MCAT BIO CH. 3 Flashcards
What are the components of an amino acid structure?
- Alpha amino group
- Variable R-group
- Alpha-carboxyl group
- Tetrahedral alpha-carbon
Draw the amino acid structure?
Page 41 in Biology MCAT
What do all twenty amino acids share?
Same nitrogen-carbon-carbon backbone
What is the unique feature of each amino acid?
Side chain (variable R-group)
What are the two common types of covalent bonds between amino acids in proteins?
The peptide bonds and disulfide bridges
What do peptide bonds link?
Link amino acids together into polypeptide chains (with a nitrogen)
What do disulfide bridges link?
Between cysteine R-groups
What is a residue based on amino acids?
Amino acid a part of a polypeptide chain
What is the first end and the last end of polypeptide chains?
The amino terminus is the first end made during polypeptide synthesis, and the carboxyl terminus is made last
What terminal residue is always written first?
The amino-terminal residue is also always written first
What is proteolysis?
Hydrolysis of a protein by another protein
What is a proteolytic enzyme? What’s another word for it?
Protein that cuts during proteolysis, protease
What bond do proteolytic enzyme cleave?
Specific means of cleaving peptide bonds
What is the important concept of denaturation based on what it involves?
It involves the disruption of a protein’s shape without breaking peptide bonds
What can proteins be denatured by?
Extreme pH, extreme temperatures or tonicity
What is the primary structure of a protein?
Sequence of amino acids
What is the secondary structure of a protein?
Folding of a polypeptide chain into shapes stabilized y hydrogen bonds between backbone NH and CO
What are the two common motifs of secondary structure?
alpha-helix and beta pleated sheets
What are the two types of beta pleated sheets?
parallel b-pleated sheets, anti-parallel b-pleated sheets
What is the tertiary structure of a protein?
Interactions between amino acid residues located more distantly from each other in the polypeptide chain
What drives the folding to form tertiary structures?
Interactions between the R-groups and with water solvent
How does water affect the tertiary structures of proteins?
- Hydrophobic R-groups tend to fold in the interior away from water
- Hydrophilic R groups tend to be exposed to water not he surface
What does the forces drive for the proteins to form into their what..?
Lowest energy conformation
What is disulfide bridge considered? 1o, 2o or 3o
3o
What is the quaternary structure?
Interactions between polypeptide subunits
What are the forces that are used in tertiary structure formation?
- Non-covalent interactions
- Van der Waals forces
- Hydrogen bonds
- Disulfide bonds
- Electrostatic interactions
What bond is not involved in quaternary structure and why?
Peptide bond; because it defines the sequence
What is a bond between two sugar molecules?
Glycosidic linkage
What is a glycosidic linkage, based on its process?
A covalent bond formed in a dehydration synthesis reaction
What is the word for a sugar molecule and two sugar molecules together?
Monosaccharides, disaccharides
What are the common disaccharides you might see on the MCAT?
Sucrose, Lactose, Maltose and Cellobiose
What is glycogen?
Serves as an energy storage carbohydrate in animals, composed of thousands of glucose units
What is starch?
Energy storage carbohydrate for plants
What is cellulose?
Polymer of cellobiose
What is important to know about cellobiose?
Does not roam freely in nature
What process causes carbohydrates to break down into Co2?
Oxidation
What is oxidation also known as, based on break down of carbohydrates?
Combustion or burning
What are carbohydrates usually used for?
Principle energy source for cellular metabolism
What is a monosaccharide? What’s the general formula?
Simple sugar, CnH2nOn
What is a lipid?
Oily or fatty substances that play three physiological roles
What are the two locations lipids are important for based on their roles?
In adipose cells, in cellular membrane
What do lipids do in adipose cells?
Triglycerides store energy
What do lipids do in cellular membrane?
Phospholipids constitute a barrier between intracellular and extracellular environments
What type of lipid is a special lipid and what does it do?
Cholesterol serves as the building block for the hydrophobic steroid hormones
What is the cardinal characteristic of the lipid?
Hydrophobicity
What polarity is water and how do polar substances react to water? What are they also called?
Polar, dissolve well in water, hydrophilic
How are carbon bonds based on polarity? How do they react to water?
Non-polar; not dissolve well in water
How do cotton shirts react to water? What about nylon shirts?
Wet when exposed because they are made from glucose polymerized into cellulose; does not become wet because composed of atoms covalently bound together in a non polar fashion
What is a synonym for hydrophobic? Synonym for hydrophilic?
Lipophilic; lipophobic
What are fatty acids composed of?
Long unsubstituted alkanes that end in a carboxylic acid
Because fatty acids are synthesized two carbons at a time from acetate…..
Only even-numbered fatty acids are made in human cells
What is. saturated fatty acid? Unsaturated?
No double bonds; one or more double bonds
What are the double bonds considered based on unsaturated fatty acids?
Z or cis
What is the shape of a unsaturated fatty acid?
Kink
How does a fatty acid chain react to being exposed to water?
Interact with each other to minimize contact with water, exposing carboxyl group to the aqueous environment
What is triacylglycerol or triglyceride?
The storage form of the fatty acid
What is the triglyceride composed of?
Three fatty acids esterified into a glycerol molecule
What are important components of the triglyceride and how does your body make sure it doesn’t harm you?
Three hydroxyl groups esterified to fatty acids; free fatty acids are reactive chemicals
Draw a triglyceride
Page 50 for the answer
Which enzyme hydrolyzes fat?
Lipase
Why are fat cells more efficient energy storage molecules than carbohydrates?
Packing and Energy content
What is packing based on fat cells?
Hydrophobicity allows fat to pack together much more closely
What is energy content based on fat cells?
Fat has more energy carbon-for-carbon than a carbohydrate
Phospholipids derived from what?
Derived from diacylglycerol phosphate or DG-P
What are bilayer stabilized by?
Van der Waals forces between long tails
What does the double bond cause to the chain that is not present in the single bonded fatty acid chain?
Tend to increase membrane fluidity
What does the unsaturated chain prevent?
Prevents the membrane from solidifying by disrupting the orderly packing of the hydrophobic lipid tails
How can we increase the fluidity of a fatty acid chain?
- Add a double bond
2. Decreasing the length
What is the important modulator of membrane fluidity? What exactly does it do?
Cholesterol; keep cholesterol at optimal levels
What are the structural determinants of membrane fluidity?
- Degree of saturation
- Tail length
- Cholesterol level
What is a terpene?
Compounds build from isoprene units (C5H8) with a general formula (C5H8)n
What are the two structures of terpene?
Cyclic or linear
What are terpenes classified by?
The number of isoprene units they contain
What is the name for two terpenes? Three terpenes? Four terpenes? Six?
- Monoterpenes
- Sesquiterpenes
- Diterpenes
- Squalene
What is important about squalene?
Biosynthetically utilized in the manufacture of steroids
What is squalene a component of?
Earwax
What are terpenoids?
Derived species built from an isoprene skeleton and functions with other elements
Why are steroids included in the lipids section?
Hydrophobicity and similar to fats
What is the basic structure of steroids and what does it relate to?
Tetracyclic ring system based on the structure of cholesterol
In what structure is cholesterol an important constituent?
Lipid bilayer
Which organ grabs and synthesizes cholesterol?
Liver
Steroids is carried into what?
Lipoproteins
What has a lipoproteins been implicated in causing which disease?
Atherosclerotic vascular disease; plaque (cholesterol build-up)
What are the four commons types of steroids?
- Tetracyclic ring
- Cholestrol
- Testosterone
- Estrogen
What are steroid hormones made from?
- Testosterone
2. Estradiol
What is an inorganic molecule?
Does not contain carbon
What type of acid is phosphoric acid?
Inorganic acid
What can phosphoric acid donate?
3 protons
What are the 3 pKas for each protons?
2.1, 7.2, and 12.4
At physiological pH, how is the phosphoric acid?
Dissociated, existing in anionic form
How are phosphates bound? What does it form?
Anhydride linkage; pyrophosphate
What is phosphate also known as?
Orthophosphate
What bond in pyrophosphate is considered the high-energy phosphate bond?
P-O-P
What is the reason the name is called high energy phosphate bond?
The fact that the hydrolysis of pyrophosphate is highly favorable
What are the three main points as to why phosphate anhydride bonds store so much energy
- Charges
- Resonance
- Interactions
What is the charges reason as to why phosphate anhydride bonds have so much energy?
The P linked together have negative charges that repel each other
What is the resonance reason as to why phosphate anhydride bonds have so much energy?
Orthophosphates has more resonance forms thus lower free energy than linked phosphates
What is the interaction reason as to why phosphate anhydride bonds have so much energy?
Has more favorable interaction with biological solvent (water) than linked phosphates
What do nucleotides contain?
- Ribose or deoxyribose sugar
- Purine or Pyrimidine
- Phosphates units
What is the phosphate unit joined to based on nucleotides?
The carbon 5 of the ribose ring
Where is the purine or pyri unit joined to based on nucleotides?
The carbon number 1 of the ribose ring
What is ATP based on RNA?
RNA precursor
Where is the energy extracted from the oxidation of foods stored?
In the phosphoanhydride bonds of ATP
Which type of specie (or not) cannot make their own ATP?
Viruses
