Exam 1 Flashcards
Elements found in biological systems
4 major subsets
- H, C, N, O
- Na, Mg, K, Ca
- P, S, Cl
- B, F, Al, Si, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br, Mo, Cd, I,W
What are amino acids?
polymer: polypeptides and proteins Major type of biological molecule They contain -an amino group (NH3) -a carboxylic acid group (COO-) -a side chain (CH3, methyl)
What are carbohydrates?
Sugars: polymer: polysaccharides
What are nucleotides?
Found in DNA and RNA: polymer: nucleic acids
They are the building blocks of nucleic acids.
What is chirality?
“Handedness” comes from the asymmetry of the alpha carbon
A carbon with 4 different substituents is considered to be asymmetric.
What are lipids?
Fats;store energy
Lipids DO NOT form polymers
What formation are all naturally occurring amino acids in humans?
L (left) formation
Exception is Glycine
Sugars (carbohydrates) can be drawn two different ways
Linear and cyclical
What is the most important lipids in human health?
Cholesterol
It can be easily identified with the 4 ring structure
What are the three major kinds of biological polymers?
Polypeptides and proteins, nucleic acids, and polysaccharides
Amino acid residues are linked by what?
Peptide bonds
How are polypeptide sequences read?
From N terminus to C terminus
How do nucleotide residues link?
Via phosphodiester bonds.
O
O-P=O
O
Where can a glycosidic bond be found?
Connecting two sugars; it is a special type of ether bond
It links the Anomeric carbon to another group.
What is the function of proteins?
Major function- carry out metabolic reactions (enzymes) and support cellular structures (cytoskeleton proteins ie keratin, actin, collagen)
Minor function- store energy (glycogen)
What is the function of nucleic acids?
Major function- encode information (DNA genetic traits)
Minor function- carry out metabolic reactions and support cellular structures
What is the function of polysaccharides?
Major function- store energy (glycogen) and support cellular structures (cellulose in plants and trees)
Minor function- encode information
Hydrophobic amino acids
Have nonpolar R groups
Hydrophilic amino acids
Have polar R groups. They can be charged or uncharged R groups.
What is the most simplest amino acid?
Glycine and it does not have chirality because both side chains are the same H group
Gly
G
Which are the hydrophobic amino acids?
Alanine (Ala, A) Valine (Val, V) Phenylalanine (Phe, F) Tryptophan (Try, W) Leucine (Leu, L) Isoleucine (Iso, I) Methionine (Met, M) Proline (Pro, P)
What are the hydrophilic polar, uncharged amino acids?
Serine (Ser, S) Threonine (Thr, T) Tyrosine (Tyr, Y) Asparagine (Asn,N) Glutamine (Gln, Q) Cysteine (Cys, C) Histidine (His, H)
Which amino acids are hydrophilic polar, positively charged
Lysine (Lys, K)
Arginine (Arg, R)
Which amino acids are hydrophilic polar, negatively charged?
Aspartate (Asp, D)
Glutamate (Glu, E)
What are amphipathic molecules that form lipid bilayers in cell walls?
Glycerophospholipids and sphingolipids
What are the classification of lipids?
Fatty acids, triacylglycerols, glycerophospholipids, sphingolipids, and isoprenoids
What are lipids (fats)?
Biological molecules that ARE soluble in nonpolar solvents and largely soluble in water
What bonds dominate lipids?
Long chain Hydrocarbon bonds
What is the polar head group on a fatty acid chain?
It is the carboxylic acids
What is the nonpolar tail of the long chain?
The hydrocarbon chain
Sphingosine and Sphingomyelin do not have what backbone found in glycerophospholipids?
They do not have a glycerol backbone
What does a cerebroside have as a head group?
A monosaccharide
What does a ganglioside have as a head group?
An oligosaccaride (oligo means more than one; a “gang”)
What is cholesterol?
An amphiphilic isoprenoid. It is the metabolic precursor of steroid hormones (estrogen and testosterone)
Which vitamins are isoprenoid derivatives?
Fat-soluble vitamins (A, D, E and K)
Which amphipathic lipid molecules form a lipid bilayer?
Triacylglycerols, glycerophospholipids, shingolipids, cholesterol, or glutamic acid?
Glycerophospholipids and sphingolipids
What is the simplest aldose?
Glyceraldehyde
What is the simplest ketone?
Dihydroxyacetone
How do you designate D and L Notation?
Identify the last chiral center in the molecule.
OH on the right=D
OH on the left=L
Most sugars in nature have the D configuration.
What are enantiomers?
Non-superimposable mirror images;have different configurations at ALL stereocenters.
What are diastereomers?
Non-superimposable non-mirror images, when there are 2 or more chiral carbons. Have different configurations at one or more (but not all) stereocenters.
What are epimers?
Special diastereomers that differ from each other in the absolute configuration at only ONE center
How do you determine the number of stereoisomers?
2 to the ‘n’ power
How does cyclization occur?
When an aldose cyclizes, the hydroxyl group on the 2nd to last carbon undergoes an intramolecular reaction with the carbonyl group of the aldehyde. The product resulting from aldose cyclization is a hemiacetal. The product resulting from ketone cyclization is a hemiketal.
Five membered ring that consists of 4 Carbons + 1 Oxygen
Furanose
Six membered ring that includes 5 Carbons + 1 Oxygen
Pyranose
What is an alpha Anomer?
A chiral carbon on a cyclical sugar with the OH group on the bottom
What is a beta Anomer?
A chiral carbon of a cyclical sugar with the OH group on the top
What is a glycoside?
A molecule consisting of a sugar linked to another molecule by a glycosidic bond.
Phosphorylated sugars
Glyceraldehyde-3-phosphate and fructose-6-phosphate are intermediates in the metabolic pathways for breaking down glucose. (Glycolysis)
How are sugars in RNA and DNA numbered?
With primes.
DNA and RNA are each furanose. What is the only difference?
In RNA, the 2’ carbon has an OH group and DNA has a H group.
What are two examples of monosaccharides derivatives?
Glucosamine (an amino group has replaced an OH substituent)
Glucuronate (a carboxyl group has replaced the terminal CH2OH)
Examples of disaccharides
Lactose and sucrose ->source of metabolic fuel
Examples of polysaccharides
Glucose polymers
Starch and glycogen -> fuel-storage
Cellulose ->structural support
Other structural polysaccharides
Bacterial polysaccharides form a biofilm (bacterial biofilms)
What is the lactose structure?
Beta(1->4) glycosidic bond
~ shape
Galactose + Glucose = Lactose
What is the sucrose structure?
Alpha(1->2) glycosidic bond
Makes a U shape
Glucose + Fructose = Sucrose (the most abundant sugar in nature)
Glucose polymers
Alpha (1->4) glycosidic bond
U shape
Starch and glycogen are storage forms of glucose
What is amylose?
A linear and helical polymer of glucose
What is Amylopectin?
A branched polymer of glucose
Alpha(1->6) glycosidic bond
Structure of cellulose
Beta(1->4)
~ shape
Cellulose is composed of glucose
Glycoproteins
Oligosaccharide chains are covalently attached to the proteins as N-linked or O-linked oligosaccharides.
Glycoproteins function as protection and as recognition markers (blood groups).
N-linked via Asn (Asparagine); amide group
O-linked via Ser or Thr
DNA and RNA are polymers of nucleotides,each of which consists of a:
- purine or pyrimidine base
- deoxyribose or ribose
- phosphate
Adenine and guanine are ______ in both ____ and ______.
Purines in both DNA and RNA
A purine has 2 rings.
Adenine has an amine group in the same location where guanine has a double bonded oxygen. Guanine has an amide group in a location that adenine does not any molecules.
Pyrimidines found in DNA
Cytosine and thymine
Pyrimadines is a single ring
Pyrimidines found in RNA
Cytosine an uracil
Uracil is missing the methyl group thymine has
NucleoSide =
Base + Sugar
NucleoTide =
Base + sugar + phosphate
How do nucleotides link?
Via sugar in phosphodiester backbone
Read sequence of bases from 5’ -> 3’
How many bonds do adenine and thymine make?
2 H-bonds
How many hydrogen bonds do guanine and cytosine make?
3 and is stronger than A and T
What does the stability of a DNA double helix depend on?
It depends mostly on stacking interactions.
What does it mean to go from genes to proteins?
Central dogma
DNA to transcription, RNA to translation to protein
True or false
DNA can denature and re-nature
True
What does it mean when water is amphoteric?
It means that water can act as an acid or a base depending on the environment
List the strengths of bonds from strongest to weakest
Covalent
Ionic
Hydrogen
van deer Waals
What is the hydrophobic effect?
The phenomenon by which nonpolar molecules aggregate to avoid contact with hydrophilic molecules, particularly water.
True or false
Nonpolar molecules tend to aggregate in nonpolar solvents
False
They tend to aggregate in POLAR solvents
Amphiphilic molecules form _______ in ________ solutions
Micelles
Aqueous
On the pH scale, 0 to 7 is considered acidic or basic?
Acidic
On the pH scale, what values are basic?
7 to 14
What does the pk describe?
An acid’s tendency to ionize
An example is acetic acid
The lower the pka for acids, the higher the strength
If the pH is acidic, will the hydrogen ions dissociate quickly or slowly?
Slowly because they do not want to give any up. The opposite is true for basic pH.
In pulmonary function, if the blood pH is acidic, what will happen to the carbon dioxide during exhalation?
More gaseous carbon dioxide is lost during exhalation causing a right shift in the chemical reaction. The opposite happens during alkalosis (left shift occurs).
What is bicarbonate reabsorption?
When a pH adjustment needs to be done and it is over a long period of time, such as hours to days, the kidneys will excrete and restore the balance.
What are amino acid residues?
Amino acids within the peptide bond are called amino acid residues because only the residual atoms remain after the condensation reaction (loss of water)
What will happen to the acidic groups amino acid side chain/terminal when pH>pK?
They will be mostly ionized with a -1 charge
What will happen to the acidic groups amino acid side chain/terminal when pH < pK?
They will be mostly unionized with a 0 charge
What will happen to the basic groups amino acid side chain/terminal when pH > pK?
They are mostly unionized with a 0 charge.
What will happen to the basic groups amino acid side chain/terminal when pH < pK?
It will be mostly ionized with a +1 charge
What is the isoelectric point, pI?
The pH at which it carries no net charge.
How do you find the pI of an acidic amino acid?
Add pKa1 and pKa3 and divide by 2.
What are the 4 levels of protein structure?
Primary- the sequence of amino acid residues
Secondary- the spatial arrangement of the polypeptide backbone
Tertiary- three-dimensional structure of an entire polypeptide
Quaternary- spatial arrangement of polypeptide chains in a protein with multiple subunits (not every protein will have one)
What are the 2 principal secondary structures?
Alpha helix and Beta sheet
Both are characterized by hydrogen bonding
What is i + 4 pattern of hydrogen bonding?
Stabilized by a characteristic pattern of hydrogen bonding of the carbonyl of one amide(i) to the NH of another amide i +4.
How do you find the pI of a basic amino acid?
Add pKa2 and pKa3 and divide by 2.
What do protein folding and protein stabilization depend on?
Non covalent forces
What happens when misfolded proteins are not immediately refolded or degraded, but instead aggregate?
They are often long insoluble fibers and can lead to disease.
An example is Alzheimer’s.
What does myoglobin transport?
O2 throughout the muscles
What does hemoglobin transport?
O2 in the blood
What are the other functions of proteins?
Immunity- antibodies
Catalysis- enzymes
Regulation of gene expression
What is the structure and sequence of myoglobin?
Monomer- 1 polypeptide chain with primary, secondary and tertiary structure
Primarily in muscles
O2 binds to the heme group in a hyperbolic manner
What is the structure and sequence of hemoglobin?
Tetramer (alpha2:beta2) 4 individual subunits
Erythrocytes
O2 binds to the heme group in a sigmoidal manner
What do the similarities and structure between myoglobin and hemoglobin indicate?
A common evolutionary origin
What is a prosthetic group?
Organic molecule bound to protein that aids protein function
Myoglobin transports _______ via the _______ in heme.
O2, Fe
What role does his residues play?
They play a key role in anchoring both O2 and iron.
How are pO2 and O2 saturation related?
They are directly related. If pO2 increases, O2 saturation increases.
Myoglobin binds to _____ in a ________ trend.
O2, hyperbolic
Does hemoglobin or myoglobin have a quaternary structure?
Hemoglobin does
Homologous proteins
Evolving from a common ancestor gene through genetic mutation
Invariant residues
- identical in homologous proteins
- essential for structure or function of the protein
- cannot be replaced by other residues
Conservative substitution
- when an amino acid can be replaced by another similar amino acid (ie Ile for Leu or Ser for Thr)
- structure or function is conserved
Variable residues
- not involved in the structure or function of the protein
- can be substituted by other dissimilar amino acids (Ile for Ser or Leu for Lys)
What is cooperativity?
Binding of O2 to one subunit induces easier binding to other subunits by conformational change.
What kind of curve does hemoglobin have?
A sigmoidal curve; sigmoidal data are indicative of cooperativity.
Which has a higher affinity of oxygen? Myoglobin or hemoglobin?
Myoglobin does
A tense hemoglobin cooperative behavior is _____?
Deoxy (missing oxygen); is not in the site of conformational change
A relaxed hemoglobin cooperative behavior is _____?
Oxy (contains oxygen); is in the conformational change site
What is the Bohr effect?
The reduction of hemoglobin’s oxygen binding affinity when the pH decreases (more acidic or an increase in hydrogen concentration
What is happening biochemically when you breathe?
It allows O2 to unbind from hemoglobin.
What decreases hemoglobin’s O2 affinity?
BPG 2,3-bisphosphoglycerate
BPG binds only to the tense (deoxy) conformation of hemoglobin.
