Micro Ch 2

subunit of a protein

• basic unit of matter
• made up of 3 major components:
• neutrons, protons, electrons

• Protons and neutrons in center of atom making up heaviest part of atom - the nucleus - , electrons for "electron cloud" around the nucleus
• Number of protons normally equals the number of electrons, so atom has no charge

• is the number of protons in it's nucleus
• an atom is distinguished by it's atomic number
• Is the bottom number next to element symbol

• the sum of the number of protons and neutrons
• (electrons are too light to contribute to the mass)
• Is the top number next to element symbol

• consists of only one kind of atom and cannot be separated into simpler parts 
• smallest unit
• are 92 naturally occurring elements

• C - carbon
• H - hydrogen
• O - oxygen
• N - nitrogen

• P ~ Phosphorus
• S ~ Sulfur

elements which have different numbers of neutrons

• most atoms are most stable when their outer shell has 8 electrons (or a full outer shell)
• *exception is hydrogen,
• Recall first shell has limit of 2 electrons

an atom that gains or loses an electron, making it no longer neutral

• positively charged ions
• "you ran over the 'cat'.. hahaha"

• negatively charged ions
• "your an 'a-hole"

• weak bonds
• formed btwn cations and anions because of strong attractions btwn positive and negative charges
• resulting product is call a salt
• Ex: NaCl = sodium chloride (table salt)

• formed when atoms share pairs of valence electrons
• strong bonds
• number of covalent bonds an atom can form is the number of electrons the atom must gain or lose to fill it's outer shell

• indicated by a dash btwn two atoms sharing a pair of electrons: C-H; double bond C=H
• "They entered into a covenant"...

• two or more atoms joined together by covalent bonds
• may be of the same or different elements

a molecule consisting of more than one element

forms when the electrons are shared equally

"No one is bi-polar. It's a happy covenant"

• those electrons found in an atoms outer shell
• particularly important in chemical bond formation

The ability of an atom to attract electrons to itself in a molecule

• when one atom in a covalent bond is significantly more electronegative than the other, the electrons are shared unequally
• slight separation of the charge is called a dipole (the atom that is pulling harder has a more negative charge, and vise versa)

• The slight separation of charge in polar covalent bond
• indicated by greek symbol Delta ( δ )
• The atom with slight positive charge is δ⁺

The atom with slight neg charge is δ^-

weak bonds that result from the attraction of the hydrogen atom in a polar molecule to an electronegative atom in the same or another polar molecule

• the ability of an atom to attract electrons to itself in a molecule
• an atom with a significantly higher electronegativity is better able to attract electrons

• a mole of a compound is the same number of molecules as a mole of another compound
• equal to 6.022 x 10²³
• Ex: One mole of sodium chloride weighs 58.4 grams, whereas one mole of potassium chloride weighs 74.55 grams

• the molarity (M) of a solution is the number of moles of a compound dissolved in 1 liter of solution
• Ex: 1 M solution of NaCl has 58.4 grams of NaCl dissolved in 1 liter of aqueous solution

• water
• making up over 70% of all living organisms by weight
• Hydrogen bonding plays a very important role in the properties of water ~ depends on temp
• the polar nature of water accounts for it's ability to dissolve a large number of compounds (If compounds are polar or have + or - charge)

• water loving
• includes salts and polar molecules

• water fearing
• do not dissolve in water because they cannot form hydrogen bonds

• Important property of aqueous solutions
• a measure of their acidity on scale of 0 -14, in which lower the number the more acidic

Measures the concentration of H⁺ in moles per liter

compounds which stabilize the pH of solutions

• ATP, energy currency of the cell
• effective energy carrier cause the 3 negatively charged phosphate groups repel each other, so bonds joining them are unstable
• Easily broken to release sufficient amt of energy to drive cellular process

• refers to the phosphate bonds in ATP
• relatively high amt of energy released when bonds are hydrolyzed makes them high energy
• symbolized by ~ (see pg 24)

• Important functional groups that modify the activity of the molecule:
• Aldehyde
• Amino
• Carboxyl
• Hydroxyl
• Keto
• Methyl
• Phosphate
• Sulfhydryl
• *Always Aim Carefully, Help Keep My Pussy Safe

• Aldehyde = carbohydrates
• Amino = amino acids

Carboxyl = Organic acids, including amino acids and fatty acids

Hydroxyl = carbohydrates, fatty acids, alcohol, some amino acids

Keto = carbohydrates, polypeptides

Methyl = Some amino acids, attached to DNA

Phosphate = nucleotides (subunit of nucleic acids), ATP, signaling molecules

Sulfhydryl = Part of the amino acid cysteine

• ADP 
• formed when terminal phosphate bond of ATP breaks

• Large molecules
• 4 major classes: 
• proteins
• carbohydrates
• nucleic acids
• lipids

• POLY means many
• Most macromolecules are polymers, formed by joining subunits together

a chemical reaction that removes H2O

Used in forming macromolecules

• the reverse of dehydration synthesis
• involves breaking down macromolecule to it's subunits by adding H2)

• Catalyzing reactions (enzymes)
• Transporting molecules
• Motility (proteins are essential components of flagella and cilia)
• Cell framework (Protein make up cytoskeleton)
• Sensing and responding to conditions outside of cell (P on cell surface recognize conditions in external environ & tell cell machinery)
• Regulating gene expression (P bind to DNA & regulate gene expression)
• *Proteins R Similar To Moms, Carry Cells Regularly

• subunits that make up proteins
• 20 major amino acids can be arranged to make infinite # of combos
• Only source of nitrogen in diet. Also has sulfur
• Held together by peptide bonds

All amino acids have a central carbon atom bonded to a carboxyl group, an amino group, and a side chain (R). The side chain (which distinguishes different amino acids) gives it's characteristic properties

type of covalent bond formed when the carboxyl group of one amino acid reacts with the amino acid of another, releasing water (dehydration synthesis)

Holds amino acids together

• results from the joining of amino acid subunits by peptide bonds
• One end of molecule has a free amino group (the N terminal or amino terminal end)
• The other end has a free carboxyl group (the C terminal or carboxyl terminal end)

*Recall in class, the backbone will be NCC NCC NCC NCC

one or more long polypeptides folded to create a functional molecule

*Distinction btwn polypeptide and protein is not always clear, sometimes used interchangably

• Primary
• Secondary
• Tertiary
• Quaternary

• Is determined by the number and sequence of amino acids in the polypeptide
• In large part, determines the final shape of the protein and it's properties
• average size polypeptide consists of about 250 amino acids

• the three-dimensional shape of localized regions
• results from folding of the various parts of the protein into two major patterns, either:
• alpha (α)- helix (spherical)
• beta (β) pleated sheet

the distinctive 3D shape of the folded entire protein

• determined primarily by sequence of amino acids and whether or not they interact with water
• The combo of strong and weak bonds btwn various amino acids results in the tertiary structure

Globular : tend to be spherical and water soluble

Fibrous : are elongated and insoluble

The specific shape that results when proteins consist of more than one polypeptide, whether identical or different

proteins that help other proteins fold properly

• a region or substructure (of a protein) consisting of sheets and helices that fold into a stable structure independently of other parts of the molecule
• different domains are associated with specific functions

• proteins that have other molecules covalently bonded to side chains of some of their amino acids
• Proteins are named after the molecules covalently joined. Ex: is sugar, is a glycoprotein; if lipid, is a lipoprotein

• High temp, extreme pH, and certain solvents can break bonds within protein, causing it's shape to change
• Becomes denatured and no longer functions
• May be reversible, may be permanent

• Diverse group of compounds that include sugars and starches. 
• Play critical roles in biology:
• Energy source
• Energy storage: organisms can store excess energy n nutrients for later by making certain carbs that function as reserve material
• Source of carbon for biosynthetic products: many microbes can make all cell parts from single carb - glucose
• Component of DNA & RNA: subunits contain sugar
• Structural components of cells: some types of cell walls are composed of sugar-containing material

all contain carbon, hydrogen and oxygen atoms in an approx ratio of 1:2:1

• simple sugars, only have single unit
• Classified by # of carbon atoms they have, most common have 5-6

• Ribose - Component of RNA
• Deoxyribose - component of DNA

• Glucose - common subunit of disaccharides
• Galactose - component of milk sugar
• Fructose - fruit sugar
• Mannose - found on surface of some microbes

• two monosaccharides joined together by covalent bonds
• joined together by dehydration reaction btwn pair of their hydroxyl group, w loss of water

Lactose = Glucose + Galactose (Milk sugar)

Maltose = Glucose + glucose  (breakdown product of starch)

Sucrose = Glucose + fructose (table sugar)

• large molecules composed of long chains of monosaccharide subunits
• Includes:
• Cellulose: principle component of plant cell walls & most abundant organic molecule on earth
• Starch: energy storage in plants
• Glycogen: energy storage product in animals and some bacteria
• Dextran: storage product in some bacterial cells
• Chitin: major organic component in exoskeleton of insects, also in cell wall of fungi
• Agar: found in cell walls of some algae, gelling agent for bacterial media

• deoxyribonucleic acid
• the master molecule of the cell
• is a double stranded helical molecule
• encodes all of the cell's properties
• Info in DNA is converted to form RNA, which is then translated to make proteins

• carry genetic info
• cells decode, convert info into sequence of nucleotides

• Is one subunit of DNA
• has 3 parts: 
• nucleobase
• deoxyribose
• a phosphate group

• can be characterized by their ring structures:
• Purines - Adenine and Guanine (Amy and Gertrude)  
• Each consisting of 2 fused rings 
• IN BOTH DNA AND RNA

• Pyrimidines - Cytosine and Thymine (Chris - in both DNA & RNA; Tim - ONLY IN DNA)
• Each consists of single ring

• Amy (Adenine) will only marry Tim (Thymine)
• Gertrude (Guanine) will only marry Chris (Cytosine)

The pair of nucleobases that bond are said to be complementary and are referred to as base-pairing rules.

Ribonucleic acid - involved in process that decodes info from DNA to crease sequence of amino acids in proteins

• In RNA, contains Uracil instead of Tim
• *Uracil is Russian guy, don't trust him with DNA
• In RNA, sugar is ribose
• RNA is shorter and exists as single chain of nucleotides

• Critically important in structure of membranes, function as gatekeepers, prevent cell leakage and keep molecules from entering cells
• Are non-polar & hydrophobic

• contain only carbon, hydrogen and oxygen
• most common are fats = fatty acids linked to glycerol
• May be liquid or solid at room temp

• are long chains of C atoms bonded to H atoms
• Most have even # of carbon atoms
• Can be divided into 2 groups based on the presence of double bonds btwn C atoms: 
• Saturated fatty acids have NO double bonds. Saturated means they have max # of hydrogen atoms
• Unsaturated fatty acids contain one or more double bonds.  Can be cis or trans
• *Those w one double bond are monounsaturated
• **Those with more than one double bond are polyunsaturated

• refers to unsaturated fatty acids
• CIS means the hydrogen atoms attached to the double-bonded carbon molecules are on the same side of the bond
• TRANS fatty acids have hydrogen atoms on opposite sides of the double bond

• Fats that contain only saturated fatty acids are typically solid at room temp, cause the straight long tails of fatty acids packed tightly together
• Fats with one or more unsaturated fatty acids tend to be liquid at room temp cause fatty acids have kinks in long tails that prevent tight packing

• contain fatty acids and glycerol as well as other carbon, hydrogen and oxygen
• Most important are phospholipids

• most important compound lipids
• contain phosphate group linked to one variety of other polar molecules
• The phosphate-containing portion is the polar head and is soluble in water (hydrophilic)
• The fatty acid portion is insoluble in water (hydrophobic)
• Essential component of cytoplasmic membranes, forms bilayer

• simple lipids that have a characteristic structure consisting of four connected rings
• Structure is quite different from fats, but classified as lipid cause insoluble in water