AP Biology Unit 1 Review

Hydroxyl Group

(-OH), Polar/hydrophilic

Carbonyl Group

(>C=O), polar/hydrophilic

Ketone

Carbonyl group is w/in a carbon skeleton (Ex: Acetone)

Aldehyde

Carbonyl group is at the end of a carbon skeleton (Ex: Propanal)

Carboxyl Group

(-COOH), polar/hydrophilic, an acid (releases H+ in ionized form)

Amino group

(-NH2), polar/hydrophilic, a base (absorbs H+ in ionized form)

Sulfhydryl Group

(-SH), polar/hydrophilic, In disulfide bridges (protein folding)

Phosphate Group

(-OPO3^2-), Strong - charge (polar)/hydrophilic

Methyl Group

(-CH3), nonpolar/hydrophobic

ATP

(adenosine triphosphate) main energy source that cells use for most of their work

triple phosphate groups bonded w/ adenosine

Dehydration Reaction

chem reaction in which 2 molecules become covalently bonded w/ the removal of a water molecule (from H or OH on either monomer)

Ends of poly/monomers must have an -H or -OH (hydroxyl group)

Hydrolysis

chem reaction in which 2 molecules are separated w/ the addition of a water molecule.

organic compound

Compounds that contain carbon

hydrocarbon

An organic molecule consisting only of carbon and hydrogen, nonpolar/hydrophobic

Types of macromolecules

carbohydrates, lipids, proteins, nucleic acids

Types of Monomers

Monosaccharides, amino acids and nucleotides

Elements of Lipids

CH (very little O)

(P in phospholipids)

Elements of Carbs

CHO

Elements of Proteins

CHON

Elements of Nucleic Acids

CHONP

Ratio of CHO in monosaccharides

some multiple of CH2O

A sugar has

a carbonyl group (>C=O) (ketone or aldehyde) and multiple hydroxyl groups (-OH)

glycosidic linkage

A covalent bond formed between two monosaccharides by a dehydration reaction.

Which is a monosaccharide?

Starch

storage polysaccharide in the form of glucose monosaccharides in plants.

spiraling, can be unbranched (amylose) or somewhat branched (amylopectin)

Glycogen

SHORT TERM storage polysaccharide in the form of glucose monosaccharides in animals (found in liver or muscles)

spiraling, extensively branched

Cellulose

structural polysaccharide in the form of glucose monosaccharides that makes up the cell wall in plant cells

Straight chains held together by hydrogen bonds

Chitin

structural polysaccharide in the form of glucose monosaccharides that makes up the exoskeletons of arthropods and cells walls of fungi

Glucose monosaccharides have N containing-attachment, unlike Cellulose

Which macromolecule is not made of polymers?

Lipids

All lipids are

hydrophobic/nonpolar (mostly hydrocarbon regions)

Glycerol

an alcohol composed of a three-C chain, each with a hydroxyl group (-OH)

serve as the backbone for a triglyceride.

fatty acid

A long carbon skeleton (16-18 C's) w/ a carboxyl group (-COOH) attached to a hydrocarbon (makes it an acid)

Fat (triglyceride)

3 fatty acids bonded to a glycerol with an ester linkage. Long term energy storage in animals

Ester linkage

a covalent bond between a hydroxyl group (glycerol) and a carboxyl group (fatty acid) created with a dehydration reaction

Saturated fatty acid

hydrocarbon chain has no double bonds between carbon atoms (max # of H's)

Sat fats are

solid at room temperature - hydrocarbon chains (tails) lack double bonds, making them flexible enough to pack together

Unsaturated Fatty acid

hydrocarbon chain has double bonds between carbon atoms (missing H's)

Trans fats

unsaturated fats that are artificially altered to be more saturated (H's added, allowing them to solidify). Unhealthy

Unsat fatty acids are

liquid at room temperature (emergent property) - hydrocarbon chains (tails) have double bonds, preventing them from packing together/creating space

Phospholipid

2 fatty acids and a phosphate group (-OPO3^2-) attached to a glycerol. amphipathic (part hydrophobic/philic)

Phospholipid tails

hydrophobic/nonpolar

Phospholipid heads

hydrophilic/polar (- charge from phosphate group)

When phospholipids are added to water

they self-assemble into a bilayer, a double-layered structure, with the hydrophobic tails pointing toward the interior and the hydrophilic heads towards the exterior (ex: cell membranes)

steroid

A type of lipid characterized by a carbon skeleton consisting of four rings with various functional groups attached.

How many amino acids are there?

20 different amino acids

peptide bond

covalent bond that forms between the carboxyl group (-COOH) of one amino acid and the amino group (-NH2) of another with a dehydration reaction

identify the amino acid

Parts of an amino acid

Central Carbon, Amino group, carboxyl group, Hydrogen, R group

protein vs polypeptide

A protein is one or more polypeptides that has been folded into a fixed structure. A polypeptide is a chain of amino acids

R group/side chain

part of amino acid extending from the backbone that determines the molecule's physical and chemical properties

can be nonpolar/hydrophobic, polar/hydrophilic, or electrically charged/hydrophilic (acid= - / basic= +)

What is the shape of a protein determined by?

the sequence of amino acids determined by DNA

How many levels of protein structure are there?

4; primary, secondary, tertiary, quaternary (2+ polypeptides)

primary structure

linear chain of amino acids determined by DNA that ends with an amino group or a carboxyl group

dictates secondary and tertiary structure due to backbone and r groups interacting between the amino acids

Secondary structure

regions stabilized by hydrogen bonds between atoms of the polypeptide backbone (NOT R groups)

the coils (alpha helixes) and folds (beta pleated sheets) of a protein

Tertiary structure

3D, overall unique shape of a polypeptide, stabilized by interactions between R groups

Largely determined by the hydrogen bonds betw. polar r groups and ionic bonds betw. +/- r groups

hydrophobic interactions

tertiary structure - when hydrophobic/nonpolar side chains end up in clusters on the inside of the protein (out of contact with water), held together by van der Waal interactions

disulfide bridges

tertiary structure- A strong (and ONLY) covalent bond formed when the sulfur of one cysteine monomer's sulfhydryl (-SH) r group bonds to the sulfur of another cysteine monomer's sulfhydryl (-SH) r group

Quaternary structure

association of two or more polypeptide subunits aggregated into one functional macromolecule (some proteins only)

Mutations in primary structure (Sickle Cell Disease example)

Mutation causes glutamic acid (normal hydrophilic r group) to be replaced by valine (hydrophobic r group) in the hemoglobin protein --> abnormal fiber-shaped cells clump together --> reduced ability to carry oxygen

Misfolding proteins

Causes malfunctional/nonfunctional proteins

-Diseases: Alzheimer's, mad cow disease, Parkinson's, dementia

Denaturation

a process in which a protein unravels/loses its native conformation (back to primary structure), thereby becoming biologically inactive, due to unsuitable chemical/physical environments breaking the interactions and bonds within it

Ex:) pH levels, salt concentrations, temperature (fevers), aqueous -> nonpolar solvent (some proteins)

Nucleic Acid polymers

DNA and RNA

gene

sequence of DNA that codes for a protein and thus determines a trait

DNA vs RNA

DNA: deoxyribose sugar, thymine base, double strand

RNA: ribose sugar, uracil base, single strand

deoxyribose sugar vs ribose sugar

deoxyribose lacks an O atom on the 2nd C of the ring

mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome

nucleotide parts

phosphate group, nitrogenous base, and pentose sugar (base + sugar = nucleoside)

N base = basic bc N usually takes up H+'s

pyrimidines

Cytosine (C) - DNA + RNA

Thymine (T) - DNA

Uracil (U) - RNA

has one 6-memebered C and N ring, differing in functional groups

Purines

Adenine (A), Guanine (G) - DNA + RNA

has a 6-membered ring fused to a 5-membered ring, differing in functional groups

phosphodiester linkage

covalent bonds from a dehydration reaction that join adjacent nucleotides between the -OH group of the 3' carbon of one nucleotide and the phosphate on the 5' carbon of the next (creates sugar-phosphate backbone (excludes base))

What direction do the polynucleotide backbones of DNA strands go in?

antiparallel/opposite of each other (5' to 3' and 3' to 5')

5’ Carbon end

phosphate group

3’ Carbon end

hydroxyl group

structure of a DNA double helix

antiparallel sugar-phosphate backbones on the outside, and bases paired on inside, held by hydrogen bonds

Base pairings (DNA)

A-T

G-C

Base pairings (RNA)

A-U

G-C

Sections of DNA (% example)

a percentage of one base is going to match its complementary base (Ex: 17% T, 17% A, 33% G, 33% C)

Comparing DNA and/or protein sequences can be used to find

closely related species

Genomics

study and comparison of genomes within a single species or among different species

proteomics

the study and comparison of all the proteins that result from an organism's genome

emergent property

a characteristic of a system that does not appear in any of the system's component parts

atomic number

the number of protons in the nucleus of an atom

mass number

the total number of protons and neutrons in a nucleus.

atomic mass

The average mass of all the isotopes of an element

isotope

Atoms of the same element that have different numbers of neutrons

radioactive isotope

An isotope whose nucleus decays spontaneously, giving off particles and energy (unstable)

potential energy

stored energy (capacity to cause change) that results from the position or shape of an object

stability of electrons

most stability: closest shell to nucleus/low energy (lost energy = heat)

least stability: farthest shell from nucleus/high energy

valence electrons

The electrons in the outermost shell (valence shell) of an atom; these are the electrons involved in forming bonds/determine chemical behavior

full valence shell = unreactive

covalent bond

A chemical bond that involves sharing a pair of electrons between atoms in a molecule

types of covalent bonds

single, double, triple pairs

an atom's valence (bonding capacity) is determined by the number of electrons needed to fill the valence shell

electronegativity

a measure of the tendency of an atom to attract a bonding pair of electrons

nonpolar covalent bond

a bond in a molecule with a neutral charge (e- are equally shared/equal electronegativity). hydrophobic

polar

a molecule with positive and negative charges (e- are unequally shared/one atom is more electronegative). hydrophilic

ion

An atom or group of atoms that has a positive or negative charge after gaining/losing electrons

cation

A positively charged ion

anion

A negatively charged ion

ionic bond

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

**electron transfer does NOT create the bond; it allows a bond to form bc it results in 2 ions of opposite charges

ionic compounds (salts)

compounds composed of cations and anions, connected by ionic bonds

hydrogen bonds

when an H atom that is covalently bonded to an electronegative atom (creating + charge in the H) attracts another atom (- charge) nearby