Bio Unit 2 REAL

Covalent bond

A bond in which atoms share electrons; it holds the atoms of a molecule together

HONC

The usual number of covalent bonds per atom: hydrogen 1, oxygen 2, nitrogen 3, carbon 4

Molecular formula

Shows the kinds and numbers of atoms in a molecule but not how they are arranged

Structural formula

A drawing that shows how the atoms in a molecule are connected

Isomers

Molecules with the same molecular formula but different arrangements of atoms, such as glucose and fructose

Emergent property

A property of a whole molecule or system that its individual parts do not have on their own

How do you use HONC to check a structure?

Count the bonds on each atom, with a double bond counting as two; every atom must match its HONC number or the structure is impossible

CO vs CO2

Example of how one atom change alters behavior: CO is a toxic gas, CO2 is the gas we exhale

H2O vs H2O2

Example of how one atom change alters behavior: water is harmless, hydrogen peroxide is reactive and damages cells

Why is a molecular formula not enough to predict a molecule's behavior?

It does not show how atoms are connected, and isomers with the same formula can have different shapes and properties

Electronegativity

How strongly an atom pulls on shared electrons; oxygen pulls more strongly than hydrogen

Polar molecule

A molecule with uneven electron sharing that creates partially positive and partially negative regions

Nonpolar molecule

A molecule whose charge is spread fairly evenly, such as a long hydrocarbon chain of carbon and hydrogen

Hydrophilic

Attracted to water and mixes with it

Hydrophobic

Not attracted to water and tends to separate from it

Like dissolves like

Polar substances tend to mix with polar ones, and nonpolar substances with nonpolar ones

Biomagnification

The increase in a contaminant's concentration at higher levels of a food chain

Hydrocarbon

A molecule made of only carbon and hydrogen; mostly nonpolar

Polar groups in biology

Groups containing oxygen or nitrogen, such as OH, COOH, and NH2, that add polarity to a molecule

Where do nonpolar substances tend to end up in the body?

In fatty tissue, because they dissolve in fat and not in water

Why do nonpolar pollutants build up in fatty tissue?

They are not easily removed by fluids that are mostly water and they dissolve well in fat

Why does biomagnification affect public health advice?

Top predators and fatty foods carry higher pollutant levels, so advice includes limiting those foods and trimming fat

Contaminant that binds protein

Stored in muscle and other tissue, so trimming fat does not remove it and it is not cleared like a substance stored in fat

Vitamins that dissolve in fat

Vitamins A, D, E, and K; nonpolar, so they are absorbed and transported with fat and can be stored in fatty tissue

Vitamins that dissolve in water

B vitamins and C; they dissolve in watery fluids and are not stored as long

Monomer

A small repeating building block

Polymer

A long chain made of many linked monomers

Macromolecule

A very large biological molecule; the four groups are carbohydrates, lipids, proteins, and nucleic acids

Dehydration synthesis

A reaction that joins two molecules and releases a water molecule

Hydrolysis

A reaction that uses a water molecule to break a bond between two molecules

Metabolism

All of the chemical reactions that take place in an organism

Anabolic reaction

A reaction that builds larger molecules from smaller ones; requires energy

Catabolic reaction

A reaction that breaks larger molecules into smaller ones; releases energy

Monomer of carbohydrates

Monosaccharide (single sugar)

Monomer of proteins

Amino acid

Monomer of nucleic acids

Nucleotide

Building blocks of lipids

Glycerol and fatty acids; lipids do not fit a simple monomer to polymer pattern

Why do lipids not fit the monomer to polymer pattern?

They are defined by being mostly nonpolar, not by a long chain of identical repeating units

How do you identify dehydration synthesis or hydrolysis from an equation?

Water among the products means dehydration synthesis; water among the reactants means hydrolysis

Rule for counting water molecules

One water is released or used per bond formed or broken; a chain of n monomers has n minus 1 bonds

How do you classify a reaction as anabolic or catabolic?

Ask whether it builds a larger molecule from smaller ones (anabolic) or breaks one down (catabolic), and state that reason

Where do the atoms of water come from in dehydration synthesis?

An OH is removed from one molecule and an H from the other, and together they form the released water

Where do the atoms of water go in hydrolysis?

Water splits, with the H added to one piece and the OH added to the other

Elements in carbohydrates

Carbon, hydrogen, and oxygen

Elements in proteins

Carbon, hydrogen, oxygen, and nitrogen (some also contain sulfur)

Elements in nucleic acids

Carbon, hydrogen, oxygen, nitrogen, and phosphorus

Element clue for proteins

Nitrogen, found with amino and carboxyl groups and a side chain

Element clue for nucleic acids

Phosphorus, found with a sugar and a nitrogenous base

Monosaccharide

A single sugar unit, such as glucose or fructose

Disaccharide

Two sugar units joined together, such as sucrose (glucose plus fructose)

Polysaccharide

A long chain of sugar units

Starch

A glucose storage polymer in plants

Glycogen

A glucose storage polymer in animals, kept mainly in the liver and muscles

Cellulose

A glucose polymer that gives plant cell walls structure

How are carbohydrates built and broken down?

Built by dehydration synthesis and broken down by hydrolysis

How does sucrose become molecules the body can absorb?

Hydrolysis breaks sucrose into glucose and fructose, single sugars small enough to be absorbed

How can starch, glycogen, and cellulose all be glucose polymers with different functions?

They differ in how the glucose units are linked and arranged, which changes the polymer's shape and function

Why can humans not digest cellulose?

Its linkages and arrangement differ from starch, so we cannot break it down; it passes through as fiber

Fatty acid

A long hydrocarbon chain with a carboxyl group at one end

Triglyceride

A fat made of glycerol joined to three fatty acids

Saturated fatty acid

A fatty acid with no double bonds between its carbons

Unsaturated fatty acid

A fatty acid with at least one double bond between carbons

Phospholipid

A lipid with a hydrophilic head and two hydrophobic tails; a main part of cell membranes

Why are fats and fatty acid tails nonpolar?

Their long chains are made mostly of carbon and hydrogen, which share electrons fairly evenly

How does a double bond affect a fatty acid tail?

It puts a bend in the tail, so unsaturated tails cannot pack as tightly as straight saturated tails

How do phospholipids behave in water?

Heads face the water and tails face each other away from water, forming the basis of cell membranes

Reaction that builds a triglyceride

Dehydration synthesis; one water is released for each bond formed

Roles of lipids

Energy storage, membranes, and signaling

Amino acid

The monomer of proteins; each has an amino group, a carboxyl group, and a side chain

Side chain (R group)

The part that differs among amino acids; it can be nonpolar, polar, or charged and affects how a protein folds

Peptide bond

The covalent bond between amino acids, formed by dehydration synthesis

Polypeptide

A chain of amino acids

Primary structure

The order (sequence) of amino acids in a polypeptide

Secondary structure

Local folding into alpha helices and beta sheets, held by hydrogen bonds along the backbone

Tertiary structure

The overall 3D shape of one polypeptide, produced by side chain interactions

Quaternary structure

The arrangement of two or more polypeptides working as one protein

Enzyme

A protein that speeds up a reaction

Active site

The region of an enzyme where the reaction occurs

Substrate

The molecule an enzyme acts on

Receptor

A protein that binds a specific molecule and triggers a response; shape and chemistry determine what binds

Where do nonpolar side chains usually sit in a folded protein in water?

In the interior, away from water

Where do polar and charged side chains usually sit in a folded protein in water?

On the surface, where they can interact with water

What can happen if a charged side chain ends up in a nonpolar interior?

It is unstable and can disrupt folding

Alpha helix and beta sheet

Examples of secondary structure

How can changing one amino acid change a protein's function?

It can change polarity or charge at that spot, alter folding and shape, and change how well the protein works

Why must a molecule's shape and chemistry match an active site or receptor?

Binding depends on 3D fit plus compatible polarity and charge

Denaturation

Loss of a protein's shape, such as from high heat or extreme pH, which reduces its function

Catalase

An enzyme that breaks down hydrogen peroxide into water and oxygen

Four examples of protein jobs

Structure (support), transport, signaling, and catalysis

Nucleic acid

A macromolecule built from nucleotides; DNA and RNA are the two main types

Nucleotide

The monomer of nucleic acids, made of a sugar, a phosphate group, and a nitrogenous base

Nitrogenous base

The part of a nucleotide that varies; base order forms the sequence

DNA

Nucleic acid with the sugar deoxyribose and the bases A, T, C, and G

RNA

Nucleic acid with the sugar ribose and the bases A, U, C, and G

Relationship between nucleotides, nucleic acids, DNA, and RNA

Nucleotides are the monomers, nucleic acids are the polymers, and DNA and RNA are the two main types

Main differences between DNA and RNA

Sugar (deoxyribose vs ribose) and one base (T in DNA, U in RNA)

How does a DNA sequence relate to a protein?

The DNA sequence carries the information that determines the protein's amino acid sequence

Which level of protein structure does a DNA change directly alter first?

Primary structure (the amino acid sequence)

Glycogen as fuel

Stored glucose in animals; a fast source of fuel kept mainly in the liver and muscles

Fat as fuel

A slower source of fuel that stores more energy per gram than glycogen