AP Bio Ch. 3 Overview Test

ARROYO MR TRAN AP BIO

What is the carbon foundation?

Valence Electrons, Geometry, Double bonds

Valence electrons (Carbon foundation)

4 valence electrons = 4 connection points

Geometry (Carbon Foundation)

Tetrahedral geometry (109.5 degrees), creates 3D depth

Double Bonds (Carbon Foundation)

Flattens the architecture into one single plane.

What makes Carbon skeleton diverse?

Length, Branching, Double Bond positioning, Stable Ring formation

Length (carbon diversity)

extending the chassis (ethane and prothane)

Branching (carbon diversity)

Adding structural offshoots (butane and isobutane)

Double Bond positioning (carbon diversity)

Locking joints to prevent rotation (1-butene and 2-butene)

Stable ring formation (carbon diversity)

Rings closing the loop into stable geometric rings (cyclohexane)

Describe Isomers

Isomers have the same components as carbon, but different arrangements.

Types of Isomers

Structural Isomers, Cis-trans isomers, enantiomers

What is structural Isomers?

Compounds that have the same molecular formula (same numbers of each atom) but different covalent arrangements of the atoms, allowing for different properties.

What is cis-trans isomers?

Isomers that have two carbons joined by a double bond, and each carbon is bonded to two different atoms/groups

What is cis-isomers?

Identical groups that are on the same side of the double bond

What is a trans-isomer?

Identical groups are on opposite sides of the double bond.

What are enantiomers?

One of two compounds that are mirror images of each other and differ in shape due to the presence of an assymetric carbon.

What is an example of enantiomers?

Right hand won’t fit left hand glove

Organisms are sensitive to small architectural changes

Ibuprofen (right hand) works perfectly, but left handed is biologically inactive

Describe Functional Groups

A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and involved in chemical reactions.

What are diverse functions? (functional groups)

Solubilizers, Stabilizers, Energizers, Non-reactive tag.

Solubilizers (diverse function)

Hydrophilic, dissolves in water

Stabilizers (diverse function)

Forms cross-links

Energizers (diverse function)

Highly reactive, negatively charged

Non-reactive tag (diverse function)

Non-reactive -CH3 (methyl group) marker/ends

Example of Functional Groups

A single molecule swap changes a female hormone into a male hormone, completely altering vertebrae physical development.

Describe Adenosine Triphosphate (ATP)

High energy nucleotide consisting of an adenine base, ribose sugar, and three phosphate groups

“Loading Spring” (ATP)

Analogy for potential energy, adding phosphate compresses spring (stores energy), removing it releases coil

Phosphate Charge (ATP)

Highly negative, causes electrostatic repulsion, making bonds unstable and energy rich.

Hydrolysis

Addition of water to break terminal bonds. Releases 7.3 kcal/mol of free energy.

Adenosine Diphosphate (ATP)

(ADP) Low-energy molecule (2 phosphates) acts like rechargable battery.

What is the two steps in the building and breaking via the flow of water?

Dehydration synthesis (building) and Hydrolysis (breaking)

Examples of Dehydration synthesis (flow of water)

Monomer building

Amino acids to proteins (linked by peptide bonds)
Sugars to complex carbs (linked by glycosidic bonds)

Glycerol & fatty acids to fats (linked by ester linkges)

Example of Hydrolysis (flow of water)

Proteins to amino acids (water splits peptide bonds)

Complex carbs to sugars (water splits glycosidic bonds)

Triglycerides to glycerol & fatty acids (water splits ester bonds)

Also allows restructuing

Example of Hydrolysis (flow of water)

A limitless variety of macromolecules are built from just 40-50 common monomers, snapped together and pulled apart by this exact same mechanism.

What are the characteristics of Starch? (Starch VS Cellulose)

Alpha Glucose
The Linkage

Helical/Branched

Energy Storage

Hydrolyzed energy

What are the characteristics of Cellulose? (Starch VS Cellulose)

Beta Glucose

Beta Linkage

Straight, parallel

Structural support

Insoluble fiber

What are lipids?

Large group of biological molecules that all mix poorly with water, mostly consist of hydrocarbon regions (nonpolar)

What is a lipids structure?

Glycerol, Ester linkages, fatty acid

What are lipids bonds?

Hydrocarbon tails, rich in nonpolar C-H bonds, these chains violently exclude water (hydrophobic)

What are lipids chemical property?

Hydrophobic with nonpolar hydrocarbon bonds

What is Lipids energy density?

A gram of fat stores more than twice as much energy as a gram of starch; crucial for mobile animals

What is the physical impact of Chemical bonds?

The bonding of saturated and unsaturated fats changes its physical property resulting in an emergent property

What are the characteristics of hydrogen bonds in saturated fats?

Tightly packed chains

Dense alignment of atoms

What are the characteristics of hydrogen bonds in Unsaturated Fats?

Rigid downward bend prevents packing

Loosely spaced due to kinks

What are the three unique traits of Saturated Fats?

ONLY single bonds, saturated with max hydrogen

Solid at room temp

Primarily animal fats

What are the three unique traits of Unsaturated Fats?

Contains Cis-double bonds, creates permanent “kink”

Liquid at room temp

Plant and fish fats

What are two special lipids?

Phospholipids and Steroids

What are phospholipids? (special lipids)

Special lipids that is amphipathic (contains hydrophobic and hydrophilic region).

Phosphate head is hydrophilic (polar)

Fatty acid tail is hydrophobic (nonpolar)

Allows natural bilayer formation (structural basis of all cell membranes)

What are Steroids? (special lipids)

Precursor for Reproductive hormones

Testosterone: Male hormones

Estrogen: Female hormones

Progesterone: Menstrual cycle, fertility, pregnancy

What is the anatomy of an Amino Acid? (5 parts)

Central Alpha Carbon

Stable Hydrogen

Amino Group

Carboxyl Group

R-Group

What is the Central Alpha Carbon? (amino acid)

Core Carbon atom, acts as central scaffold attaching all four components

What is Stable hydrogen? (amino acid)

Single Hydrogen atom connected directly to central Alpha carbon

What is Amino Group? (amino acid)

Basic functional group containing nitrogen that acts as a base accepting proton

What is a Carboxyl Group? (amino acid)

Acidic functional group containing carbon and oxygen, acts as an acid donating a proton

What is an R-group? (amino acid)

Variable chemical structure unique to each 20 standard amino acids, determines distinct size, charge, polarity, and chemically behavior

What does an Amino acid form? (amino acids)

Polymer (polypeptide chain) consisting of a continuous unbranched sequence of amino acids, folds into functional protein.

How is the polypeptide chain formed by an Amino acid? (amino acids)

Dehydration synthesis

Covalent peptide bonds form between a carboxyl group of one amino acid and an amino group of another

Releases a water molecule

What is the process of protein folding to function? (protein folding)

Primary, Secondary, Tertiary, Quaternary

What is the Primary structure level? (protein folding)

Shape: Specific LINEAR sequence of amino acids, determined by DNA

Bonding: Peptide bonds

What is the Secondary structure level? (protein folding)

Shape: Helieces & Sheets

Bonding: Backbone interactions stabilized by hydrogen bonds

What is the Tertiary structure level? (protein folding)

Shape: 3-D subunit

Bonding: hydrophobic clustering, disulfide bridges, hydrogen bonds, van DER Waals, ionic bonds

What is the Quaternary structure level? (protein folding)

Shape: combined subunits

Bonding: Two or more polypeptide subunits assembled by R-groups into a functional macromolecule

What is the Domino effect of sickle cell disease?

Protein folding fails resulting in biological consequence

Cause (sickle cell)

Primary error

Single point mutation in primary amino acid sequence

Replaces hydrophilic glutamic acid (Glu) with hydrophobic Valine (Val) at position 6

Effect (sickle cell)

Tertiary alteration: In low-oxygen condition warps to hide hydrophobic valine patch

causes hemoglobin to aggregate into long rigid fibers at Quaternary level

Biological Consequence (sickle cell)

Rigid protein fibers deform the red blood cell

Changes from flexible disc into rigid sickle shape

Physiological Symptoms (sickle cell)

Sickled red blood cells clog blood vessels and reduce oxygen transport throughout body

What is the order of limited common building blocks of monomers?

Limited Monomers →sequenced Monomers →Folding polymers →3D functional structures

Limited Monomers (infinite diversity)

Nature uses 40-50 common building blocks

(ex. what elements or amino acids use, like 26 letters of alphabet)

Sequenced Monomers (infinite diversity)

Sequence dictates folding

Precise linear arrangement of blocks dictate chemical interactions

(ex. order of amino acids)

Folding Polymers (infinite diversity)

Folding dictates shapes

Internal interactions force the molecule to spontaneously fold into a 3D architecture

(ex. chemical properties - hydrophobic, polar, etc.)

Shapes & Functional Structures (infinite diversity)

Shapes dictate function

Dynamic processes are direct emergent properties of 3D molecular shapes that match and interact with another molecule