Section 1: Chemistry Flashcards
What are atoms made up of?
Neutrons, Protons, and electrons
2 or more atoms held together by chemical bonds are called…
Molecules
Chemical bonds result from ____ interactions
electron
This is the ability of an atom to attract electrons
Electronegativity
What are the 3 bonds types?
Ionic
Covalent (polar and non-polar)
Hydrogen
This type of bond is a transfer of electrons from one atom to another due to different electronegativities
Ionic bond
This type of bond is the sharing of electrons between atoms with similar electronegativites
Covalent
This type of covalent bond is the equal sharing of electrons (identical electronegativites)
This type is the unequal sharing of electrons due to different electronegativities that forms a dipole
Nonpolar
Polar
This type of bond is a weak bond between molecules with a hydrogen attached to a highly electronegative atom while also attracted to a negative charge on another molecule (F,O,N)
Hydrogen bond
What are the 5 qualities of water?
Excellent solvent High heat capacity Ice floats Cohesion/surface tension Adhesion
This quality of water results from dipoles of H2O being able to break up charged IONIC molecules
Excellent solvent
This is defined as the degree in which a substance changes temperature in response to gain/loss of heat
The temperature of large water bodies are very stable in response to temperature changes of surrounding air, a large amount of energy is required to warm up water. So it has a….
It also has a high heat of _____
Heat capacity
High heat capacity
Vaporization
This quality of water results from water expanding as it freezes, becoming less dense then it’s liquid form.
H bonds become rigid and form a crystal that keeps molecules separated
Ice floats
This quality of water results from attraction between LIKE substances due to H-bonds; the strong cohesion between H2O molecules produces a high…
cohesion/surface tension
This quality of water is due to attraction to unlike substances; capillary action; ability of liquid to flow without external forces (like against gravity)
Adhesion
Organic molecules have what atoms?
Macromolecules form _____ which form ______
Carbon
Monomers which form polymers
How many of carbon’s 6 electrons are available to form bonds with other atoms?
4
This functional group of organic molecules is polar and hydrophilic
hydroxyl (OH)
This functional group of organic molecules is polar, hydrophilic, and is a weak acid
carboxyl (COOH)
This functional group of organic molecules is polar, hydrophilic, and a weak base
NH2
This functional group is polar, hydrophilic, and are present in acidic molecules
Phosphate (-PO3)
H3PO4, etc
This functional group of organic molecules is polar and hydrophilic. It can be an aldehyde or ketone
Carbonyl
This functional group of organic molecules is nonpolar and hydrophobic
Methyl (CH3)
This type of biochemical structure forms monosaccharides, disaccharides, and polysaccharides
Carbohydrates
This type of carbohydrate is an alpha or beta sugar molecule base on position of anomeric carbon
An OH pointing up is ____
An OH pointing down is ____
Beta
Alpha
This type of carbohydrate is two sugar molecules joined by a glycosidic linkage
Disaccharide
What type of linkage occurs between saccharide molecules?
What type of reaction creates this bond?
Glycosidic
Dehydration
This type of carbohydrate is a series of connected monosaccharides
They are joined by what type of synthesis?
They are broken down by….
Polysaccharides
Dehydration (loss of water from reacting molecules, forms a water molecule)
Hydrolysis (water is used and added to molecules)
This type of carbohydrate is a polymer of α-glucose molecules
Where does it store energy?
Starch
Plant cells
This type of carbohydrate is a polymer of α-glucose molecules, but is stored in animal molecules
How is it different from starch?
Glycogen
Polymer branching. Starch is branched every 30 residues and glycogen is branched every 8-12 residues
This carbohydrate is a polymer of β-glucose; structural molecule for walls of plant cells and wood
Cellulose
This type of carbohydrate is a polymer of β-glucose, but each one has a nitrogen containing group attached to a ring.
Chitin
Where is chitin used as a structural molecule?
Fungal cell walls and exoskeleton of insects
This type of biochemical molecule is hydrophobic
Used for insulation, energy storage, structural in membrane, and endocrine system (hormones)
Lipids
This is three fatty acid chains attached to a glycerol backbone
Triglycerides (triacylglycerols)
This type of triglyceride, or fatty acid, has no double bonds
This type of triglyceride or fatty acid has double bonds
Saturated fatty acid
Unsaturated fatty acid
Which have a higher boiling point, unsaturated or saturated fatty acids?
Why?
Saturated
They stack more tightly(densely). They form plaques which is why they are considered unhealthy
This biochemical molecule is a lipid derivative of two fatty acids and a phosphate group attached to a glycerol back bone
What term describes their hydrophobic/hydrophilic tendencies?
Phospholipid
Ampiphatic (both hydrophilic and hydrophobic = membrane bilayer)
This biochemical molecule is a lipid derivative of three 6 membered rings and on 5 membered ring, form hormones and cholesterol
Steroids
This lipid derivative is an ester of long chain fatty acids and monohydroxylic alcohols. It is used as protective coating or exoskeleton
waxes
These lipid derivatives are fatty acid carbon chains with conjugated double bonds and six membered rings at each ends
Carotenoids
This lipid derivative produces colors in plants and animals
Carotenoids (carotenes and xanthophylls)
These lipids are 4 joined pyrole rings. Often complexed with a metal, like heme and iron in Hb, chlorphyll with Mg)
Porphyrins (tetrapyroles)
You should probably review what all those lipid structures look like and quiz yourself!
You know you want to.
Specialized fat cells whose cytoplasm contains nothing but triglycerides
Adipocytes
These are similar to phospholipids but have a carbon group instead of a phosphate group
Glycolipids
Lipids are SOLUBLE/INSOLUBLE
insoluble
Since lipids are insoluble, how are they transported in the blood?
Lipoproteins
This structure is a lipid core surrounded by phospholipids and apolipoproteins
Lipoproteins (used to transport lipids in the blood)
Cell membranes need to maintain a certain degree of ______ and are capable of changing fatty acid composition to do so
Fluidity
In cold weather, to avoid rigidity, cells incorporate more mono and __________ fatty acids into the membrane as they have lower melting points and are more kinked to increase fluidity
In warm weather climates, cells show the opposite trend
Polyunsaturated fatty acids
Which has a higher boiling point, unsaturated or saturated fatty acids?
Which has a lower melting point?
Unsaturated have higher boiling point
Unsaturated have lower melting point
Tricky business!
Explain why unsaturated fatty acids have a higher boiling point but a lower melting point
Double bonds increase bond polarity
But a more kinked structure leads to less dense packing
What is the structure of amino acids?
hydrogen group, amine group, carboxyl group, and a variable R group
What is the storage protein in milk?
Casein
What is the storage protein in egg whites?
ovalbumin
What is the storage protein in corn seeds?
Zein
This is the transport protein which carries oxygen around the body
Hemoglobin
These are the transport proteins which carry electrons around the body
Cytochromes
Does ATP contain ribose or deoxyribose?
Ribose!
What enzyme catalyzes the reaction that breaks the the α-glycosidic bonds in starch?
Amylase
These catalyze reaction in both the forward and reverse direction based upon [substrate] (the concentration of substrate)
Enzymes
What determines an enzyme’s efficiency?
Temperature and pH
Do enzymes change the spontaneity of a reaction?
No!
Enzymes are almost always considered to be proteins, but what else can act as an enzyme?
RNA (a nucleic acid)
These are NON PROTEIN molecules that assist enzymes
Cofactors
This is the term for the unioned cofactor and the enzyme
What is the term for when the protein is not combined with its cofactor?
Holoenzyme
Apoenzyme/apoprotein
Can cofactors be both organic and inorganic?
Yes
These are organic cofactors
These are inorganic cofactors
Coenzymes
Metal ions
What is it called when a cofactor strongly bonds to an enzyme?
Prosthetic Group
This classification of protein structure is one made entirely of AAs
This classification are functional and act as carriers or enzymes
These are fibrous, structural (like collagen)
These are made of a simple protein and nonprotein
Simple
Albumins and Globulins
Schleroproteins
Conjugated
This type of protein is bound to a lipid
This type of protein is bound to a carbohydrate
This type of protein is bound to a pigmented molecule
This type of protein is complexed around a metal ion
This type of protein contains a histone or protamine, is bound to nucleic acid
Lipoprotein
Mucoprotein
Chromoprotein
Metalloprotein
Nucleoprotein
This is the structure of proteins that is the sequence of AAs
Primary structure
This is the structure of proteins that is the 3d shape due to H-bonding between amino and carboxyl groups of adjacent amino acids
Secondary structure (Alpha helix, beta sheet)
This is the structure of proteins that is the 3d structure due to noncovalent interactions between amino acid R groups (subunit interactions)
Tertiary structure
What are the interactions between R chains that can cause tertiary structure to form?
H bonding Ionic Bonding Hydrophobic Interactions Disulfide Bonds Van der waals
All proteins have a primary structure, and most have a secondary structure. Larger proteins can have a tertiary and quarternary structure. Of these proteins, there are two main broad categories:
Globular and Fibrous
This category of proteins is somewhat water soluble, has many fxns: enzymes, hormones, membrane pumps/channels/receptors, inter and intracellular storage and transport, osmotic regulation, immune response, etc
Globular Proteins
This category of proteins is not water soluble, made from long polymers, maintain + add strength to cellular and matrix structure
Fibrous proteins
_____ proteins are mostly comprised of secondary structure
_____ proteins are mostly comprised of tertiary structure
Fibrous
Globular
DNA is a polymer of ______
nucleotides
What are the parts of a nucleotide?
Nitrogen base, five carbon sugar deoxyribose, and a phosphate group
What are the purines?
What are the pyrimidines?
Adenine, guanine = purines
cytosine, thymine = pyrdimidines
Which nitrogen base pair has 3 H-bonds?
Which has two?
C-G
A-T
What is the name for a nucleic acid structure which is only comprised of a sugar and nitrogen base?
nucleoside
DNA is comprised of two ANTIPARALLEL/PARALLEL strands of a double helix
Antiparallel
RNA is a polymer of nucleotides that contain ___, not ____
What nitrogen base is replaced by uracil in RNA?
ribose, not deoxyribose
Thymine (pairs with adenine)
Is RNA usually single or double stranded
RNA is usually single stranded
What are the 4 principles of cell doctrine/theory?
- All living organisms are composed of one or more cells.
- The cell is the basic unit of structure, function, and
organization in all organisms. - All cells come from preexisting, living cells. 4. Cells carry hereditary information
This theory proposes that self-replicating ribonucleic acid (RNA) molecules were precursors to current life (based on deoxyribonucleic acid (DNA), RNA and proteins).
RNA world hypothesis
RNA STORES GENETIC INFORMATION like DNA and CATALYZES CHEMICAL REACTIONS like an ENZYME protein, so it may have played a major step in the evolution of cellular life.
RNA is unstable STABLE/UNSTABLE compared to DNA, so more likely to
participate in chemical rxns (due to its extra hydroxyl group).
RNA world hypothesis
RNA is unstable compared to DNA, due to its hydroxyl group, so it is more likely to participate in chemical reactions
What is the central dogma of genetics?
iological information cannot be transferred back from protein to either protein or nucleic acid;
DNA ->RNA -> proteins
Which type of microscopy is basic, the phase contrast doesn’t kill or stain tissue?
Light microscopy
This type of microscopy is high magnification and resolution but kills tissue (scanning and magnification)
Electron Microscopes
This type of microscopy is used to observe chromosomes during mitosis
Fluorescence microscopy
Centrifugation spins and separates liquified cell homogenates into layers based upon
Which layer is the most dense?
What’s next?
What’s next?
Density
Nuclei Layer
Mitochondria
Ribosomes
How do catalysts accelerate the rate of a rxn?
They lower the activation energy
Metabolism =
catabolism + anabolism + energy transfer
Concentration of ___ and _____ determines which way a rxn will go
Reactants and products
When the rate of forward and reverse rxns is the same, there is 0 net production, and the reaction is in
Equilibrium
Enzymes are ___ proteins that act as catalysts
They are specific for what?
Do enzymes change after a reaction?
Do they only catalyze reactions in the forward direction?
Where do substrates bind enzymes? What occurs?
Globular
Substrate
No.
No, both forward and reverse
The substrates binds at the active site. Induced fit occurs.
Cofactors are nonprotein molecules that assist enzymes usually by donating or accepting some component of a
rxn like….
These are organic cofactors that usually donate or accept electrons
electrons
Coenzymes
Are vitamins coenzymes or metallic ions?
Inorganic cofactors are usually _____
If metal ions bind covalently, it becomes a
Coenzymes
metal ions
Prosthetic group
This is a common source of activation energy
How is new ATP formed (what reaction)?
ATP
Phosphorylation
ATP is formed from _______ + phosphate using energy from an energy rich molecule like _____
ADP
Glucose
Is ATP potential energy?
No, but it contains potential energy
These are enzymes that have both an active site for substrate binding and an allosteric site for the binding of an allosteric effector (activator or inhibitor)
Allosteric Enzymes
This is a substance that mimics the substrate and thereby inhibits the enzyme by binding the active site.
It’s effects can be overcome by
Competitive Inhibitor
Increased substrate concentration
What changes with competitive enzymes?
Kmax is increased, Vmax is unaffected
This is a substance that inhibits enzyme binding by binding elsewhere than the active site of an enzyme, the substrate can still bind.
Noncompetitive Inhibition
What changes in noncompetitive inhibition?
Km is unchanged, Vmax decreases
This is the property of enzymes where the enzyme becomes more receptive to additional substrate molecules after one substrate molecule attaches to an active site
What class of structures is this usually seen in?
What was the example in class?
Cooperativity
Quaternary - enzymes with multiple subunits that each have an active site
Hemoglobin (NOT myoglobin)
