Biochemistry Flashcards
Biochemistry: def
study of chemistry in living things
What are the 2 types of substances?
- Inorganic
- Molecule does not contain C + CO2 - Organic
- Molecule contains C
What are the types of organic compounds?
- Protein
- Lipids
- Carbohydrates
- Nucleic Acid (DNA)
Molecular Formula: def
shows type of elements and number of atoms
Structural Formula: def
shows arrangement of atoms in space
Monomer: def
identical or similar small sub-units
Polymer: def
larger molecules made by joining monomers
What are some strong bonds and why are they important in living organisms?
Covalent bonds: sharing of a pair of electrons between 2 atoms to join atoms in a molecule together
What are some weak bonds?
- Hydrogen Bond: weak attractions between slightly negative end of the one molecule (O, N) and a slightly positive H in another molecule (dictated by dotted lines)
- Hydrophobic Interaction: association of hydrophobic molecules or parts of molecules to each other, because they are excluded from water
- London’s Force: random movement of electrons causes momentary slight positive and negative charges in atoms causing attraction
- Ionic Bond: electrostatic attraction of oppositely charged ions
Why is water crucial for life?
- Has a high specific heat capacity
- Acts as a solvent by surrounding ions or polar molecules
- As the particles slow down and get closer, they repel
- Sticks together (cohesion)
Which types of molecule are hydrophilic?
- Ionic compounds
- Dissociate into ions
- Ion-dipole attraction - Polar covalent compounds
- Anything charged (sugars, alcohols)
Which types of molecules are hydrophobic?
- Large nonpolar molecules
- Fats and oils - Smaller nonpolar molecules are only slightly soluble in water
- Oxygen gas and carbon dioxide gas
What happens when water autoionizes?
One water molecule transfers an H+ ion to the other, resulting in OH (aq) and H₃O (aq)
What is an acid?
- Dissociates to release H+
- Increases cocnentration of H3O
- Sour
What is a base?
- Dissociates to form OH
- Increases the concentration of OH
- Bitter
- Slippery
What is an indicator and what are some examples?
A substance that changes colour as the concentration of H and OH changes
- Litmus paper
- Phenophthalein
- Universal indicator
What do acid-base buffers do?
- Resists change in pH when acid or base is added
- Absorbs protons from acids
- Releases protons upon the addition of a base
What are some examples of acid-base buffers?
- The pH of blood is 7.4
- eg. Bicarbonate (HCO3) buffers the pH levels in order to make sure the body functions properly
- eg. Protein
What is the basic structure of an organic molecule?
- Carbon backbone (R) with functional groups attached (CₓHᵧ)
- Carbon has 4 valence electrons so can form chains, branch chains, and rings
Functional Group: OH
Hydroxyl
- Alcohols (eg. Ethanol)
R-O-H (bent)
Functional Group: O=C
Carbonyl
- Aldehyde/Ketone (eg. Formaldehyde, acetone)
C; -R, =O, -H
C; -R, =O, -R
Functional Group: COOH
Carboxyl
- Organic Acids (eg. Citric Acid)
C; -R, -OH, =O
Functional Group: NH2
Amino
- Amines (eg. Amino Acids)
N; -R, -H, -H
Functional Group: SH
Sulfhydryl
- Thiols
R - S - H (bent)
Functional Group: PO4
Phosphate
- Phospho (eg. Phospholipids, nucleotides)
O; -R, -P-O negative, =O, -O negative
Is ionic bonding weak?
Yes, in living organisms as the ions just dissociate
What can perform the condensation/hydrolysis reaction?
Also, what to remember to draw?
- Hydroxyl and Carboxyl
- Phosphate in low pHs can pick up H
- Hydroxyl and Hydroxyl
- Carboxyl and Carboxyl
- Amino and Carboxyl
- Amino and Hydroxyl
DRAW WATER!
What is a dehydration synthesis reaction?
Formation of covalent bond through loss of water molecule used to join monomers
What is hydrolysis?
Addition of water to break covalent bond between monomers
When do linkages form?
Formed when 2 functional groups undergo a condensation reaction
Why are linkages important?
Links units of organic molecules into macromolecules that make up living organisms
Ether: functional groups, molecules found in
- Hydroxyl and Hydroxyl
- Ethers
Glycosidic: functional groups, molecules found in
- Hydroxyl and Hydroxyl (sugars)
- Dissacharides + Polysaccharides
Ester: functional groups, molecules found in
- Hydroxyl and Carboxyl
- Fatty Acids + Phospholipids
Phosphodiester: functional groups, molecules found in
- Hydroxyl and Phosphate
- Nucleic Acids + Phospholipids
Peptide: functional groups, molecules found in
- Carboxyl and Amino
- Proteins
What is the structure of carbohydrates?
- C, H, O
- Ratio of 2 H: 1 O
- Hydroxyl and Carbonyl (aldose sugar at end, ketose sugar in the middle)
What are the functions of carbohydrates (3)?
- Source of energy for cells
- Cell identity marker on membranes
- Form cell walls in plants or exoskeletons in anthropods
What is a monosaccharide (carb)?
- Single unit sugars
- Those with 5+ carbons form ring structures when dissolved in water
What are some examples of monosaccharides?
Ribose (RNA), deoxyribose (DNA), glucose (energy, structure), ribulose (photosynthesis)
What are glucose’s 2 isomers?
Fructose, galactose
What is a dissaccharide (carb)?
- 2 unit sugars
- Two monosaccharides joined in a dehydration synthesis reaction, forming glucosidic linkage
How do you make maltose, sucrose, and lactose?
Glucose + Glucose = Maltose + water (alpha 1,4)
Glucose + Fructose = Sucrose + water (alpha)
Glucose + Galactose = Lactose + water (beta 1,4)
What is a polysaccharide (carb)?
- Many units of sugars (polymer) joined in a dehydration synthesis reaction, forming glycosidic linkage
- Polar, hydrophillic
- Can’t dissolve easily
How do animals and plants access the glucose from polysaccharides?
Animals and plants possess amylase which breaks the alpha 1,4 glucosidic linkages from end of molecule + a second that breaks the alpha 1,6 glycosidic linkages allowing the glucose to be used as fuel
What are examples of polysaccharides?
Amylose (starch) Amylopectin (starch) Glycogen Cellulose Chitin
What is Amylose?
- Straight chain polymer
- Alpha gluclose in alpha 1,4 glycosidic linkage
- In plants
What is Amylopectin?
- Branched chain polymer
- Alpha glucose in alpha 1,4 and 1,6 glycosidic linkages
- In plants
What is Glycogen?
- Highly branched chain polymer
- Alpha glucose in alpha 1,4 and 1,6 glycosidic linkages
- In animals
How do you test for carbohydrates?
- Starch turned black in the presence of iodine solution
- Sugar turns red in the presence of Benedict’s solution when heated
What is the basic structure of a lipid?
- Not a polymer
- Consist of C, H, O
- Lots of H: little O
- Hydrophobic
What are some examples of a lipid?
Fats, oils, wax, hormones, cholestorol
Which of the macromolecules are polymers?
All but lipids
Tell me about saturated fatty acids; their structure, their source, and their room temperature
- Carboxyl + hydrocarbon in ester linkage
- Animal sources
- Only single bonds
- Straight so can stack and form many London forces
- Solid in room temperature
Tell me about UNsaturated fatty acids; their structure, their source, and their room temperature
- Carboxyl + hydrocarbon in ester linkage
- Plant sources (and fish oil)
- C=C causes a bend in C chain so they don’t stack closely
- Few London forces between molecules because of less interaction bt molecules
- Liquid at room temp
What do fats do, and how are they made?
- Involved in energy storage
- Dehydration synthesis reaction between a glycerol molecule and a fatty acid
What is the structure of a triglyceride?
Dehydration synthesis between glycerol and 3 fatty acids
What is a glycerol?
Alcohol with hydroxyl
What is the structure and function of a phospholipid?
2 fatty acids in ester linkage to hydroxyl + phosphate group attached to nitrogen group in phosphodiester linkage to hydroxyl
It is amphipathic and crucial for cell membranes
What is the structure, some examples, and function of a steroid?
- 4 carbon rings in their structure, not dehydration synthesis
- eg. Steroid hormones, cholesterol
- Crucial for cell membrane and hormones
How does soap work?
Hydrophobic end faces grease to emulsify it
Hydrophillic end faces out and washes away water
How do you test for fats?
Paper becomes translucent
What is the structure of proteins?
Monomer amino acids joined in peptide linkage via dehydration synthesis to form peptides
Composed of amino group and carboxyl attached to central carbon
Distinguished between R groups
What are the different groups of amino acids?
- Electrically charged: form ionic bonds
- Polar: form H bonds
- Nonpolar: hydrophobic interaction hold R groups together
- Thiol Containing: Sulfhydryl groups form disulfide bridge with one another
What is the primary level of proteins?
Polypeptide chain of amino acids linked by peptide linkages
What is the interaction in the primary level of proteins?
Covalent peptide linkage between amino and carboxyl
Strongest
What is the secondary level of proteins?
1+ polypeptide chains individually coiled into an alpha helix or beta sheet
What is the tertiary level of proteins?
Folding of coiled polypeptin chain to form globular protein
What is the quaternary level of proteins?
Assembly of 2+ folded sub-units (polypeptide) with beta and alpha chains
What is the interaction in the secondary level of proteins?
H bonding between polar amino acids
What is the interaction in the tertiary level of proteins?
- Hydrophilic and hydrophobic R groups (dipole-dipole, London forces)
- H bonding
- Disulfide bridges (covalent)
- Charged R groups (forming ionic bonds)
What is the interaction in the quaternary level of proteins?
- Hydrophobic interactions
- H bonding
- R group interaction
- London forces
Weak bonds, easiest to disrupt
How does salt solutions cause protein denaturation?
disrupt ionic and H bonds (charges)
How does heat cause protein denaturation?
increased motion of particles disrupts weak bonds maintaining shape except for disulfide bridge
How do organic solvents cause protein denaturation?
nonpolar R groups are soluble in the solvent which will cause the protein to invert (hydrophillic and hydrophobic sides switch)
How do changes in pH cause protein denaturation?
disrupt ionic and H bonds (H+ ions)
What are the functions of protein (8)?
- Transport of O₂ (hemoglobin)
Needs iron ion as cofactor in its structure - Immune System (antibodies)
- Enzymes - catalyze reactions
- Structural (hair, nails, antlers, hooves)
- Contractile Proteins - movement
- Cell Signals - protein hormones (insulin)
- Membrane Transport - carrier proteins
- Energy Storage - during starvation
How do you test for proteins?
When Biuret’s solution is added to a protein, the solution turns violet
What are the 2 types of nucleic acid?
- RNA (polymer)
2. DNA (polymer)
How are nucleic acids formed?
Joining nucleotides in dehydration synthesis reactions
What are the functions of nucleic acid (2)?
- Genetic information of the cell
- Involved in protein synthesis
What kinds of molecules are the functional groups and how polar are they?
All polar or ionic
Phosphate > Carboxyl > Amino > Hydroxyl > Carbonyl > Sulfhydryl
What are the 4 types of macromolecules?
- Proteins
- Polysaccharides
- Lipids
- Nucleic Acids
What are the most abundant elements in the body and their electronegativities?
C, H (low EN)
O, N (high EN)
What is chitin and cellulose?
Beta glucose units joined in a beta 1,4 glycosidic linkage
