Biochemistry Flashcards
1
Q
Essential elements
A
Carbon (c), Hydrogen (h), Oxygen (o), Nitrogen (n) –> 96% of all living matter
Phosphorus (p), Sulfur (s) –> other 4% (CHONPS)
2
Q
Molecules
A
Compounds compromised of ONLY nonmetals helf together by COVALENT bonds
3
Q
Covalent bonds
A
bond of life (strongest bond), intramolecular force (atoms within molecules)
4
Q
Polar Covalent Bonds
A
cheat : any bond between H & N, O, and F, electrons are shared unequally between two nonmetals, LARGE difference in electronegative
5
Q
Nonpolar Covalent Bonds
A
electrons shared equally, similar ectronegativity
6
Q
Electronegativity
A
Tendency of an atom to attract electrons to itself when it’s bonded to another atom
7
Q
Weak Bonds
A
intermolecular force, attractions between different molecules, short term attachment (most important = Hydrogen bonds)
8
Q
Hydrogen Bonds
A
formed between polar molecules, H atom and the O, F, or N of a second polar molecule, strongest of the weak bonds
9
Q
Molecules of Life
A
water, carbohydrates, proteins, lipids, nucleic acids (not only organic but are POLYMERS)
10
Q
Organic Molecules must have…
A
At least one C-C bond
11
Q
Water Structure
A
polar covalent molecule, high electronegativity (h+, o-)
12
Q
Water’s H-bonding
A
H-bonds form between pos H atoms of one polar molecule and the neg O atoms of neighboring H20 molecules (extensive h-bonding gives water its unique structure & properties that are needed for life on earth)
13
Q
Unique Water Properties (4)
A
- cohesion and adhesion
- Medium of life (facilitates the chemical processes of cells)
- Moderates Temperature (result of its specific heat of vaporization)
- Surface Tension (facilitates the processes (chemical reactions) of cells)
14
Q
Cohesion
A
When two of the SAME polar molecules form H-bonds with each other
15
Q
Adhesion
A
when two DIFFERENT polar molecules form H-bonds with each other
16
Q
Because of cohesion water…
A
H20 molecules H-bond to each other and resist being pulled apart
17
Q
Because of adhesion water…
A
H20 molecules H-bond to other polar molecules or charged particles and resist being pulled apart
18
Q
Capillary Action
A
COHESION & ADHESION create a continuous water column from the roots to the leaves, responsible for the movement of H20 against gravity from soil to the leaves of the plant for photosynthesis, water enters through microscopic veins in roots and then travels up to the leaves as H20 molecules are being evaporated off the surface of a leaf
19
Q
Medium of Life
A
H20 is the solvent of life - most of the important molecules are polar and therefore soluble, H2O facilitates the movement of materials across cell membranes (allows for diffusion and osmosis), buffers chemical reactions of cells (allows cells to resist changes in pH)
20
Q
Water Moderates Temperature
A
H2O can resist changes in temperature as a result of its high specific heat and heat of vaporization
21
Q
Cohesion between water molecules = ___ specific heat
A
HIGH
can absorb a great deal of E without a significant increase in temperature as most of the absorbed used to disrupt H-bonds between the H2O molecules
22
Q
Cohesion between water molecules = high heat of _____
A
VAPORIZATION
H2O molecules have to absorb a high amount of heat E in order to change from liquid phase to a gaseous state as most of the E absorbed must first be used to break the H-bonds between the H2O molecules
23
Q
How does water help regulate Earth’s temperatures?
A
most of the solar E absorbed is utilized to heat large bodies of water (high specific heat, high heat of vaporization)
24
Q
Evaporative Cooling
A
Organisms are composed mainly of H2O therefore they can moderate (resist sudden changes) their temperatures (evaporation of water to cool organisms)
exs. sweating in humans, urohydrosis in birds, licking in Kangaroos
25
Ice is ____ dense than H2O
LESS
frozen water molecules spread apart into a lattice --> creates air spaces in the solid ice
h2o expands as it solidifies (*ICE FLOATS*)
26
Surface Tension
the surface of liquid water exposed to the air is difficult to puncture --> cohesion between water molecules slows evaporation of water from a large body of water --> allows for the continued presence of large bodies of water on Earth (also allows water to bead up on waxy surfaces ex. leaves)
27
Importance of Carbon
only true nonmetal that has 4 valance electrons
can have a maximum of 4 covalent bonds around it
28
Organic Molecules
Molecules that contain at least one C-C bond (carbons covalently bonded to each other)
29
Diversity of Carbon Molecules
*carbon tends to bond to itself in long chains that form the skeletons of organic molecules*
1. carbon chains may very in length
2. can very in shape - either straight, branched or arranged in rings
3. can have multiple bonds (double & triple) that very in number and location
30
Carbon Skeleton Attachments
distinctive properties of an organic molecule depend not only on the arrangement of the carbon skeleton but also on the attachments to that skeleton
attachments are required to complete the octet for each carbon atom most common attachment is Hydrogen
31
Functional Groups
Specific groups of atoms that attach to the carbon-hydrogen core of organic molecules and help to give the molecules particular function
* most of the cell's molecules have 2 or more different functional groups
32
Hydroxyl group
(-OH) - functional group
can be found at a terminal carbon or within the chain
33
Carbonyl Group
(-CO) - functional group
can be found at a terminal carbon or within the chain
34
Amino Group
(-NH2) - functional group
35
Carboxyl Group
(-COOH) - functional group
O = C - OH
ONE carbon simultaneously DOUBLE BONDED to oxygen and bonded to a hydroxyl group
can ONLY be found at a terminal carbon
36
Sulfhydryl group
(-SH) - functional group
can be found at a terminal carbon or within the chain
form DISULFIDE BONDS
- special covalent bonds that are found ONLY in proteins
37
Phosphate Group
(-PO42-)
NEGATIVELY charges
can be found at a terminal carbon or within the chain
38
Importance of functional groups
help to give each type of molecule its distinctive properties
allow molecules to form WEAK BONDS with other molecules
most functional groups are POLAR (hydrophilic) --> makes the molecules with these attachments POLAR
POLAR molecules can H-bond to other POLAR molecules which allows POLAR molecules to attach temporarily
39
Molecular Shape
all molecules have SPECIFICITY (characteristic 3D shape)
result of carbon skeleton and functional groups
40
Isomers
molecules that have the SAME chemical formulas but DIFFERENT arrangements of atoms (structure) and therefore different properties
a.k.a same chemical formula + different arrangements = different properties
41
Structure defines function
structure = function
shape of a molecule DETERMINES its function
42
If the shape of a molecule changes then the function...
changes
43
The molecular shape is crucial to ...
molecule recognition
44
if different molecules are complementary in shape they...
interact
ex. receptors and hormones
45
Polymers
Biological molecules are composed of covalently bonded smaller molecules called MONOMERS
Chains of monomers COVALENTLY BONDED
varying length and sequence of monomers = different polymers (DIVERSITY)
*larger polymers are also known as MACROMOLECULES*
46
Monomers
Small organic molecules (C2-C6)
building blocks of polymers, every type of polymer has a limited # of monomers
47
Properties to ALL polymers (3)
1. composed of a limited set of unique monomers
2. synthesized by joining monomers together via a chemical reaction called DEHYDRATION SYNTHESIS
3. broken down into monomers by adding water molecules via a chemical reaction called hydrolysis
48
Dehydration Synthesis
Chemical reaction used to join together monomers and create polymers by removing H2O molecules
results in the loss of an H2O molecule between reacting monomers - *special covalent bond is formed*
ratio of H2O molecules removed to # of special covalent bonds formed is 1:1
cells can create infinite # of DIFFERENT polymers - by changing # or sequence of monomers
49
The ratio of H2O molecules to number of monomers
The number of water molecules released by dehydration synthesis is always one less than the TOTAL number of monomers joined together
50
Covalent bonds created via dehydration synthesis are ____ , why?
SPECIAL
made by removing water and thus can be broken by adding water
51
Hydrolysis
A chemical reaction that breaks down polymers into monomers by the addition of H2O molecules
*monomers remain intact because it ONLY breaks the special covalent bonds formed via dehydration synthesis*
52
PROTEINS ***
True polymers
Contain C,H,O,N and sometimes S
the most structurally sophisticated molecules - instrumental to ALL LIFE PROCESSES
53
Types of Proteins
structural proteins, storage, transport, hormonal, receptor, contractile/ motor, enzymes (catalysts that speed up reactions)
54
Protein Monomer =
Amino Acids
55
Amino Acids
Need 4 bonds to be stable
C2 molecule
Amino group (NH2) attached to one carbon
56
Variable side chain attachment is the ____
R group
attached to the same carbon with the amino group
57
Types of amino acid side chains
nonpolar - hydrophobic, uncharged side chains
polar - hydrophilic, uncharged side chains
basic - hydrophilic positively charged side chains
acidic - hydrophilic, negatively charged side chains
58
Peptide Bonds
Covalent bond created via dehydration between amino acids
formed between the carboxyl end of one amino acid and the amino group of a second amino acid
** TO RECOGNIZE** - look for a carbon double bonded to an oxygen next to a nitrogen
59
Protein Structure
MOST structurally sophisticated
chains formed together by peptide bonds must FOLD to create a unique 3D structure required for function
60
Primary Structure
Unique amino acid sequence held together by peptide bonds (covalent bonds)
what DNA codes for
61
Secondary
A - helix or B - sheet (can have both within a certain protein)
caused by H-bonding between the carboxyl and amino groups
does NOT involve the R-groups of the amino acids
62
Tertiary
when single polypeptide chain forms a globular shape
result of mainly weak bonds between the r groups of the amino acids
hydrogen bonds
disulfide bonds (bridges) can form between cysetine side chains holding a folded polypeptide in place
*MINIMUM LEVEL OF STRUCTURE THAT MUST BE ACHIEVED TO HAVE FUNCTION*
63
Quarternary
aggregation (clustering) of two or more different polypeptides
result of weak bonds (mostly h) between the polypetide chains
64
Denaturation
*proteins*
most of protein shape is determined by weak bonds (h-bonds) and therefore heavily influenced by environment
can occur when exposed to pH alterations, high salt concentration, or HIGH TEMPS
proteins have limited capacity to renature
65
When a denatured protein has unraveled and lost it's shape it has become ____
biologically inactive
66
Denaturation only breaks weak bonds so when a protein denatures it loses _____ structure
4, 3, or 2
67
Chaperones
proteins that assist the folding of other proteins into their 3 shape
can be used after denaturing OR when a protein is newly synthesized
**NOT available for all proteins**
68
What happens to proteins during a fever?
Body increases temperature to speed up the creation of white blood cells (immune system cells) to fight infection (bacterial or viral) --> the longer the body
69
Cytoskeleton Microtubules
*big*
largest cytoskeleton fiber
can be created & disassembled
are what compose cell fibers during cell division
compose flagella and cillia
provide tracks for motor proteins
70
Intermediate Filaments
*medium*
intermediate cytoskeleton fiber
permanent structures
involved in maintaining cell shape and anchoring organelles
71
Microfilaments
Narrowest cytoskeleton fiber
can be created and disassembled
involved in muscle cell contraction
72
CARBOHYDRATES
true polymers *limited set of monomers, created by dehydration synthesis, broken down by hydrolysis*
composed of C,H,O in a 1:2:1 ratio
- ose ending
often known as sugars and starches
73
3 major biochemical functions of carbohydrates
1. Immediate source of energy
2. Glucose storage
3. structure
74
Carbohydrate Monomers
MONOSACCHARIDES
glucose, fructose, galactose, riose, deoxyribose
most common = glucose (C6H12O6)
75
Glycosidic Linkage
Special covalent bond between two monosaccharides via dehydration synthesis
(covalent bond - weakest of the strong bonds)
76
Carbohydrate Polymers
Disaccharides, Polysaccharides
can be either linked or branched
77
Disaccharides
Two monosaccharides joined together by glycosidic linkage (created by dehydration synthesis)
IMMEDIATE e-source for cells
sucrose, maltose, lactose
78
Polysaccharides
HUNDREDS of monosaccharides joined by GL created by DS
function in GLUCOSE STORGE or CELL STRUCTURE
79
Polysaccharide examples
Cellulose - structure, plant cell walls
Chitin - structural, strengthens exoskeletons in insects and fungal cell walls
Glycogen - animal GLUCOSE STORAGE stored
in liver & muscle cells
Starch - plant glucose storage potatoes and grains
80
LIPIDS
mainly C,H,O and sometimes P
diverse group of molecules
NOT all are considered true polymers, NO true monomers
81
"sort of" monomers in lipids
FATTY ACIDS & GLYCEROL
only found in 2/3 lipid families
82
The unifying lipid property is:
LIPIDS ARE HYDROPHOBIC
extremely NON-POLAR
mainly chains/rings of HYDROCARBONS
comprised entirely of non-polar covalent bonds
83
Glycerol
lipid "monomer"
3 carbon chain that contains 3 hydroxyl groups
84
Fatty Acids
lipid "monomer"
long hydrocarbon chain with a carboxyl group
85
fatty acids that contain ONLY single bonds between C atoms are :
SATURATED
86
fatty acids that contain DOUBLE bonds between C atoms
UNSATURATED
contain at least one double bond between Carbons
create a kink wherever there is a double bond
87
Ester Linkage (BOND) * lipids*
Covalent bond created via DS between the glycerol (hydroxyl group) and the fatty acid (carboxyl group)
88
Triglycerides
true polymer
created by dehydration synthesis using 3 fatty acids and 1 glycerol
major function - LONG TERM E STORAGE
89
Triglycerides are held together by ____ ester linkage bonds
3
removes 3 H2O molecules (E-Linkage created by dehydration synthesis)
90
Triglycerides FATS:
trig in animals
solid @ room temp
ONLY saturated fatty acids (fatty acids stack close together)
91
Triglycerides OILS:
trig in plants
liquid @ room temp
unsaturated fatty acids - the kinks from the unsaturated fatty acids prevents the fatty acids from stacking close together
92
Nutrient Polymers we Consume
Carbohydrates, proteins, fats (triglycerides)
93
Triglyceride = ____ + __ fatty acids
while
Phospholipids = ______ + __ fatty acid tails
GLYCEROL & 3
PHOSPHATE HEAD & 2
94
Phospholipids
Major component of ALL biological membranes
modified polymer (only PARTIALLY created by DS)
1 glycerol molecule attached to 2 fatty acids & a phosphate group
95
Phospholipids have a ___ head:
HYDROPHILIC
polar - negatively charged phosphate group
comprised of the glycerol + phosphate
96
Phospholipids have _____ tails:
HYDROPHOBIC
non-polar - fatty acid hydrocarbon chains
tails comprised of the fatty acids
97
STEROIDS
NOT a polymer (not created by DS)
functions: animal cell membrane, cell communication as hormones
c-skeleton of 4 fused rings
98
Cholesterol
most Abundant steroid in humans
ONLY steroid utilized in animal cell membranes
99
NUCLEIC ACIDS
C,H,O,N, & P
True polymers - limited monomers, created via dehydration synthesis, broken down by hydrolysis
functions: store & transmit hereditary info, high E molecules
100
Nucleotides
Nucleic acid monomer
3 component structure:
1 - 5-carbon sugar (Deoxyribose)
2 - phosphate group @ the 5'C
3 - nitrogenous base (A,T,C,G) @ the 1'C
** ONLY distinction between a nucleotide & nucleic acid is the nitrogenous base**
101
Nitrogenous Base Categories
Purines = 2 fused carbon rings that contain N atoms
- Adenine & Guanine
Pyrimidines = one carbon ring that contains N atoms
- cytosine, thymine, uracil
102
Phosphodiester Bond
Covalent bond formed between 2 nucleotide during DS
3' Carbon of one phosphate and the phosphate 5' carbon of a second nucleotide
103
Types of nucleic acids
DNA, RNA, ATP
104
DNA
DEOXYRIBONUCLEIC ACID
true polymer
CODE FOR PROTEINS
5-carbon sugar in nucleotides is DEOXYRIBOSE
contain ONLY the nitrogenous bases
AGTC
105
DNA has a ____ stranded helix
DOUBLE
each strand has a sugar-phosphate backbone held together by PHOSPHODIESTER bonds
strands are ANTIPARALLEL one 5' --> 3' other is 3' --> 5'
106
DNA strands are held together by _____ bonds
H-BONDS
between the bases
107
purine to pyrimidine pairs are called ____
COMPLEMENTARY BASE PAIRING
108
purine = pyrimidine
A = __
__ = C
A = T
*held together by 2 hydrogen bonds*
G = C
*held together by 3 hydrogen bonds*
109
RNA
RIBONUCLEIC ACID
true polymer
involved in protein synthesis
SINGLE strand
5-carbon sugar in nucleotides is RIBOSE
nucleotides contain
AGCU
110
ATP
ADENOSIN TRIPHOSPHATE
modified nucleotide
5-c sugar = ribose
nitrogen base adenine
3 phosphate groups
made by cellular respiration or fermentation
E molecule of life because it contains high E bonds (phosphate - phosphate bonds)
