Unit 1 - Biochemistry Flashcards
What is an independent variable?
- The condition manipulated by the experimenter
- Time is a common independent variable
What is a dependent variable?
- The condition that is affected by the independent variable
- What is measured/recorded
What is a control variable?
- The conditions kept the same
- Ex., temperature, group under study
What formula is used to determine the number of electrons in each shell?
2n2
Explain how you can identify protons, neutrons, and electrons in a given element
- Protons: the atomic number
- Electrons: depends on the charge; neutral = the same number as protons
- Neutrons: the mass number – the atomic number (or will be indicated)
What are ionic bonds?
Chemical bonds that occur between two elements that wish to gain or lose electrons (typically a metal and non-metal) to complete or lose an outer shell.
What are covalent bonds? Polar vs. nonpolar?
Chemical bonds that occur between two elements that wish to share electrons (typically a non-metal and non-metal) to feign completion of an outer shell.
Covalent bonds can either be polar (covalent between non-identical elements) or nonpolar (covalent between the same elements).
- Polar bonds have partial charges, depending on the element that has a stronger attraction for electrons
- Nonpolar bonds are completely neutral
What are hydrogen bonds?
Hydrogen bonds occur between hydrogen and FONS. These are all partial attractions that are created by polar bonds.
Four Properties of Water
Explain cohesion in water
Cohesion
- Water molecules form hydrogen bonds with one another, resulting in high surface tension
Four Properties of Water
Explain adhesion in water
Adhesion
- Water molecules form hydrogen bonds with other polar molecules, counters gravity by bonding to cell walls
What makes water a good temperature moderator?
Water as a Temperature Moderator (ie sweating?)
- Hydrogen bonds can absorb more eat then standard bonds due to their strong intermolecular forces
Four Properties of Water
What makes water a good solvent?
Water as a Solvent
- Often called the universal solvent, as it is polar and can break up most substances
What are functional groups?
Groups of atoms that determine the characteristics and chemical reactivity of a substance
What is an isomer?
Isomer: two molecules are isomers if they have the same chemical formula (Ex., C2H6O) but different molecular structures.
What do you call a molecule with a single bond? double bond? triple bond?
Alkane, alkene, alkyne
What is a peptide bond? State the formula.
A peptide bond is a special type of amide linkage found between 2 amino acids
(O=C-N-H)
What are “linkages”?
Functional groups of different molecules frequently interact to form bonds called linkages, which are always found in the middle of molecules.
Describe disulfide linkage
A disulfide linkage refers to the linkage formed between 2 thiols when H2 is removed
- S-S
Describe amide linkage
An amide linkage occurs when the elements of water are removed between an amine and a carboxyl group
- O=C-N
Describe an ester linkage
An ester linkage occurs when the elements of water are removed between an alcohol and carboxyl group
- O-C=O
Describe anhydride linkage
An anydrige linkage occurs when the elements of water are removed between 2 carboxyl groups
- O=C-O-C=O
Describe an ether linkage
An ether linkage occurs when the elements of water are removed between 2 alcohol groups
- Often found in carbs
- C – O – C
Define monomer and give an example
Monomer: small building blocks of polymers (ex., glucose, a monomer, makes up glycogen, a polymer)
Define polymer and give an example
Polymer: large molecules composed of smaller building blocks (ex., DNA is comprised of nucleotides)
Define thermodynamics
Thermodynamics: the study of energy flow. In biology, this is called bioenergetics
Define redox reaction
Redox reaction: oxidation and reduction reactions generally occur together, as electrons are highly reactive. As one molecule is oxidized, another is quickly reduced. These are called redox reactions.
Living System Reactions
What is condesnation?
Condensation occurs when two molecules are joined by a covalent bond by the removal of H2O
- Sign: H2O is a product, but not the only product
Living System Reactions
What is hydrolysis?
Hydrolysis occurs when large molecules are split into smaller ones by the addition of H2O
- Sign: H2O is a reactant with something else and “splits” it to create the products
Living System Reactions
What is an exothermic/exergonic reaction?
Exothermic reactions occur when energy is released/lost
- Sign: energy is a product
Living System Reactions
What is an endothermic/endergonic reaction?
Endothermic reactions occur when energy is gained/absorbed
- Sign: energy is a reactant
Living System Reactions
What is oxidation?
Oxidation occurs when any substance is combined with oxygen OR loses an electron
- Sign: oxygen is a reactant and creates a combined product OR an electron is a product
Living System Reactions
What is reduction?
Reduction occurs when oxygen is removed in a reaction OR when an electron is gained
- Sign: oxygen is a product OR an electron is a reactant
Living System Reactions
What is neutralisation?
Neutralisation occurs when acids and bases react to produce a salt and water. This is called a neutralisation reaction since the solution is no longer acidic or basic
State the four biologically important molecules
There are four types of these molecules (called macromolecules):
- Carbohydrates
- Lipids
- Proteins
- Nucleic Acids
What are carbohydrates?
Molecules that consist of C:2H:O.
There are 4 subtypes of carbohydrates:
- Monosaccharides (single sugars)
- Disaccharides (2 single sugars)
- Oligosaccharides (3-10 simple sugars)
- Polysaccharides (long chains)
Explain monosaccharides
Monosaccharides (single sugars)
- Most are classified by the number of carbons they contain (Ex., triose has 3 carbons, tetrose has 4)
- Exceptions include glucose (major energy supply for plants and animals), fructose, and galactose, which are all isomers of each other
Explain disaccharides
- Disaccharides (2 single sugars attached together via a special ether linkage called a glycosidic linkage)*
- Ex., sucrose (fructose + glucose), lactose (glucose + galactose) and maltose (glucose + glucose)
Explain oligosaccharides
Oligosaccharides (3-10 simple sugars)
Explain polysaccharides
- Polysaccharides (complex carbohydrates consisting of many monomer units forming long chains)*
- They have two major functions: structural support (ex., cellulose, chitin) and energy storage (ex., starch, glycogen)
What are lipids?
- Hydrophobic molecules consisting of C:H:O and ending in OH.
- They are involved in energy storage, hormones, and cell membranes.
There are 3 subtypes of lipids:
- Oils and Fats
- Phospholipids
- Steroids (Sterols)
Explain oils and fats
Oils and Fats
- These are produced by condensation reactions between 1 molecule of glycerol and 3 molecules of fatty acids (long CH hydrocarbon chains) (an ester linkage, ex triglyceride)
- They are the most common energy-storing molecules in living organisms
Explain phospholipids
- Phospholipids*
- These are mostly found in cell membranes and are composed of 1 glycerol, 2 fatty acids, and 1 polar nitrogen groups. The polar nitrogen head is hydrophilic (loves water) and the nonpolar fatty acids are hydrophobic.
Explain steroids
- Steroids (Sterols)*
- Steroids are composed of 4 fused “rings” with several functional groups and are synthesized from cholesterol. They function as hormones (ex., testosterone)
What are proteins?
- Proteins are composed of amino acids and possess two functional groups: amine and carboxyl.
- Proteins function as enzymes, hormones, hemoglobin, and antibodies.
There are 3-4 steps to the structure of a protein:
- Primary
- Secondary
- Tertiary
- Quaternary
Explain the steps of the protein structure
- Primary*
- This refers to the specific sequence of amino acids in the protein
- Secondary*
- This refers to the coiling or folding of the amino acid chain
- Tertiary*
- This refers to the three-dimensional globular structure (multiple folding)
- Quaternary*
- This refers to the interaction of 2 or more tertiary structures (not all proteins have this)
What are nucleic acids?
- Nucleic acids are used to store genetic information.
- They are the only molecules that can produce clones of themselves.
- Examples include DNA, RNA (helps DNA synthesis proteins), and ATP.
- Five types of nitrogenous bases are found in nucleic acids: adenine, thymine (not RNA), guanine, cytosine, Uracil (RNA’s thymine replacement) (ring like with lots of N)
Define essential amino acids
Essential amino acids are amino acids that cannot be made by the body. As a result, they must come from food.
What are catalysts?
- A molecule that speeds up the rate of a chemical reactions
- These are not consumed in the reaction; they are not reactants
- They function by reducing the required activation energy of a reaction
What are enzymes?
- Enzymes are biological catalysts, influenced by temperature, shape, pH
- They are proteins with complex and changing shapes and:
- Are highly specific about their substrate
- Their activity can be regulated (enhanced/supressed)
What two ways can a substrate interact with an enzyme?
There are two ways the substrate can interact with the enzyme: the lock-and-key model in which the substrate fits perfectly, or the induced-fit model, where the substrate is induced to fit perfectly.
What is allosteric control?
Enzymes have control sites where a specific substance can bind to and alter the enzyme shape. There are two types of these substances:
- The activator, which primes the enzyme (turns it “on”)
- The inhibitor, which distorts the enzyme (turns it “off”)
What is end-product inhibition (a.k.a. feedback inhibition)?
End-product inhibition occurs when the enzyme is switched off due to an increased concentration of the end product. There are two types of this inhibition:
- Competitive inhibition, where an end-product similarly shaped as the enzyme binds at the active site
- Non-competitive inhibition, where an end-product binds away from the active site; at the control site. This is an example of allosteric control.
Define metabolism
Metabolism: any chemical reaction in the body.
Define anabolism
Anabolism: small molecules building up into larger ones (Ex., amino acid à protein)
Define catabolism
Catabolism: large molecules breaking down into smaller ones
Define ATP
ATP: adenosine tri-phosphate - a nucleic acid. When ATP is called upon, it releases one of its 3 phosphates, becoming ADP and releasing energy for the cell. This process can be reversed.
Draw an amino acid with peptide bond
Draw glucose
Show this reaction: glycerol + fatty acids –> triglyceride
ESTER
Draw an enzyme control diagram
