All of Chapter 1 Flashcards
Chapter 1
Atoms have what at their core?
A nucleus at their core and are surrounded by electrons
- a nucleus is composed of protons and neutrons
Atomic number
Number of protons in the nucleus of an atom
Protons, neutrons, electrons
Protons: positively charged, Neutrons: no charge, Electrons: negatively charged
Mass number
Number of protons and neutrons in the nucleus
Neutral atoms may have diff # of neutrons, and are known as what?
Isotopes
- Ex. Carbon-12, Carbon-13 (1 xtra neutron), Carbon-14 (3 xtra neutrons)
What are isotopes?
Element that has the same # of protons, or atomic number, but a diff # atomic mass cuz of the change in neutron number!
- most isotopes r stable but decay over time
What are radioactive isotopes/radioisotopes?
Has a unstable nuclei that break apart: radioactive - subatomic particles are released as well as some radiation
What are valence electrons?
Electrons involved in bonding btw atoms
- possess the highest energy (outermost electrons)
Common uses for radioisotopes? 4 uses
C-14: carbon dating, tracing cancer
Ca-45: measures bone formation rate
K-40: fossil dating
Ra-226: cancer treatment
Intermolecular bonds
Bonds formed between atoms and interaction of valence electrons
- ionic
- covalent
- polar covalent
What are core electrons?
Electrons when under normal reaction conditions are chemically inert
Ionic bonds
Exchange or transfer of electrons from one atom to another
- bonding makes atoms more stable
- opposite charges attract each other
Covalent bond
Sharing of electrons.
- valence electrons are shared between atoms. usually 2 nonmetals
What are the 4 main types of biochemical reactions?
- Acid-base/ Neutralization Reaction
- Acid-Base Buffer Reactions (not rlly apart of it)
- Redox Reaction (Oxidation, Reduction)
- Hydrolysis and Condensation (dehydration synthesis) reaction
Biomolecules
covalent bonds give structure to biomolecules, and non-covalent bonds give dynamics
- Ex. phosphodiester bonds in DNA give structure to DNA & act as a backbone
- Ex. ionic bonds, hydrogen bonds in protein folding
What are the 4 major macromolecules
- Carbohydrates
- Lipids (Fats)
- Proteins
- Nucleic Acids
What forms the backbone of biomolecules, and forms covalent bonds with metals
Carbon
Polymerization
Creates richness of life - holds the molecules
Aqueous Solutions (aq)
Can be classified as either acidic, basic, or neutral
Acidic Solutions
High concentration of Hydrogen Ions (H+)
Basic Solutions
High concentration of hydroxide ions (OH-)
Neutral Solutions
Have an equal amount of hydrogen and hydroxide ions
Inorganic
Carbon molecules not bonded with hydrogen
Organic
Carbon molecules bonded with hydrogen
Most of the biosphere is composed of..
Carbon, Hydrogen, Nitrogen, Oxygen
Hydrocarbons
Made of only carbon and hydrogen
Ex. methane, ethane, propane (generally non-polar because of low electronegativity)
Pure water undergoes what?
Autoionization, where 2 water molecules in every 550 mill reaction with each other to produce a hydronium ion (H3O+) - acidic, and a hydroxide ion (OH-) - basic.
Functional groups and what r the 6 ones?
Handles that stick out on biomolecules exhibit particular chemical properties and account for an organic molecule’s reactivity
ex. carboxyl + amino –> peptide bond
- hydroxyl
- carbonyl
- carboxyl
- Amino
- Phosphate
- Sulfhydryl
Intermolecular bonds
interactions btw molecules that hold 2 or more molecules to one another. much weaker then intramolecular bonds
London Dispersion forces
Weak forces of attraction between all atoms and molecules.
Dipole-Dipole Forces
Hold polar molecules together. stronger than london forces
Hydrogen Bonding
Very strong dipole-dipole forces that form between the electronegative H of one polar molecule and the electronegative N, O, or F of another.
Water molecules are held together by..
Hydrogen bonds. which are actually forces between molecules and not true bonds
- due to the polar covalent bonding within each molecule, water will have a positive and negative pole attracting each other.
Water is a solvent and dissolves substances easily, why?
It’s because of the polarity.
- when ionic solids dissolve, the anions and cations dissociate (ionic bonds are broken)
Insoluble
Substances that cant dissolve in water
Hydrophilic
If a substance is polar, it will dissolve in water and form hydrogen bonds
Ex. salts
Hydrophobic
If a substance is nonpolar, it will not dissolve in water, nor form hydrogen bonds
Ex. fats and oils
prop of water: Cohesion
Water molecules form hydrogen bonds with one another
effect: High surface tension
prop of water: Adhesion
Water molecules form hydrogen bonds with other polar materials
Effect: capillary action causes water to creep up a narrow glass tube and paper.
Ex. Transpiration
prop of water: High density at 4°C
Below 0°C, water molecules form a crystalline lattice. H-bonds spread apart, low density.
Effect: ice floats on liquid water allowing for aquatic life in winter
prop of water: High Specific Heat Capacity
Hydrogen bonding causes water to absorb much heat before its temp. increases & also causes it to lose huge amounts of heat before its temp. decreases
Effect: temperature moderation. Helps organisms maintain a constant body temperature
prop of water: High Specific Heat of Vaporization
Hydrogen bonding causes liquid water to absorb a large amount of heat to become a vapor (gas)
Effect: evaporation cooling. Allows for organisms to dissipate body heat by evaporation from skin and tongue
acid is a proton donor or acceptor?
proton donor
base is a proton donor or acceptor?
proton acceptor
Polar Functional Groups
Alcohols (-OH) and Carboxyls (-COOH) are polar due to the electronegative Oxygen. so sugars and alcohols are very soluble (hydrophilic) in water since they have polar hydroxyl groups
Acidic Functional Groups
The carboxyl (-COOH) group will make a molecule acidic, hence the term ‘carboxylic acidddd’
Basic Functional Group
The Amine (-NH2) group will make a molecule basic
Isomer
- organic compounds w the same molecular formula but diff structures
- glucose, galactose, and fructose are all examples of an isomer
- all share the same formula C6H12O6, but different structures
Structural isomer
two or more compounds with the same atoms bounded differently
ex. glucose and fructose
Steroisomers
two or more compounds with their atoms bonded the same way but arranged differently in space
Stereoisomers: Geometrical isomers
Different physical properties (melting point) but same chemical properties
Ex. Glucose and galactose
- glucose has a hydroxyl group on carbon 4 below the plane of the ring
- galactose has one above the place of the ring
- alpha and beta glucose are dis
Stereoisomers: Optical isomers (enantiomers)
Mirror images, have the same physical & chemical properties but differentiate through enzymes and proteins in the cell
- occur when a carbon atom is bonded to four different atoms or groups
Ex. our hands; glove only fits on one hand, like right on right hand the same way biomolecules cant interact with a specific optical isomer of a compound but cant fit the other
Monomers
Building blocks, repeated small units
Polymers
Long molecules built by linking repeating building blocks in a chain
Carbohydrates
Largest of organic molecules and most abundant
- most immediate source of energy for cellular respiration
Oligosaccharides (few sugar units)
Contains two (disaccharides) or three sugar monomers
Monosaccharides
Simplest form of a carbohydrate
- 3-7 carbon long
- names usually end in -ose
- glucose, galactose, fructose
Sucrose –> a-glucose + b-fructose
1-2 Glycosidic linkage
Maltose –> a-glucose + a-glucose (or b-glucose)
held together w/ 1-4 glycosidic linkage
Glycosidic linkages (oligosaccharides)
Covalent bonds formed through a condensation/dehydration synthesis reaction that links monosaccharides into oligosaccharide
Dehydration Synthesis and Hydrolysis Formula
Dehyrdation synthesis: C6H12O6 + C6H12O6 –> C12H22O11 –> H2O
Hydrolysis: C12H22O11 + H2O –> C6H12O6 + C6H12O6
Lactose –> b-glucose + b-galactose
found in milk
Polysaccharides
- Polmer of monosaccharide subunits, linked together in the same way; condensation reactions producing glycosidic bonds
- Energy storage (starch and glycogen) and structural support (cellulose and chitin)
Starch
- produced by plants
- stored in chloroplasts, amyloplasts and other plastids
- mixture of amylose and amylopectin
Amylose
- straight chain polymer of a-glucose w/ 1-4 glycosidic linkages
- tends to form a-helix shape in water due to hydrogen bonding
- slightly soluble
Amylopectin
- Branched-chain polymer of a-glucose
- 1-4 glycosidic linkages (main chain) and 1-6 linkages (branch points)
- insoluble in water due to hydroxyls interaction with water due to large number of branch points
Glycogen
- produced by animals and stored in liver and muscles
- same linkages as amylopectin but more branched –> higher number of 1-6 linkages
Cellulose
- Major component of cell walls
- structural forms of polysaccharides
- straight chain polymer with b-glucose held together by 1-4 glycosidic linkage
Acid-Base Buffer Reaction
Chemical systems that resist changes in pH. they are substances that can donate H+ ions when they are required and remove them when there are too many in a solution
Redox Reaction
Oxidization: atom, ion, molecule loses electron (RA: reducing agent)
Reduction: atom, ion, molecule gains electron (OA: oxidizing agent)
Hydrolysis Reaction
- opposite of condensation reactions
- larger molecules are broken down
- catabolic since they break apart large molecule
Chitin
- 2nd most abundant organic material in the world
- used in hard exoskeleton of insects and lobster and in cell walls of fungi
- similar to cellulose except a nitrogen-containing group is attached to carbon-2
Acid-Base Neutralization Reaction
transfer of hydrogen ions btw molecules
acid: high concentration of hydrogen ions (H+_=)
base: high concentration of hydroxide ions (OH-)
neutral: equal amount of (H+) and (OH-)
Condensation (Dehydration synthesis) Reaction
- formation of water by removing 2 hydrogen molecules and 1 hydrogen molecule
- require energy
- Anabolic cuz they form larger molecules by joining smaller ones
Lipids (fats)
- Hydrophobic, non-polar, insoluble in water
- slippery, oily, waxy
- fats are large macromolecules made from smaller subunits, they are not polymers: not a continuing chain
Reducing Sugars
- Sugars that have a free anomeric carbon can be oxidized
What are the 4 families of lipids?
- Fats
- Phospholipids
- Steroids
- Waxes
Fats: Tricylglyceros/Triglycerides
- 3 fatty acids attached too glycerol via a condensation reaction
- fat molecules don’t retain their acidic properties once esterlinkage is formed, become large polar molecukes
- fatty acids are 16 or 18 carbon atoms long
- more carbon atoms, more nonpolar the molecule is
Triacylglycerol formation
- condensation reaction between a hydroxyl group of glycerol and the carboxyl group of a fatty acid
- forms an ester linkage
- not a true polymer
Saturated fats (bad)
- produced by animals
- hydrocarbon chains saturated with H atoms
- contributes to cardiovascular disease
Unsaturated Fats (good)
- contains one or more polar bonds
- polyunsaturated double bonds
- monounsaturated - almonds, avocado, cashews (any type of nuts), olive oil
- produced by plants and fish
- linked to a decline of inflammation in the body - less heart disease
Hydrogenation
- industrial process where H-atoms are added to double bonds in unsaturated fatty acids –> semi-solids
- trans fats cant be broken down
Phospholipids
- glycerol molecule attached to 2 fatty acid chains, and a phosphate
- amphipathic hydrophilic heads (phosphate group) and hydrophobic tails (fatty acids)
- when in water, they form spheres called micelles or produce bilayers (liposomes)
Steroids
- compact hydrophobic molecules containing 4 fused hydrocarbon rings and several functional groups
- diff steroids have diff functional groups attached to
- lacks a fatty acid chain
Cholesterol
- Precursor of all steroid hormones (ex. sex hormones), vitamin D, bile salts
- present in cell membrane
Waxes
- long-chain fatty acids linked to alcohols or carbon rings
- hydrophobic with firm, pliable consistency
- used as waterproof coatings by plants (leaves, stems, etc)
Lipoprotein
protien-lipid complexes that carries fat in the blood
What is HDL?
High-Density Lipoprotein
- good cholesterol
- high protein/fat ratio
- scavengers
- collect fat from body –> liver (opposite for LDL)
What is LDL?
Low Density lipoprotein
- bad cholesterol
- high fat/protein ratio
- transports fat from liver –> body
Omega fats
essential fatty acids that cannot be made by the body
- ex. cats need omega-3 oils in their diet since they don’t produce omega fats which is essential
Protein
- large molecule that has many amino acid subunits that are joined by peptide bonds folded into a 3D shape
Primary (1°) Structure
- linear structure
- slight change in amino acid sequence can affect proteins structure and its function
- can cause serious disorders
sicklel asmmeia
Seconday Structure
- “local folding”
- alpha helix and beta pleated sheet
- folding along short sections of polypeptide
Tertiary (3°) Structure
- “whole molecule folding”: interactions btw distant amino acids
Quaternary (4°) Structure
- more than one polypeptide chain bonded together: only then does polypeptide become functional protein
Nucleic acid
- directs growth and development of every living organism
- DNA, mtDNA, RNA, and ATP
- DNA and RNA are polymers that are made up of monomer units called nucleotides
DNA (Deoxyribonucleic acid)
- source of genetic info
- directs cellular activity
- desoxyribose sugar, 4 nitrogenous bases, phosphate group
Nitrogenous bases
- 4 diff ones found in DNA
- divided into Pyrimidines & purines
- Purines have 2 rings, adenine and guanine
- Pyrimidines have 1 ring, thymine and cytosine
- to rmbr pyrimidines keep da y’s together (pyr, thy, cy)
Base pairing rule (nitrogenous bases)
- adenine always binds w thymine w 2 H-bonds
- guanine always bonds w cytosine w 3 H-bonds
- A=T requires less energy to separate than G=C
RNA (Ribonucleic acid)
- polymer made up of nucleotides
- composed of ribose sugar, phosphate group, and 4 nitrogenous bases
- Uracil replaces thymine in RNA
- RNA is single stranded
- synthesized in the 5’–>3’ direction. (condensation reaction)
ATP (Adenosine triphosphate)
- important nucleic acid composed of a single nucleotide
- a monomer unit that is made up of a nitrogen base called adenosine, a ribose sugar, and 3 phosphate groups
- energy-providing molecule
- other forms : ADP (diphosphate), AMP (monophosphate)
Enzyme
- biological catalyst that speeds up reactions
- they r globular proteins
- w/o the presence of enzymes, biochemical reaction would not occur fast enough to sustain life
Substrate
- molecule/reactant that will undergo an enzymatic reaction
- binds to active site of an enzyme, fits in the enzyme nicely
Active site
- region of the enzyme that binds to the substrate
Carboxyl group
organic acids
Carbonyl group
Aldheydes, Ketones
Hydroxyl group
Alcohols
Amino group
amino acids
Phosphate group
Nucleotides, nucleic acids
Sulfhydryl group
many cellular molecules
Disaccharide
- carbohydrate molecule made from two monosaccharides
- maltose
- sucrose
- lactose
Monosaccharide
- simplest form of carbohydrate, one simple sugar unit
- glucose
- galactose
- fructose
- ribose
- deyoxyribose
Polysaccharide
- molecule that contains many linked monosaccharides
- starch
- glycogen
- cellulose
- chitin
