Biochemistry Exam Flashcards
ionic bond
a chemical bond that forms due to the complete transfer of electrons from one atom to another.
The atom that gains electrons is given a negative charge, while the atom that gives up electrons is given a positive charge.
covalent bond
A covalent bond is a chemical bond that forms via the sharing (not complete transfer) of electrons.
When the electrons are shared unequally, the bond is polar covalent.
When the electrons are shared equally, the bond is nonpolar covalent.
hydrogen bond
Hydrogen bonds are intermolecular, which means they occur between two or more different molecules.
a weak chemical bond that forms when a hydrogen atom with a partial positive charge of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule
electronegativity
the attraction of an atom for the electrons of a covalent bond
(i.e. electronegativity of oxygen atom in a water molecule results in polarity)
structure of water
Two hydrogen atoms with partial positive charges joined by a single covalent bond to an oxygen atom with a partial negative charge to form H2O
Cohesion
the attraction of water molecules to other water molecules through hydrogen bonds
-causes surface tension and helps hold together the column of water being transported upwards within the xylem during transpiration
Adhesion
the attraction between water molecules and another substance due to the polarity of the water molecule
-allows water molecules to cling to the cell walls of the xylem during transpiration to resist downward pull of gravity
Moderation of Temperature
- Water freezes at 0˚C and boils at 100˚C
- due to high specific heat (1 cal/g/°C), water is a heat bank and resists changes in temperature by absorbing or losing a large quantity of heat for each degree of temperature change
- evaporative cooling allows for the molecules with the most kinetic energy to evaporate and convert to the gaseous state, cooling the surface
- maintain homeostasis in organisms, stabilization of the temperature of land and bodies of water, moderates climate
Expansion during Freezing
Water expands as it freezes and becomes less dense due to its crystalline structure formed by hydrogen bonds
- Ice floating at the top of lakes and ponds insulates the water below preventing them from freezing solid as well as allowing life to exist below the frozen surface
Solubility
the chemical property of water referring to the ability for a given substance (the solute) to dissolve in the solvent
- based on the polarity (positive and negative charge) of the molecule
- cations (+) are attracted negatively charged oxygen regions of water molecule while anions (-) are attracted to the positively charged hydrogen regions
- as a result, water molecules surround the individual ions and dissolves the solute through the formation of a hydration shell
Transport happens on three different scales:
- Transport of water & solutes by individual cells
- Short distance transport at the tissue & organ level
- Long distance transport through the xylem & phloem across the entire plant
transport by individual cells
Osmosis
- Water transport across a semi permeable membrane based on solute concentration
Water Potential (Ψ)
- A property that predicts the flow of water based on solute concentration & physical pressure
transport at the tissue & organ level
Lateral transport: Short distance movement through
plant tissues
-plasmodesmata are pores in cell walls that allow cytoplasms to fuse together in cells of the same tissue- faster transport and communication
transport over long distances
Bulk flow of fluid through the whole plant:
- Water & solutes move through the xylem
- Sugars move through the phloem
water’s pathway
Water and mineral salts from the soil enter through the root epidermis with the aid of root hairs and mycorrhizae. Water is then transported to the root cortex and then to the xylem. The transpiration-coheion-tension mechanism is the main source of water’s movement from the xylem to the leaves. Transpiration pull occurs as the oustide air has a lower water potential than the air inside the leaf. This results in diffusion of water vapor from the leaf to the atmosphere (diffusion). Lost water is replaced by water in the xylem due to
cohesion.
- transpiration requires no energy
stomata
allows gas exchange to occur, water to evaporate during transpiration
-guard cells regulate the opening and closing of stomata in response to stimuli
pH
A scale that compresses the range of H+ and OH concentrations by using logarithms. It is the negative log of hydrogen ion concentration
• pH=-log[H+]
acids
a substance that increases the [H+] in a solution by releasing H+ ions
base
a substance that reduces the [H+] in a solution by directly accepting H+ ions (weak) or dissociating to release OH- to bond with H+ ions in the solution to form H2O
buffer
a substance that minimizes changes in the concentraion of OH- ions and H+ ions in a solution by accepting or releasing H+ ions
- usually composed of weak acid and corresponding base
carbon structure
CH4
Carbon’s diversity arises from its ability to bond with four other atoms (covalent)
Tetravalence: carbon with single covalent bonds will form tetrahedrons
Carbons with double covalent bonds will form planar molecules
4 valence electrons; can bond to four other atoms
hydrocarbons
– Molecules consisting of only carbon & hydrogen
– Not found often in cells, but rather are organic
molecules have regions that are hydrocarbons
– Ex: hydrocarbon tails found in fats
Isomers
molecules with the same molecular formula but different
structures and properties
Structural Isomers
changes location of covalent bonds to create new molecules
Geometric Isomers
cis - special group on the same side
trans - special group on opposite sides
covalent bonds remain unchanged, but rather differs in the spatial arrangement and position of atoms and arrangement about a double bonds
Enantomers
differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images
Dehydration Synthesis
Monomers are connected by a dehydration reaction:
– One monomer provides the hydroxyl group & the
other provides a hydrogen to form a water molecule that is removed
- this process is repeated continuously
Hydrolysis
Monomers are removed from polymers by hydrolysis – Adding water molecules breaks the bonds between monomers
– One monomer receive the hydroxyl group & the other gets the hydrogen
monomer
the repeating units that serve as the building blocks of a polymer
polymer
a long molecule consisting of many similar or identical building blocks linked by covalent bonds
general characteristics of carbohydrates
monomer: monosaccharides
polymers: disacchardies, polysaccharides
bond type: glycosidic linkage
- 3-7 carbons with carbonyl group and multiple hydroxyl groups and many structural isomers
monosaccharides
• Use multiples of CH2O
• Glucose (C6H12O6) is essential for life due to its role in cellular respiration
• In solution, glucose & most sugars form rings
– The first carbon bonds to the oxygen on carbon 5
disaccharides
Two monosaccharides connected by glycosidic linkage
• Sucrose (table sugar) is the most common & is how plants transport carbohydrates
polysaccharides
Thousands of monosaccharides
– Storage material until hydrolyzed into sugar for cells
• Starch: plant storage made of glucose monomers; stored in plastids.
• Glycogen: human storage found in the liver and muscles
– Building material for protective structures
• Cellulose: part of the tough cell wall of plants
• Chitin: builds exoskeletons in arthropods & found in fungi cell walls
lipids
monomers: fatty acids and glycerol
polymers: phospholipids, fats, steroids
bond type: ester linkage
Little or no affinity for water due to the molecular structure
– Mainly hydrocarbons
– Smaller than traditional macromolecules
Fats
Formed through dehydration reaction of one glycerol and three fatty acids by an ester linkage
– Called triacylglycerol (triglyceride)
Saturated Fats
- have no double bonds between carbon atoms in the fatty acid chain (saturated with hydrogen).
- solid at room temperature due to the ability of molecules to tightly pack together
- animal fats (ie butter, lard)
Unsaturated Fats
- one or more double bonds formed by the removal of hydrogen atoms from the carbon skeleton
- kink in hydrocarbon chain wherever a cis double bond occurs
- liquid at room temperature
- plants and fish fats (ie olive oil, fish oil)
Energy Storage of Fats
adipose in animals
seeds in plants
Phospholipids
Glycerol with two fatty acids and a phosphate group
– Phosphate head is hydrophilic and fatty acid tail is hydrophobic
– Creates double layer in water
• Main component of cell membranes (the phospholipid bilayer)
Steroids
Carbon skeletons consisting of four fused rings
– Differentiation due to attached functional group
• Cholesterol is a steroid found in animal cell membranes
– High levels in the blood leads to cardiovascular disease
• Sex hormones are steroids that acts as messengers
– Testosterone & estrogen
Proteins
monomers: amino acids
polymers: polypeptides
bond type: peptide bond
One or more polypeptides folded into a specific
conformational shape
Protein function
– Structural support – Storage – Transport – Hormonal – Cellular communication – Movement – Defense against foreign substance – Speed up chemical reactions (enzymes)
Proteins have • Incredibly diverse structures & functions due to _____________________________
three dimensional shape
nonpolar and nonpolar amino acids form
hydrophobic interactions (Van der Waal)
polar and polar amino acids form
hydrogen bonds
positively charged base and negatively charged acid form
ionic bonds
sulfhydryl interacts to form
disulfide bridge
amino acid structure
– Amino acids (with an amino & carboxyl group) are the
monomers
– It is the side group (R) that determines the behavior of the amino acid
– All proteins are made from 20 amino acids
nonpolar amino acids
carbon and hydrogen
ie methyl
polar amino acids
hydroxyl and carbonyl
negatively charged acidic
carboxyl group
positively charged base
amino group
Amino acid polymers
A peptide bond is formed between two amino acids
– Carboxyl group bonds with amino group of the next amino acid
Protein Structure: Primary
The unique sequence of amino acids
Protein Structure: Secondary
Folds & coils in the polypeptide chain due to hydrogen bonds between repeating sections
- α helix
- β pleated sheet
- due to attraction of negatively charged carboxyl group and positively charged amino group
Protein Structure: Tertiary
Overall shape of the polypeptide due to the interactions between side chains (R groups)
- Hydrophobic interactions
- Disulfide bridges
- Ionic bond
- Hydrogen bond
Protein Structure: Quaternary
-same type of interactions as tertiary structure
Two or more polypeptide chains create one protein
Denaturation of Proteins
• The environment can impact the conformation of protein causing denaturation
– pH
– Salt concentration
– Temperature
