Quiz 1 - Biochem (Basics) Flashcards
What is Biochemistry?
A field that bridges bio and chem, studying the chemistry of the molecules that make life possible
What are the chemical foundations of life?
Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur
What do the six important elements provide?
Provides the underlying structure of the biological molecules (carbohy, proteins, lipids, nucleic acids)
Explain the classifications for InTRAmolecular bonds
-Covalent Bonds (sharing); polar (unequal), non-polar (equal)
-Ionic Bonds (transfer)
What are organic molecules?
Organic molecules are CARBON BASED, (involve carbon atoms bonded to each other and to Hydrogen (also maybe N,O,P,S)
What are chemical bonds?
The attraction between atoms
What are the types of chemical bonds
-InTRAmolecular bonds (within mol)
-InTERmolecular bonds (between mol)
What is the difference between Covalent and Ionic Bonds?
Covalent bonds involves the sharing of electrons to achieve stable valence shells, and this is between non-metals. Whereas Ionic bonds involves the transfer of electrons between atoms to achieve stable valence shells. metal-nonmetal.
Define Electronegativity
A measure of how strongly an atom attracts electrons.
What are the electronegativity rules?
If the electronegativity difference is:
0 - 0.5 = non-polar cov
0.5 - 1.7 = poalr cov
> 1.7 = ionic
What factors determine polarity?
- Geometry; sym vs asym
- Bond Polarity (elecneg diff)
Explain a water molecule in terms of polarity
in a water molecule, the oxygen atom is much more electronegative than the hydrogen atom, thus the electron pair is pulled more towards oxygen, making the O partially negative, leaving the H partially positive.
Why is Polarity important in bio?
-It affects physical properties of a substance - eg. solubility “LIKE DISSOLVES LIKE”
- Determines strength and type of intermolecular attraction between molecules
How do you determine polarity?
It depends on bond polarity and molecular shape
-Sym arrangement of polar bonds will result in a nonpolar mol (dipoles will cancel)
-asym arrangement of polar bonds will result in polar mol
explain the number of bonds an atom forms
- Relates to the number of electrons needed to fill the valence shell
Single = 1 shared pair of val elec
Double = 2 shared
Triple = 3 shared
Do ionic bonds have structural diagrams? Why or why not?
Ionic compounds do not share electrons, there is no covalent bonds- so NO structural diagrams
How is Lewis-d-d diff from bohr?
It only shows the valence electrons
What are the type of INTERmolecular bonds?
-London Forces (van der)
-Dipole-dipole
-Hydrogen Bonds
Give 4 points to explain INTERmolecular bonds
-Bonds BETWEEN molecules
-Responsible for many biological properties
-Weaker than intramolecular bonds within molecules
-Sometimes referred to as “van-der-waals interactions” (distance-dependent
Explain London forces
- Weakest intermolecular force
-Due to temporary equal distribution of electrons as they randomly move about nuclei forming temporary dipoles
-only forces that hold non-polar molecules together
Explain Dipole-dipole interactions
-Stronger than London Forces (weaker than ionic of covalent bonds)
-partial positive of one molecule attracts partial negative of adjacent molecule
-only has a significant effect if molecules are close together
Explain hydrogen bonds
-Strongest force
-due to dipole-dipole forces that form between partially positive hydrogen of one polar molecule and the partially negative atom (usually N, O or F) of an adjacent polar molecule
What is the chemistry of water?
-Colourless, odourless, tasteless
-Exists as a solid, liquid, and gas at normal temperatures
-Highly polar
What is the difference between hydrophilic and hydrophobic
Hydrophilic means water LOVING, whereas hydrophobic is the opposite (non polar mol)
What are some bio significances of water
-Help control body temp
-Keeps eyeballs moist
-Lubricates joints
-required for photosynthesis
What are the unique properties of water?
-Water is a versatile solvent
-Water clings
-Water absorbs heat
-Ice floats
Explain how water is a versatile solvent
-More substances dissolve in water than in any other liquid
-“Like dissolves like”
-Water can dissolve ionic compounds; hydration shells
Explain how water clings
theres 2 types
COHESION - water mol cling to other water mol; result in surface tension
ADHESION: Water mols h-bond with other polar mols; result ; capillary action.
Overall; water clings through h-bonding
Explain how water absorbs heat
Water can absorb a lot of heat without a significant temperature increase because the heat first goes into breaking hydrogen bonds. Only after these bonds are disrupted can the kinetic energy of the water molecules increase, leading to a rise in temperature.
What is a specific heat capacity?
Amount of heat required to raise or lower the water temperature by 1 degree. Water has a HIGH SHC
What is the bio sig of water having a high heat capacity?
-water temp is very stable even when air temp is not
-since organisms are made of mostly water, then they too resist temp change because of its high specific heat capacity
SHC results in evaporative cooling; what is this?
-as liquid evaporates, surface that remains behind cools down
bio sig:
global climate is moderated
keeps leaves cool as water evaporates from leaves
cools organisms that pant
cools organisms that sweat
Explain the differences in water and methane
Water is polar, methane is non-polar. This means water absorbs more heat before changing state (h-bonds)
Water has a higher heat of vaporization (energy absorbed as it changes from a liquid to vapour)
Explain how ice floats
solid water is less dense than liquid water (one of few substances that are less dense as a solid than a liquid) so ice floats.
How does water become ice; explain density.
at 0 degrees, kinetic energy decreases and molecules become locked in a “crystalline lattice structure” with each water molecule bonding to 4 partners. This bonding structure keeps the molecules at “arm’s length” - far enough apart to make ice ~10% less dense than liquid water
What would happen if ice was more dense than water?
ice would freeze at the bottom of oceans, making ecosystems die.
What so special about carbon?
-Great ability to form complex mol (proteins, DNA, carbohy)
-Carbon has 4 valence electrons, maiing it vv compatible
what are the major atomic components of organic mols
Carbon, Hydrogen, Nitrogen, Oxygen
What is the history of organic chem?
Prevailing early belief; VITALISM - a “life-force” outside the realm of physics or chemistry was responsible for the processes of life; believed that only living organisms could produce organic compounds because chemists could not artificially synthesize organic compounds
what is Urea
a nitrogen-containing compound found in urine
-produced when there is an excess of amino acids in body, synthesized in liver->kidney
Who was the german chemist?
Wohler. he “accidentally” made urea (an organic compund) from inorganic salts
Who was stanley miller?
a man who perfromed a classic experiment in which he found that organic molecules could arise spontaneously under conditions thought to have existed on early Earth.
what were the scientists’ results?
Organic molecules can be made from abiotic (non-living, inorganic) sources
What is mechanism?
the view that physical and chemical laws govern all natural phenomena
What are the four types of carbon skeletons?
- Length
- Branching
- Double bond position
- Presence of rings
What are hydrocarbons?
-Combos of C & H
-Non polar (not soluble in h2o; hydrophobic)
-Stable
-Very little attraction between molecules
Ex: Methane
Explain hydroxyl
- OH
-organic comp w/ OH = alcohols
-Polar due to elecneg O
-names typically end in -ol
What are the six functional groups?
-Hydroxyl
-Carbonyl
-Carboxyl
-Amino
-Sulfhydryl
-Phosphate
Explain Carbonyl
C=O
- If C=O at end mol = aldehyde
- If middle = ketone
Explain Sulfhydryl
- SH
-THIOLS
-stabilize the structure of proteins
Explain Carboxyl
- COOH
- C=O & single bond to OH
-Polar
-ACIDS
Explain Amino
- NH2
-Nitrogen w/ 2 H
-AMINES; polar
Explain phosphate
-PO4
-highly polar
-ATP
-ORGANIC PHOSPHATES
