally is a protein macromolecule

Carbohydrate

class of molecules that provide short and long-term energy

Elements that make up Carbohydrates and the ratio of them

Carbon, Hydrogen, and Oxygen in a 1:2:1 ratio

Monosaccharides

monomers of carbohydrates

Disaccharides

Carbohydrate polymer made of only two monosaccharides

Polysaccharide

Carbohydrate polymer made of 3 or more monosaccharides

Starch

a storage polysaccharide that consists of only glucose monomers

Glycogen

a storage polysaccharide for animals that consists of only glucose monomers

Cellulose

major component in the tough plant cell walls

What is special about Cellulose's bonds

the glycosidic bonds are alternating from top and bottom

Chitin

used by insects and crustaceans to build their exoskeleton

Lipids

diverse compounds that are grouped together because they do not mix well with water

Hydrophobic

water-fearing

Fat/Triglycerides

made of 1 glycerol and 3 fatty acids; long-term energy storage

Unsaturated Fatty Acid

fatty acid that is not at the maximum number of hydrogen atoms because there are double bonds between the carbon; liquid at room temp; healthy

Monounsaturated Fatty Acid

An unsaturated fatty acid that contains only one double bond

Polyunsaturated Fatty Acid

An unsaturated fatty acid that contains multiple double bonds

Saturated Fatty Acid

fatty acid that is at the maximum number of hydrogen atoms because there are no double bonds in it at all; solid at room temp; unhealthy

Trans Fats

happens unsaturated fats go through hydrogenation(adding hydrogen) and become converted to saturated fats; major health risks

Phospholipids

consists of 2 fatty acid tails, a phosphate group, and a glycerol; a major component of cell membranes

Lipid Bilayer

two rows of phospholipids in the cell membrane faced opposite directions with phosphate heads pointing to the outside and inside of the cell

Steroids

a lipid with a carbon skeleton that has 4 fused rings

Cholesterol

important part of animal cell membranes and making steroid hormones

Protein

a macromolecule class that is involved in nearly every dynamic function in the human body and are very diverse

Amino Acids

monomers of protein; made of a amino group, carboxyl group, central carbon, hydrogen atom and R group

Amount of different Amino Acids

20 different Amino Acids; they differ because of the different R groups

Determines the Function of a Protein

Shape of the Protein

Peptide Bond

covalent linkage of two or more amino acids joining together by dehydration synthesis/reaction

Dipeptide

protein polymer made of only two amino acids

Polypeptide

protein polymer made of 3 or more amino acids forming a chain; synonymous with "Protein"

Denaturation

when a protein(polypeptide) unravels, losing it's function

Causes of Denaturation

changes in temperature, changes in pH

Primary Structure

linear sequence of amino acids in a long chain

Secondary Structure

a coiled polypeptide(alpha helix) that is stabilized by hydrogen bonds; can also be folded into a beta pleated sheet(also stabilized by hydrogen bonds)

Tertiary Structure

overall 3D shape of a polypeptide(which determines the function of a protein) resulting from interactions among R groups(such as hydrophobic & hydrophilic R groups, and ionic boning between R groups)

Quaternary Structure

multiple polypeptides coming together to make one protein

Energy

the capacity to cause change or to perform work

Kinetic Energy

energy of motion

Heat(thermal energy)

type of kinetic energy associated with the random movement of atoms or molecules

Potential energy

energy that matter possesses as a result of its location or structure

Why do molecules possess potential energy?

the arrangement of electrons in the bonds between their atoms

Chemical energy

a type of potential energy available for release in a chemical reaction

Thermodynamics

the study of energy transformations that occur in a collection of matter

First Law of Thermodynamics (Law of Conservation of Energy)

Energy can be transferred and transformed, but cannot be created or destroyed

Why can organisms not recycle their energy?

during every transfer or transformation, some energy becomes unusable--it becomes unavailable to do work

Entropy

a measure of disorder of randomness

Second Law of Thermodynamics

energy conversions increase the entropy of the universe

Cellular respiration

the chemical energy stored in organic molecules is converted to a form that the cell can use to perform work

Exergonic Reaction

chemical reaction that releases energy

Endergonic Reaction

chemical reaction that requires a input of energy

Metabolism

all of the chemical reactions in an organism

Metabolic pathway

a series of chemical reactions that either builds or breaks down a complex molecule

Energy Coupling

the use of energy released from exergonic reactions to drive essential endergonic reactions

ATP(Adenosine Triphosphate)

adenine, ribose, and a chain of three negatively charged phosphate groups

Hydrolysis of ATP

exergonic reaction that releases energy a phosphate group and forms ADP(adenosine diphosphate)

Phosphorylation

the transfer of the third phosphate group (from ATP) to some other molecule

Three main types of cellular work

Chemical, Mechanical, and Transport

Phosphorylation of ADP

uses energy from other exergonic reactions to add the third phosphate group back onto ADP to form ATP; creates ATP

Activation Energy

an energy barrier that must be overcome before a chemical reaction can begin; energy must be absorbed to weaken bonds so they can break and form new bonds in the chemical reaction

What macromolecule class are most enzymes apart of?

Most enzymes are Protein; some RNA molecules can act as enzymes

Substrate

the specific reactant that an enzyme acts on

Active site

the shape of the area where a enzyme and substrate meet

Enzyme Specificity

enzymes are specific because the active sites must be opposite/matching to fit specific substrates

Induced Fit

The substrate sinking into the enzyme's active site changing the shape of the active site slightly and contorting/weakening substrate bonds

Cofactors

nonprotein helpers for enzymes which bind to the active site and function in catalysis

Coenzyme

cofactors that are organic molecules

Competitive Inhibitor

reduces and enzyme's productivity by blocking substrate molecules from entering the active site

Noncompetitive inhibitor

binds to the enzyme in a place that is not the active site causing the active site to change shape and not fit the substrate

Allosteric site

the place a noncompetitive inhibitor binds to in an enzyme

Role of Inhibitors

important regulators of cellular metabolism

Feedback inhibition

prevents the enzymes from producing a surplus of a product by using the product as a inhibitor

Nucleic Acids

Polymers of the Nucleic Acid macromolecule class

Gene

the inherited sequence of DNA that programs amino acid sequences for polypeptides

DNA(deoxyribonucleic acid)

first type of Nucleic Acids(polymers) that provides instructions for its own replication and the building of proteins; Double helix shape, double strand

What does the "Deoxy" in DNA stand for

it means without oxygen because deoxyribose has one less oxygen atom than ribose

RNA(ribonucleic acid)

second type of Nucleic Acids(polymers) that takes the instructions from DNA and actually makes the protein; goes through transcription then translation to build a protein; single helix shape, single strand

Transcription

The mRNA forms itself as the opposite/matching bases of one of the DNA strands(after it leaves the nucleus and goes to the rRNA)

Translation

tRNA reads the mRNA and tries to find a matching triplet so it can drop of a amino acid it is carrying. those amino acids will bond together by peptide bonds and form a chain

Nucleotides

monomers of Nucleic acids; Consists of a 5-carbon sugar, a negatively charged phosphate group, and a nitrogenous base

Nucleotide arrangement in DNA

The Nucleotides are Antiparallel

Polynucleotide

a long chain that is made of nucleotides

Sugar-phosphate backbone

repeating pattern of sugar-phosphate-sugar-phosphate in a polynucleotide strand

Types of Nitrogenous bases

DNA: Adenine(A), Thymine(T), Cytosine(C), Guanine(G)