Lecture 2: Chemical Basis of Life Flashcards
Compound
A substance consisting of 2+ diff. elements combined in a fixed ratio
Many compounds in living organisms contain ____ , ____ , ____ , & ____
C, H, O, & N
DNA: C, H, O, & N
Carbs: C, H, O
Proteins: C, H, O (in some cases N)
Proton
+ electrical charge
Electron
- (-) electrical charge
Neutron
Electrical neutral
How do atoms make their outermost shell full?
By sharing their electrons –> covalent bond formed
Which atoms are the most abundant in biological molecules and readily form covalent bonds?
- Hydrogen
- Oxygen
- Carbon
- Nitrogen
- Phosphorus
- Sulfur
All biological building blocks are organized around carbon atoms forming _____ or _____ bonds
3 or 4
Electronegativity
The extent o/ an atom’s ability to attract an electron
Non-polar covalent bonds
Electrons are equally shared between atoms that form the covalent bond
- e.g. C—C, C—H
Polar covalent bond
Covalent bonds between atoms that have diff. electronegativity —> unequal sharing o/ electrons
- e.g. O–H bonds in H2O
Ionic bond
One atom loses 1+ electrons to another atom
- Results in formation of positively (cation) and negatively (anion) charged ion
How are ionic bonds formed?
Formed as the result o/ attraction between OPPOSITELY-charged ions
- e.g. NaCl
Why are ionic bonds so rare in cells?
Ionic bonds are weak and break easily in H2O
- e.g. Salt dissolving in water
Why are hydrogen bonds important in cells?
Electrostatic attraction between a proton in one molecule + electronegative atom in the other
Why are Van der walls interactions important in cells?
- Weak attractive force between atoms or nonpolar molecules
- Caused by a short change in dipole moment caused by a momentary transfer of orbital electrons to one side of one atom or molecule, causing a corresponding shift in surrounding atoms or molecules.
How is chemistry in living things different from that in the rest of the world?
Fewer elements, more water! (Cells are 70% water)
Why is so special when it comes to cells?
- Both O–H bonds are highly polarized
- All 3 atoms readily for H-bonds
- It’s an excellent solvent
- It determines the interaction between all types o/ molecules within the cell and actively participates in these reactions
Hydrophilic molecules
- “Water-loving”
- Ones that can form H-bonds in aqueous solutions and dissolve in H2O
- e.g. sugars, some amino acids, etc.
Hydrophobic
- “Water-hating”
- Molecules can’t form H-bonds and are insoluble in water
- Hydrophobic interactions hold these structures together
- e.g. fats
What are the macromolecules found in cells?
- Proteins
- Carbs
- Nucleic acids
What are the 4 classes of biological macromolecules?
- Carbs
- Lipids
- Nucleic acids
- Proteins
General principles of macromolecular polymerization
- Macromolecule synthesis proceeds by the stepwise polymerization o/ monomers
- H2O molecule is removed w/ addition of each monomer
- Addition o/ each monomer to a growing macromolecule requires energy
- Synthesis occurs in a particular diction, and the 2 ends o/ polymer chain are chemically diff. from each other
What are the functions of carbohydrates?
- Energy storage
- Cell structure
- Modification on other macromolecules (e.g. glycolipids)
Name examples of carbohydrates
Simple sugars- glucose, fructose, etc
What are di- and oligo-saccharides?
Simple sugars joined linearly by glycosidic bonds
- e.g. Sucrose, Lactose, etc.
Name examples of polysaccharides.
Glycogen, starch, cellulose
Branched polymers are found in which organisms? What are they used for?
a. Animals
b. Energy storage
Helical polymers are found in which organisms? What are they used for?
a. Plants
b. Energy storage
Unbranched polymers are found in which organisms? What are they used for?
a. Plants
b. Structure
What functions do nucleic acids serve?
- Serve & transmit genetic info.
- Some serve as enzymes
What are the two major types o/ nucleic acids?
- DNA
- RNA
- mRNA
- tRNA
- rRNA
- Various small RNA molecules
What are nucleotides made up of?
- Pentose sugar
- Nitrogenous base
- Phosphate group linked to pentose sugar
What is the difference between a nucleoSIDE and a nucleoTIDE?
Nucleoside: Nitrogenous base + sugar
Nucleotide: Nitrogenous base + sugar + 1+ phosphates
What are the functions of nucleotdes?
- Monomeric units o/ nucleic acids
- High-energy compounds
Adenosine triphosphate (ATP)
Adenosine nucleoside + 3 phosphate groups
What is the pentose sugar present in DNA?
Deoxyribose
What is the pentose sugar present in RNA?
Ribose
What are the nitrogenous bases present in DNA?
- Adenine
- Guanine
- Cytosine
- THYMINE
What are the nitrogenous bases present in RNA?
- Adenine
- Guanine
- Cytosine
- URACIL
What bond holds the base pairs in DNA together?
Hydrogen bond
How do lipids differ from other macromolecules?
- Not synthesized by linear polymerization o/ monomers
- Heterogenous category grouped together based on their shared distinctive hydrophobic character
Why are lipids still considered macromolecules?
- High molecular weights
- Presence in important cellular structures, especially membranes
What are the major cellular functions of lipids?
- Membrane structure
- Energy storage
- Signaling molecules
What are triacylglycerols (Triglycerides)?
Glycerol molecule + 3 fatty acids
T/F: Triacylglycerols are more unsaturated in animals.
FALSE, they’re more SATURATED
- Typically solid at room temp. (e.g. fat on meat)
T/F: Triacylglycerols are more unsaturated in plants.
TRUE, typically liquid at room temp. (e.g. vegetable oils)
What is the most abundant class of phospholipid in biomembranes?
Phosphoglycerides
What is a phosphoglyceride composed of?
- 2 fatty acyl chains esterified to 2 hydroxyl groups in glycerol phosphate
- A polar head attached to the phosphate group in glycerol phosphate
What are the functions of cholesterol?
- Regulate membrane fluidity
- Precursor to steroid hormones
- Amphipathic
What are sterols made up of?
Cholesterol and its analogs
What functions do proteins have?
- Catalyze reactions (enzymes)
- Structural roles
- Movement
- Transport across membranes
- Receive and transmit signals (between and within cells)
- Defense (protect against disease)
Proteins are ________ polymers o/ amino acids
Linear
What are the common features of proteins?
- Central alpha carbon atom bonded to 4 diff. chemical groups
- 1 amino (-NH2) group
- 1 carboxyl or carboxylic acid (-COOH) group
- 1 hydrogen (H) atom
- 1 R group
Amino acids are linked by what type of bond?
Peptide
Proteins (or polypeptides) are composed o/ amino acid that joined together by _______________.
Dehydration synthesis reactions
How is a peptide bond formed?
When H2O is removed
________ defines function.
Structure
Primary structure of proteins
- Sequence o/ amino acids in a polypeptide chain
- Read from N-terminus to C-terminus
- All info. needed for higher-level structure is provided by the amino acid sequence
Secondary structure o/ proteins
- Local regions o/ structure formed by H-bonding between H in amino group + O in carboxy group o/ peptide backbone
What are the most common elements of secondary structure?
Alpha helix- spiral arrangement o/ amino acids
- Looks like a coiled telephone cord
Beta sheet- sheet-like conformation composed o/ extended pleated strands
- Looks like a pleated skirt
Tertiary structure o/ proteins
- Global 3D structure o/ a single polypeptide chain
- Controlled almost completely by R group interactions
- Influenced by covalent & non-covalent interactions
What determines the 3D protein conformation?
Amino acid sequence
What are the types of non-covalent interactions?
- Hydrogen bonds
- Ionic bonds
- Van der Waals interactions
- Hydrophobic interactions
What are the types of covalent interactions?
Disulfide bonds
Quaternary structure o/ proteins
Overall architecture o/ a protein comprised o/ multiple polypeptide chains
- Multimeric protein/protein complex- a protein comprised o/ multiple polypeptides
What factors/conditions might cause a folded protein to unfold (denature)?
- Extreme temps.
- Extreme pH
- High salt
- Mechanical agitation
Why is a denatured protein a bad thing for a cell?
Denaturation breaks H-bonds & Van der Waals interactions
- These bonds hold the 3D shape o/ the protein
- No proper shape —> no function
What is protein phosphorylation?
- Like a chemical switch that can turn a protein “on” or “off
- Phosphate group is added to a protein
- This alters the protein’s shape + function, making it less active in carrying out its specific function within the cell
