Unit 2 Biochemistry Flashcards
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<p>Cations</p>
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<p>= positive ions with more protons then electrons</p>
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<p>Anions</p>
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<p>= negative ions with more electrons then protons</p>
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<p>Beryllium Bohr Short form</p>
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<p>Be 2e-)2e-</p>
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<p>Sulphur Bohr short form</p>
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<p>S 2e-) 8e-) 6e-</p>
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<p>3 Main types of Intramolecular bonds:</p>
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<p>-Ionic (electron transfer)
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<br></br>-Covalent (two or more non metals share one or more pairs of electrons)
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<br></br>-Polar covalent (a covalent bond that occurs when there is an unequal sharing of electrons causing a dipole - the molecule has a positive and negative pole)</p>
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<p>Ionic Bonds</p>
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<p>= typically between metals and non metals, always a transfer of electrons from one atom to another that results in stable bonding For both atoms.</p>
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<p>Covalent bonds</p>
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<p>= when two or more NON METALS share one or more pairs of electrons. Results in a stable electron arrangement in their outer orbit.</p>
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<p>Polar Covalent Bonds</p>
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<p>= covalent bond that occurs when there is an unequal sharing of electrons. When one atom pulls stronger than the other, resulting in different polar charges at the ends of the molecule (aka DIPOLE)</p>
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<p>Dipole</p>
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<p>= molecule with one end slightly positive and the other slightly negative. The more electronegative an atom, the stronger they are at pulling the electrons to them. The higher electronegative atom will be the one slightly negative.</p>
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<p>3 Types of Intermolecular Bonds</p>
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<p>- London dispersion forces / van der Waal forces
<br></br>- Dipole-Dipole
<br></br>-Hydrogen bonding</p>
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<p>London forces</p>
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<p>= all molecules have them, very weak forces of attraction, momentary dipoles are created by the electrons in the compound that are constantly emotions. Which are constantly in motion (WEAKEST intermolecular force)</p>
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<p>Dipole-dipole forces</p>
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<p>= MEDIUM hold polar molecules together, the opposing dipoles attract</p>
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<p>Hydrogen bonding</p>
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<p>= STRONGEST formed between electropositive hydrogen dipole and an electronegative dipole of oxygen, chlorine or fluorine</p>
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<p>4 Main Types of Biochemical Reactions</p>
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<p>- hydrolysis
<br></br>-condensation
<br></br>-redox reactions
<br></br>-neutralization</p>
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<p>Hydrolysis</p>
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<p>a reaction that uses water to help break down molecules. Examples such as carbohydrate lactose into galactose glucose, or protein to amino acids (in presence of enzymes)</p>
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<p>Condensation</p>
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<p>= when two molecules combine together to form one molecule. OFTEN water is produced, which is why it’s also known as dehydration synthesis. Examples being an upstream amino meets a downstream amino acid to create protein and water.</p>
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<p>Redox Reaction</p>
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<p>an electron transfer between two substances (an oxidation and reduction process)</p>
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<p>An important redox reaction used by animals to make energy</p>
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<p>CELLULAR RESPIRATION, combines glucose and oxygen to produce carbon dioxide, water and energy (ATP)</p>
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<p>Neutralization</p>
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<p>= an ACID and a BASE reaction to produce water and a salt. Happens often in digestive system.</p>
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<p>Oxidation</p>
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<p>= process of losing electrons</p>
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<p>Reduction</p>
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<p>= process of gaining electrons</p>
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<p>what are 3 molecules that PURE water contains</p>
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<p>H2O, H+ ions, and OH- ions</p>
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<p>how our hydrogen ions and hydroxide ions produce in pure water?</p>
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<p>a natural process called ionization</p>
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<p>ionization</p>
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<p>the dissociation of a molecule into ions</p>
definition of Acids
substances that when dissolved in water increase the concentration of H+ (hydrogen ions).
definition of Bases
substances that when dissolved in water increase the concentration of hydroxide ions (OH-)
4 properties of Acids
- sour taste
-conducts electricity
- Turns litmus paper red
- Has a pH below 7
4 properties of Bases
- bitter taste
-slippery feel
- litmus paper turns blue
-pH above 7
why is pure water neutral
it contains an equal number of hydrogen and hydroxide ions
acidity of an aqueous solution is expressed in terms of wht
hydrogen ion concentration in mol/L
pH is measured on a logarithmic scale expressed in this formula
pH = -log(10 subscript)[H+]
the stronger an acid or base...
the more they completely ionize when dissolve in water
weak acids and bases are
reversible and can proceed in both directions
what is the strength of most organic acid and bases
weak
when an acid and base react what is produced
a salt and water
what is the salt produced from in a neutralization reaction
the metal cations
what is the water produced from in a neutralization
non-metal anions
acid-base buffers
solutions that are able to maintain nearly constant pH levels. Despite fluctuating environmental conditions.
how do acid-base buffers maintain pH levels
by taking up excess hydrogen or hydroxide ions, neutralizing excess acid or base
examples of acid base buffers in body
-proteins (red blood cells)
- amino acids (glycine amino acid)
- carbonic acids
optimal pH level of blood
7.4
what buffer operates in blood and extracellular fluid to maintain pH level
carbonic acid-bicarbonate buffer
how is carbonic acid bicarbonate buffer made + chemical equation (give it in molecular formula as well as identify name of each molecule)
by the reaction of carbon dioxide with cater to form carbonic acid that ionizes to form bicarbonate and hydrogen
H2O + CO2 <-> H2CO3 <-> HCO-(3subscript) + H+
polymer vs macromolecule
-Polymers are mostly made up of smaller repeating units (monomers)
- Most macromolecules are due to polymerization (becoming polymer macromolecule)
- Some macromolecules are due to chemical bonding of more atoms
- main difference is that polymers contain repeating units that represent the monomers whereas not all macromolecules have a monomer in their structure.
-macromolecules are an umbrella term
name this functional group, polarity, solubility, acidtiy, general structural features
Hydroxyl group
Properties: polar, hydrophilic
Structurally the addition of an -OH group, a hydroxyl
name this functional group, polarity, solubility, acidtiy, general structural features
Sulffhydryl group
Polar, hydrophilic
Contains an SH group, sulfur with hydrogen
name this functional group, polarity, solubility, acidtiy, general structural features
Carbonyl group
polar, hydrophilic
Has a carbon double bonded to an oxygen, but the carbon is connected to 2 different sides
name this functional group, polarity, solubility, acidtiy, general structural features
Carboxyl group
acidci, polar, hydrophilic
similar to a carbonyl group, has a carbon double bonded to an oxygen, and is connected to the R group but additional a hydroxyl (OH) group
name this functional group, polarity, solubility, acidtiy, general structural features
Amino group
Basic, polar, hydrophilic
it is a nitrogen attached to R group plus two hydrogens, characterized by the presence of nitrogen
name this functional group, polarity, solubility, acidtiy, general structural features
phosphate group
acidic, polar, hydrophilic
a phosphorus attached to four oxygens (one double bond, two hydroxyls, and oxygen attached to R group)
these reactions break down
catabolic
these reactions build up
anabolic
what reaction is required to form polymers and why
condensation reaction/dehydration synthesis because water must be removed to join the molecules together
what are the four macromolecules of life
carbohydrates
proteins
lipids
nucleic acids
uses for carbohydrates
building materials for energy ; cell identification and communication
2 groups of carbohydrates + examples of each
Simple = Monosaccharides, Disaccharides, Oligosaccharides (glucose, lactose)
Complex = Polysaccharides (Starch, Glycogen, Cellulose, Chitin)
two types of monosaccharides + how they are identified
aldoses and ketoses ; identified by the location of their carbonyl functional group
the three aldoses and location of their carbonyl functional group
Ribose, glucose, and galactose [carbonyl group on the endmost carbon-opposite of hydroxyl group]
the two ketoses and location of their carbonyl group
ribulose and fructose [ carbonyl group located on the second carbon, opposite end of the hydroxyl group]
the most important monsaccharide used for immediate energy ; considered the energy currency of the body
glucose
Isomers
= same chemical formula but different arrangement of atoms and different chemical properties.
Glucose and Galactose have the same chemical formula but different arrangement of atoms - what kind of isomerism is this and what is their chemical formula
structural isomers ; C6H12O6
which molecule is this and label which is alpha and which is beta, explain the distinction of the two
glucose; the alpha glucose has the first carbon's hydroxyl group "down" or opposing the sixth carbon direction, while beta glucose hydroxyl group is "up" or same as sixth carbon direction
what form do 5 carbon or more monosaccharides take in water? when dry?
ring structures in water ; linear/chain structures when dry
what kind of sugars are usually consumed in food
disaccharides
what covalent bonds are formed to join monosaccharides together
glycosidic linkages
what does the prefix oligo mean
few
how many sugars are in oligosaccharides
about 3-10
glucose + glucose =
matltose + water
glucose + fructose =
sucrose + water
glucose + galactose =
lactose + water
name the two molecules, how you know, and what products are likely to be formed, with which type of reaction
two alpha glucose, based of position of hydroxyl. two glucose form maltose and water ; and anabolic reaction and condensation/dehydration synthesis reaction
how many monosaccharides are typically in a poly saccharides
several hundred to several thousands
4 types of polysaccharides
Starch
Glycogen
Cellulose
Chitin
2 types of glycosidic bonds
Alpha (α) + Beta (β)
describe Beta (β) glycosidic bonds
when the carbon-1 on the first carbohydrate and the carbon-4 on the other carbohydrate are covalently bonded and the -OH group on the Carbon-1 above the glucose ring
describe Alpha (α) glycosidic bonds
means that the carbon-1 on the first carbohydrate and carbon-4 on the other carbohydrate are covalently bonded and the -OH group on the Carbon-1 below the glucose ring
describe amylose and what kind of carbohydrate it is
starch molecule ; made up of a chain of glucose bonded in alpha 1-4 glycosidic links
describe amylopectin and what kind of carbohydrate it is
starch molecule ; made up of 2 by 3 branched chain of glucose bonded in alpha 1-6 glycosidic links
main energy storage for molecules
glycogen
what converts excess glucose into glycogen
muscles and liver
what is glycogen composed of
alpha1-4 links and alapha 1-6 links for branches
composed of beta 1-4 links, not coiled or branched chains, ideal building material for plants/cell walls
cellulose
undigestiable carbohydrate ; form of fibre that aids in egestion/BM ; can be used for paper or fabrics
cellulose
describe the beta 1-4 glysodic linkages in cellulose
glucose change where the glycosidic linkages are up and down of glucose as the glucose molecules are upside down every other in relation to each other
chitin is a polymer of
N-acetylglucosamine
what is the composition of N-acetylglucosamine
it a glucose molecule with a nitrogen group attached to the second carbon
this carbohydrate is used in surgical thread and exoskeletons due to strength
chitin
function and monomers of proteins, and 6 examples of them
- involved in almost everything cells do
- can be enzymes, immunoglobin, hemoglobin, keratin, fibrin etc.
- amino acid monomers
what determines the type of protein
the number of, type, and arrangement of amino acids in the protein
how many amino acids are there
20
3 distinct parts of amino acids
- amino group (NH2)
- carboxylic acid group (COOH)
- a radical/R group/side chain that disttinguishes the amino acids from one another
how does the R group in an amino acid make them different
- it can determine if the amino acids polarity/solubility and acidity
name the 9 essential amino acids and why they are essential
histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine
essential because we cant manufacture them in our cells and must obtain from our diet
Final stage of a protein
= called conformation / folded / compact
What shape generally are proteins
- globular // rolled up into balls
What is conformation the result of
- amino acid sequence it contains and how they interact with each other (molecularly/polarity)
4 Stages of Protein Structure
Primary protein structure = sequence of a chain of amino acids
Secondary Protein structure = when sequence of amino acids are linked by hydrogen bonds
Tertiary protein structure = occurs when certain attractions are present between alpha helices and pleated sheets
Quaternary protein structure = a proteins consisting of more than one amino acid chain
Polypetide chain
- simple chain of amino acids
What determines a proteins sequence of amino acids
Dna of a gene
Describe proteins in primary structure
- 1 degree structure ; simple chain of amino acids/polypeptide chain ; can be an combo (20 to the power of X)
Describe Secondayry protein structure
- 2 degree; polypeptide chain begans folding and coiling as it grows ; either alpha helix (tight coils of H bonds every 4th peptide bond) or a beta pleated sheets (hydrogen bonds formed between parallel stretches to form sheets)
Disulphide bridges
- covalent bonds between sulphur atoms ; most common bonds occuring in tertiary protein stage
Describe tertiary Protein structure
- 3 degree structure ; additional folding between pleated sheets and alpha helix chains ; caused by the varied radical groups ; disuphide bridges forms that help build the globular structure which can be the final structure
Describe the Quaternary protein stage
- 4 degree stage ; not all proteins have this ; sometimes 2 or more polypeptide chains join to make a functional protein ; this structure depends on how the polypeptides join together
Describe 5 characterstics of lipids
Group of organic molecules that dissolve in non-polar substances, but generally not in water (insoluble in water)
Efficient energy storage molecules that yield about twice the amount of chemical energy per gram that carbs or proteins
Important for physical and thermal insulation for the body, key components for cell membranes and act as raw materials for the synthesis of hormones
Mostly made up of hydrogen, carbon and oxygen
Some form chains other rings
4 Families of Lipids
- Fats ; Phospholipids ; Steroids ; Waxes
3 traits of Fats
- Most common for of energy storage and insulation in plants and animals
Composed of one glycerol and a maximum of 3 fatty acid chains
Fatty acid chain contains between 16-18 carbons and has a terminal carboxylic acid
Define and describe how a fat molecule is formed
- dehydration synthesis where hydroxyl from the glycerol combines the the H from the carboxylic acid to create ester linkage and water. This process is called esterification
Describe 4 traits each of Saturated and Unsaturated Fatty Acids
Describe the structure of a phospholipid
Describe the permeability of the phospoholipid bilayer
Sterols
= subgroup of steroids which are also lipids ; compact hydrophobic molecules containing four fused hydrocarbon rings
define Cholesterol
a sterol ; important because it affects membrane’s fluidity, provided support to membrane and acts as a messenger in cell communication during development. Can also be converted to Vitamin D. Too much cholesterol can lead to clogged arteries and cardiovascular disease.
gametes
(egg and sperm cells)
Steroids molecules of derivatives of what molecule, and examples
derivatives of - choloesterol (estradiol ; testosterone ; progesterone)
4 traits of waxes
Hydrophobic
Long-chain fatty acids linked to alcohols or carbon rings
Waxes often form waterproof coatings such as beeswax, paraffin
Used to manufacture items such as fuel, candles
4 places where nucleic acids are found
DNA (deoxyriobnucleic acid)
RNA (ribonucleic acid)
ATP (adenosine triphosphate)
Nucleotide coenzymes (NAD+, NADP+, and FAD)
Monomers of nucleic acids
- nucleotides
Describe nucleotide structure
Consist of nitrogenous base, five carbon sugar (ribose group), and a phosphate group
Phosphate and ribose groups are joined together by a phosphodiester linkage.
