Unit 1-5 AP bio review

Hydroxyl identification

-OH

Amino identification

-NH2 or -NH3+

Methyl identification

CH3

Carbonyl identification

C=O, could be aldehyde or ketone depending on where the group is on the molecule (middle or end)

Ketone identification -C=O in the middle of a molecule

Aldehyde identification -C=O at the end of a molecule

Sulfhydryl identification -SH

Carboxyl identification

-COOH or -COO-

Phosphate identification

-PO4

Properties of Hydroxyls

Polar/hydrophilic; found in carbohydrates

Ketone description

Found within a carbon skeleton (the carbon double bonded to oxygen has carbons on either side), important in energy reactions

Aldehyde description

Found at the end of a carbon skeleton (the carbon double bonded to oxygen has a hydrogen on one side), very reactive

Properties of Amines

Basic, Polar/Hydrophilic, accepts H+ ions from the environment

Properties of Sulfhydryls

Polar/Hydrophilic; help stabilize proteins by allowing formation of disulfide bridges

Properties of Methyls

Nonpolar/Hydrophobic, can be added to DNA molecules to deactivate the gene

Properties of Phosphates

Polar/Hydrophilic; important in energy transfer

Properties of Carboxyls

Polar/Hydrophilic; acidic

When amino acids join together join together, the

N-C-C is the center of the molecule is known as its backbone and is a defining feature of amino acids

A highly electronegative atom on the end of an R-group willcause

the amino acid to be polar and a series of hydrocarbon on the end of an R-group will cause the amino acid to be polar

In Carbs, sugars occur

as a ring structure

monosaccharides, disaccharides, polysaccharides

single rings, double rings, and larger ring structures

In solutions, single rings can dynamically change from

straight chains to rings back to straight chains

glucose can be found as in

isomer

an isomer is a

compound the that has the same chemical formula but a different physical structure

Sugars can be joined together in long chains to form macromolecules called

starch, cellulose, and glycogen.

A plant's starch and an animal's starch are easily

broken down into sugars for energy.

Cellulose is made primarily in plants

can be broken down by a few organisms in the world

lipids are

hydrophobic

lipids may have a few polar bonds associated with oxygen, depending on the specific molecule, but on the whole

lipids consist mostly of hydrocarbons

fatty acids can exist alone as a single chain of

hydrocarbons, or can join a glycerol molecule to form larger molecules with multiple chains

fatty acids that contain no double bonds are considered

saturated

fatty acids that contain at least one double bond are considered

unsaturated

saturated fats are

solid at room temperature because the chains pack together more densely than do unsaturated fats, which are liquid at room temperature and less dense.

saturated fats tend

to be found in land animals; unsaturated fats tend to be found in plants and fish

purine

a nitrogenous base that has a double-ring structure; one of the two general categories of nitrogenous bases found in DNA and RNA; either adenine or guanine

pyrimidines

thymine and cytosine

macromolecule (polymer) Polysaccharide complex carbohydrate monomer

monosaccharides

what type of bond when joining 2 monomers together through dehydration synthesis of monosaccarides

glycosidic linkage

fat (lipid) monomer

glycerol, fatty acids

type of bond formed when joining 2 monomers through dehydration synthesis of lipids

ester bond

polypeptide (protein) monomer

amino acids

type of bond formed when joining 2 monomers through dehydration synthesis of polypeptides

peptide bond

nucleic acid monomers

nucleoacides (phosphate + nitrogenous bases + sugars)

type of bond formed when joining 2 monomers through dehydration synthesis

phosphodiester bond

dehydration synthesis (condensation) reaction

-monomers join to build macromolecules (polymers) using dehydration synthesis reactions.
-H from one monomer and OH from the other monomer are REMOVED. The H and OH combine to form WATER.

every sugar/carbs have

lots of oxygen Most likely a 1:1 ratio.

Hydrolysis

-Macromolecules are BROKEN DOWN into smaller molecules
-WATER is ADDED which causes the bond joining monomers to break
-It is the reverse of dehydration synthesis

Covalent bonds

is the term used to describe the bond type in which atoms share electrons

covalent bond example

oxygen is sharing electrons with hydrogens. Oxygen is more electronegative compared to hydrogen, resulting in an unequal sharing of electrons between oxygen and hydrogen

covalent bonds result in

polarity, when there are differences in atomic electronegativities, ex. a water molecule has polarity

Hydrogen bonds

is a weak bond interaction between the negative and positive regions of two separate molecules

hydrogen bond example

water can form hydrogen bonds w/ other water molecules or with other charged molecules.

When two of the SAME molecules form hydrogen bonds with each other this is

cohesion

when two different molecules form hydrogen bonds with each other is called

adhesion. ex. amino acid and water

the hydrogen bonds between water molecules bond can result in

surface tension

cohesion, adhesion, and surface tension allow water to demonstrate additional chemical behaviors known as

emergent properties

surface tension

is a result of increased hydrogen bonding forces between water molecules at the surface. ex. water droplet on a penny.

capillary action

result of both adhesive and cohesive properties of water. ex plants can access water from soil through this capillary action ability through the roots.

monomers are

chemical subunits used to create polymers

polymers is a

macromolecule made of may monomers

example a dehydration synthesis creates carbohydrates

carbohydrate monomers have hydroxides (OH) and hydrogen atoms (H) attached. One monomer will lose an entire hydroxide while the other monomer will only lose the hydrogen form of a hydroxide. A covalent bond will form where the hydroxide and hydrogen atom will be removed. The hydroxide (OH) and hydrogen (H) join forming a water molecule

hydrolysis crates cleave covalent bonds

is the opposite of dehydration synthesis. polymer are hydrolysis (broken down) into monomers during hydrolysis reaction. Covalent bonds between monomers are cleaved (broken) during hydrolysis reaction. A water molecule is hydrolyzed into subcomponents is added to a different monomer.

another example of dehydration synthesis is that they create proteins

-protein monomers are called amino acids. each amino acids has an amino group (NH2) terminus and a carboxyl group (COOH)
-a hydroxide (OH) is lost from the carboxyl group of one amino acid and a hydrogen atom (H) is lost from the amino group of another amino acid.
-a covalent bond will form between the monomers in the location where the hydroxide and hydrogen atom were removed.
-the hydroxide (OH) and hydrogen atom (H) will join forming a water molecule (H2O)

proteins undergo hydrolysis reactions

-covalent bonds between amino acids can be broken
-a water molecule is broken and each sub component of water (H&OH) will be bonded to different amino acids.
-result is separate amino acid monomers.

covalent bonds are used to

connect monomers together

dehydration synthesis reaction

to create biological macromolecules and water is an additional product

hydrolysis reaction

use water to break down biological macromolecules

what is the R group in an amino acid? How does it affect the functional properties of the amino acid

amino acid differ in R group, the atoms attached to the central carbon. The R group can be hydrophobic, hydrophilic, or ionic.

describe how the unique chemical and physical properties of water influence the life on earth

The properties of a compound depend on the chemical bonds that hold its atoms together. Most ionic compound will be a solid at room temperature, have extremely high melting and boiling points, The rigid crystal network also makes them hard, brittle, and poor conductors of electricity; No moving electrical charges means no current will flow. They often dissolve easily in water, separating into positive ions and negative ions. The separated ions can move freely, so solutions of ionic compounds are good conductors of electricity. Covalent compounds have almost the exact opposite properties of ionic compounds. Since the atoms are organized as individual molecules, melting or boiling a covalent compound does not require breaking chemical bonds. Therefore, covalent compounds often melt and boil at lower temperatures than ionic compounds. Unlike ionic compounds, molecules stay together when dissolved in water, which means covalent compounds are poor conductors of electricity. Covalent bonds do not always form small individual molecules; Bonds can make the same element look different.

list the key differences between DNA and RNA and and between the purines and pyrimidines

DNA uses deoxyribose and RNA uses Ribose as their Nitrogenous bases. DNA consists of ACGT, while RNA is used on ACGU. DNA is used in the first step; it can be used for DNA replication and transcription. And RNA is used in translation which is translated onto aminoacids, and proteins later. DNA makes two strands, while RNA makes one strand
PURINES: are LARGER because they have a TWO ring structure are adenine and guanine
PYRIMIDINES: only have ONE ring and are Cytosine & Thymone

primary structure of proteins

determined by the sequence of amino acids held together by covalent bonds, peptide bonds
-established by covalent bonds
amino acid monomers are joined forming polypeptide chains

secondary structure of protein

arises through the local folding of the amino acid chain into elements such as alpha-helices and beta-sheets
-

tertiary structure of protein

is the overall 3D shape of the protein and often minimizes free energy. Various types of bonds and interactions stabilize the protein at this level
-

quanternary structure of protein

arises from the interactions between multiple polypeptide units

what factors in the environment surrounding a protein can cause it to denature?

-increase in temperature can cause rapid molecular movements and this can break hydrogen bonds and hydrophobic interactions
-alterations in the concentration of H+ (pH) in the solution of the exposed carboxyl and amino groups. this can disrupt the patterns of ionic attractions and repulsions
-high concentration of polar substances such as urea can disrupt the hydrogen bonding that is critical to protein structure
-nonpolar substances may also denature a protein in cases when hydrophobic groups are essential for maintaining the protein's structure

anabolic reactions

link simple molecules to form more complex molecules. require a small input of energy because strong bonds within the smaller molecules must be broken down to form the more complex molecules.
EX: sucrose requires the breaking of strong O-H bonds in glucose and fructose.

catabolic reactions

break down complex molecules into simplistic ones and release the energy that was used to make the complex molecules.
EX: when sucrose is hydrolyzed, energy is released by the formation of more stable (lower energy) bonds within the monosaccharides.

covalent bonds are very

strong and takes a lot of energy to break them.

ionic bond

A chemical bond resulting from the attraction between oppositely charged ions.

unique chemical and physical properties of water influence on earth

Water is often nicknamed the "universal solvent" as it can dissolve other substance. Those which dissolve well are hydrophilic (eg. salts, sugars, acids), where as those which do not are called hydrophobic (eg. fats, oils). Water has a high specific heat (the amount of energy needed to raise the temperature of 1 gram 1 degree Celsius) and a high heat of vaporization (the energy needed to turn a liquid into a gas) due to the many hydrogen bonds and then breaking the hydrogen bonds. The high specific eat allows water to keep the Earth's climate moderate, protecting us from any huge changes in temperature. The high heat of vaporization is important in humans when they sweat. The change from a liquid to a gas is what creates the cooling sensation. A high surface tension exists with water. Due to cohesion, water molecules have hydrogen bonds which attract to one another. This is important in transpiration, as the water molecules stick to each other as they move up a tree.

hydroxyl group properties and general features

polar, hydrophilic, characterized by presence of H&O simple structure

sulfhydrol group properties

polar, characterized by presence of S, simple branched structure

methyl group properties

nonpolar, characterized by presence of H and C, simple structure

carbonyl group properties

polar, bound to 2 organic side groups, double bond to oxygen increases of polarity

carboxyl group properties

charged, ionized to released carboxyl groups can release H+ ions into a solution, they are considered acidic, characterized by central C bound to O and OH

amino group properites

charged, accepts H+ or form NH3+ since amino groups can remove H+ from solution, they are considered basic, branched structure

phosphate group properties

charged ionizes to release H+. Since phosphate groups can release H+ into solution, they are considered acidic, characterized by presence of P and has a complex structure

carbs

store energy, provide fuel, and build structure in body, main source of energy, structure of plant cell wall.

nucleic acids

stores and transfers energy

lipids

insulators and stores fat and energy

protein

provide structural support, transport, enzymes, movement, defense

to determine polarity

if the R group at the end has an oxygen, sulfer, or nitrogen

what type of bond joins carbohydrates together to form a polymer, like the polysaccharide cellulose

glycosidic linkage

what type of bond joins amino acids together to form a polypeptide chain

peptide bonds

how many fatty acid chains are attached to a molecule of glycerol to make a triglyceride

3

fatty acid tails of a phospholipid is

nonpolar

what part of the phospholipid is hydrophobic

the fatty acid tails

if a fatty acid chain has a c=c

it is unsaturated because of the c=c double bonds

would a saturated or a nonsaturated fatty acid chain be liquid at room temperature?

unsaturated because of the double bonds chain to be bent

in what level of protein structure can you expect to find hydrogen bonding between R groups

3rd