Exam 1 Flashcards
What are the four major classes of organic molecules in living organisms?
Carbohydrates, lipids, proteins, and nucleic acids
What is an important characteristic of covalent bonds?
They store a lot of energy
What are hydrocarbons?
Molecules consisting of carbon and hydrogen atoms
Are hydrocarbons polar or nonpolar?
Nonpolar, and when functional groups are added, they confer chemical properties to the molecule.
When are triple bonds found in hydrocarbons?
Only in two-carbon hydrocarbons such as ethyne
When are single and double bonds found in hydrocarbons?
In linear and ring hydrocarbons
What are some general structures of hydrocarbons?
Linear unbranched chain, linear branched chain, or a structure with one or more rings
Match the bond type to the molecule: single, double, triple and ethane, ethene, and ethyne
Ethane- single, ethene- double, ethyne- triple
Which functional groups are most commonly found in biological reactions?
Hydroxyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl groups, which are linked by covalent bonds to other atoms in the molecule (usually represented by R)
Are lipids polar or nonpolar?
Primarily nonpolar and water-insoluble
List the three common types of lipid molecules and their function
Neutral lipids- stored and used as an energy source
Phospholipids- form cell membranes
Steroids- serve as hormones regulating cellular activities
True or false: neutral lipids have no charged groups (nonpolar)
True
What are the two types of neutral lipids?
Oils (liquid at biological temperatures) and fats (semisolid)
What is a fatty acid? Is it polar or nonpolar?
A fatty acid has a single hydrocarbon chain with a carboxyl (COOH) group at one end. The carboxyl group gives organic molecules acidic properties because the -OH group releases the H as a proton in aqueous solutions, turning it into an ionized form. Fatty acids are nonpolar.
How are triglycerides formed?
Formed through a process called dehydration synthesis between 3-carbon glycerol (an alcohol) and three fatty acid side chains. A covalent bond called the ester linkage forms between the COOH fatty acid and the OH of glycerol, which eliminates the polar group of glycerol and forms a nonpolar molecule
What is the hydroxyl group and what are some of its properties/applications?
Hydroxyl (–OH) can be found in molecules like alcohols. It is polar and hydrogen bonds with water, which facilitates dissolving of organic molecules. It allows an alcohol to link with other molecules through dehydration synthesis reactions.
Where is the ester linkage in triglycerides located?
Between the O in glycerol and the C in the fatty acid
How many molecules of water are formed through formation of triglycerides?
3
What roles do triglycerides play?
Serve as energy reserves in animals because they can store more than 2x the calories per gram as carbohydrates.
A layer of fatty tissue under skin acts as insulation in mammals and birds.
Triglycerides also help make bird feathers waterproof
What is a typical number of carbons in a fatty acid?
14 to 22; as chain length increases, the fatty acid becomes less water soluble and more oily
What is a saturated fatty acid? Where are they found?
A fatty acid that binds the maximum number of hydrogen atoms, meaning only single bonds exist between carbon atoms. These fatty acids can be found in solid animal fats such as butter
What are mono and polyunsaturated fats?
Fatty acids with one double bond are mono; acids with 2 or more are polyunsaturated.
Why are unsaturated fatty acids usually fluid at biological temperatures?
The presence of double bonds causes “bends” in the structure that mean the molecules cannot pack as tightly together.
Which are healthier- saturated or unsaturated fats?
Unsaturated fats.
What are examples of unsaturated fats?
Vegetable oils.
Is stearic acid saturated or unsaturated? (no bends)
Saturated
Is oleic acid saturated or unsaturated?
Unsaturated
What are trans fats?
Trans fats are formed through adding hydrogen to vegetable oil, which makes the liquid into a solid fat. This is called hydrogenation. Trans fats are also found in products such as milk, butter, cheese, meats, etc. in trans fats. In the process of hydrogenation, cis fatty acid configurations are transformed into trans fat configurations and this gives them more qualities of saturated fat but they are not a good source of energy and they are harder to process
Why are trans fats bad?
They raise the level of LDL cholesterol in the blood, which increases the risk of heart disease.
How can LDLs contribute to heart disease?
Atherosclerosis occurs due to buildup of plaques in coronary arteries; these plaques form from a buildup of excess cholesterol.
What is the structure of phospholipids?
Glycerol, 2 fatty acids as the nonpolar tails, a phosphate group as part of the polar head
Order goes polar unit–phosphate group– glycerol then the two nonpolar fatty acids
What type of fatty acid composes the tails?
One saturated, one unsaturated
What is the function of phospholipids?
They help form cell membranes; the polar ends are exposed to water and their nonpolar ends collect in a region that excludes water
What is a micelle?
Micelles are lipid molecules that orient with their polar head toward water and their nonpolar tails away from water in a circle
What is the structure of a phospholipid bilayer?
2 molecules thick- polar groups face water and hydrocarbon chains form nonpolar, hydrophobic regions in the interior
What are waxes?
Fatty acids combine with long-chain alcohols or hydrocarbon structures to form waxes, which are harder and less greasy than fats
What are the functions of waxes?
Help animals keep skin, hair, or feathers protected, lubricated, and pliable; plants also secrete waxes that form a protective exterior layer to reduce water loss and resist infection.
What are steroids?
Lipids with structures based on 3 hexane carbon rings and 1 pentane carbon ring. They control development, behavior, and many internal biochemical processes. The sex hormones that control differentiation of sexes and sexual behavior is one example.
What makes sterols unique?
They have a single polar OH group at one end of the ring framework and a nonpolar hydrocarbon chain at the other end
What role does cholesterol play?
It is an important part of animal cell membranes; sterols called phytosterols also occur in plant cell membranes
What are some structural differences between estradiol (an estrogen) and testosterone?
Estradiol has 3 double bonds in first ring an an OH group. In the pentane ring it has a CH3 and an OH group. Testosterone has an =O instead of -OH and an extra CH3 between the first two rings
What is the name for CH3?
Methyl
What do chlorophylls and carotenoids do?
They are pigments that absorb light and help convert it to chemical energy in plants
True or false: lipid groups combine w/ carbs to form glycolipids and w/ proteins to form lipoproteins with important strucural and functional roles in cell membranes
true
Define isomers
Molecules with the same molecular or empirical formula but different molecular structures
What are structural isomers?
Same chemical formula but the arrangement of atoms are different, such as glucose and fructose
What are stereoisomers?
They differ in how the groups are attached, auch as in mirror image molecules and L and D sugars
What is the carbonyl group?
Has C double bonded to O, usually found in aldehydes and ketones. Molecules with carbonyl groups are major building blocks for carbohydrates and participate in the reactions supplying energy for cellular activities.
Carboxyl
C double bonded to O and bonded to OH, gives organic molecules acidic properties because -OH releases the hydrogen as a proton in aqueous solutions, converting it into an ionized form. Found in carboxylic acids.
Amino
NH2, acts as an organic base by accepting a proton. Found in amines and amino acids.
Phosphate
P bonded to 3 O and double bonded to an O, found in organic phosphates such as glyceraldehyde-3 phosphate and nucleic acids. They react as weak acids because one or both OH groups release H. Can also bridge two organic building blocks. Added to or removed from molecules as part of reactions that conserve or release energy or to alter activity.
Sulfhydryl
Found in thiols. -SH. Easily converted into a covalent linkage where it loses hydrogen atoms. Two sulfhydryl groups form a disulfide linkage.
R-SH+ HS-R = R-S-S-R+ 2H + 2e-
Define enatiomers
Mirror image molecules
Are glucose and fructose structural or steroisomers?
Structural
Are galactose and glucose stereo or structural isomers?
Stereo
Describe and illustrate the dehydration synthesis process
In dehydration synthesis, water is removed and largr molecules are formed. The OH bonds join together to form a water molecule, leaving an O to join the monomers.
Describe and illustrate the hydrolysis process
Hydrolysis involves the breakdown of large molecules through the addition of water. Polymers are broken down into monomers through the addition of water.
What is a carbohydrate?
Molecules with a 1:2:1 ratio of carbon, hydrogen, and oxygen. The empirical formula is CH2O.
What is a key factor about C-H bonds?
They hold a lot of energy
How many C atoms do monosaccharides have?
3-7
What are two monosaccharides called?
Disaccharide
What are polysaccharides?
Carbohydrate polymers with more than 10 linked monosaccharide monomers
What function do carbohydrates serve?
They can act as energy storage molecules; glycogen and starch are some examples. They can also be structural saccharides, such as cellulose.
What are the simplest carbs?
Monosaccharides
T or F: All monosaccharides occur in linear form
True
Give some examples of common hexoses. Why do we care about these?
Glucose, fructose, and galactose. these 6 carbon sugars play important roles
Why are isomers important in sugars
Enzymes can recognize different structural and steroisomers of the basic 6-carbon skeleton which alloes it to distinguish between glucose, fructose, and galactose.
If a monosaccharide has 3 or 5 carbons, what is it called?
Triose and pentose.
How are glucose rings formed?
Monosaccharides with 5+ carbons can fold back through an interaction between two functional groups. The hydroxide on the 5th carbon combines with the carbonyl group on the first carbon, crearing C OH2.
Distinguish alpha and beta glucose.
Alpha= below the plane, beta= above the plane. They are enatiomers (mirror images)
How are disaccharides formed?
Monosaccharides covalently synthesized via dehydration.
How is maltose formed?
A glycosidic bond between two alpha-glucose molecules with oxygen as a bridge between the 1 carbon and 4 carbon creating an alpha 1->4 linkage
How is sucrose formed?
Alpha 1-2 linkage between glucose and fructose.
Draw structures of glucose, fructose, and galactose
Use slides
How is lactose formed?
beta 1-4 linkages between galactose and glucose.
What polysaccharide do plants use for energy?
Starch such as amylose, which is formed from alpha 1-4 glucose lincages which creates a coiled structure
What do animals use for energy?
Glycogen, which is formed from glucose alpha 1-4 chains and side branches are linked by alpha 1-6 linkages (side chain starts on third linear glucose)
What do plants use for structural support?
Cellulose, which is made from glucose units joined end to end by beta 1-4 linkages. Thousands of cellulose chains line up in an arrangement reinforced by H bonds between the chains to form cellulose microfibrils in plant cells.
What do arthropods and fungi use for structural support
chitin, which contains glucose and nitrogen groups. It uses beta 1-4 linkages.
What functional group do ketones and aldehydes fit in?
Carbonyl
Distinguish ketones and aldehydes
Ketones have a C=O connected to two R groups, while Aldehydes have a C=O connected to an R and an H
Polymer is to nucleic acid as monomer is to:
Nucleotide
What is the name of the bond that connects nucleotides?
Phosphodiester
What are the components of a nucleotide?
Nitrogenous base, 5-carbon sugar, and a phosphate group
What is the 5-carbon sugar in a deoxyribonucleotide and in a ribonucleotide?
deoxyribose and ribose
What are the purines?
adenine, guanine
what are the pyrimidines?
cytosine, uracil, thymine
Is it purines or pyrimidines that have two rings?
Purines
What is a nucleoside?
structures that only have a nitrogenous base and a 5 carbon sugar
What are nucleotides in terms of nucleosides?
Nucleoside phosphates
What are some examples of nucleotides?
ATP, ADP, AMP (3,2,1 phosphate groups respectively)
Describe some structural characteristics of uracil
one carbon ring with two carboxyl groups
Structural characteristics of thymine
One ring, two carboxyl groups, and a methyl group
Structural characteristics of cytosine
Amino group and carboxyl group
Structural characteristics of adenine
purine so two rings, amino group
Structural characteristics of guanine
Two rings, amino and carboxyl group
How do you distinguish between deoxyribose and ribose?
Look at the 2’ carbon- either H or OH will be bonded depending on whether ribose or deoxyribose
Where do the phosphate bonds occur in nucleotides?
Phosphate groups bond to the 5’ carbon in the sugar
Describe the phosphodiester bond
5’ Ch2-o-p-o-c (hydrolysis reaction); a bridging phosphate group between the 5’ and 3’ of next carbon
Describe the structure of DNA
the sugar phosphate backbone consists of alternating sugars and phosphates where 5’ connects with phosphate group to 3’ of next sugar; in the other strand this same thing occurs in opposite direction.
How do nucleotides pair up?
A-T or A-U in RNA and C-G
How many bonds between A and T and C and G?
2 and 3 respectively
Describe how each nucleotide bonds to eachother
CNC from hexane face eachother; for AT it is NHO and NHN in order; for GC it is OHN NHN NHO
Can one nucleotide chain determine another?
Yes, that of its partner chain in the double helix
Can RNA fold back on itself and create hybrid nucleic acids with DNA?
Yes, this is where uracil comes into play
What does Atp do?
Main energy currency of cell
NAD+ and FAD+
main electron carriers
Describe the process of DNA replication
- Parent strand with 2 complementary strands of base paired nucleotides
- Two strands unwind from eachother
- Each old strand serves as a template for addition of new ones
- New and old strands join together, creating two new exact copies of old one
List the functions of proteins
Structural support, enzymes, movement, transport, recognition and receptor molecules, regulation of protein and DNA, hormones, antibodies, toxins, and venoms.
What monomers are proteins composed of?
Amino acids
What functional groups do amino acids contain?
Amino (NH2) and carboxyl (COOH) groups
Give the function an example of a structural support protein
Microtubule fibers and microfilament fibers inside cells, collagen, and cell wall proteins of plant cells
Examples and function of enzymatic proteins
Increase the rate of biological reactions; DNA polymerase, rubisco, digestive enzymes
Membrane transport proteins
Speed up transport across cell membranes; ion transporters move ions like Na+ and K+ into the cells, aquaporins, glucose transporters
Motile proteins
Produce cellular movements; myosin acts on microfilaments to produce muscle movements; kinesin acts on microtubules involved in cell division
Regulatory proteins
Promote or inhibit the activity of other cellular molecules. Nuclear regulatory proteins turn genes on or off to control the activity of DNA; protein kinases add phosphate groups to other proteins to modify activity.
Receptor proteins
Hormone receptors bind hormones at the cell surface or within cells and trigger cellular responses; cellular adhesion molecules help hold cells together
Hormonal proteins
Carry regulatory signals between cells; insulin regulates sugar levels; growth hormones regulate cell division and growth
Defensive proteins
Defend against invading molecules and organisms; antibodies recognize and bind and eliminate foreign bodies
Storage proteins
Hold amino acids and other substances in storage forms; ovalbumin is a storage protein of eggs and apoplipoproteins hold cholesterol for transport
How many amino acids and how many classes of amino acids are there?
20 amino acids split into five classes based on side groups: nonpolar, polar, charged, negatively charged, and positively charged amino acids
Why is cysteine an important amino acid?
Cysteine has a CH2-SH side group, which contains a sulfhydryl side group which can produce disulfide linkages that help form the 3D shape of the protein.
How is proline different?
It has a ring structure that includes the central carbon atom. The central carbon binds to a -COOH and =NH (imino) group on the other side
Can R groups interact with other amino acids and atoms?
Yes
How can amino acids act as acids or bases?
The amino group can be basic by accepting a H+, and carboxyl can be acidic by donating a H+
What is the bond between amino acids called?
Peptide bonds, which form polypeptides (the subunit of proteins)
How is a peptide bond formed?
Dehydration synthesis between amino of one acid and carboxyl of the other
What are the N and C terminal ends of a polypeptide chain?
The C terminal is the carboxyl side and new amino acids are only added to this side. The N terminal is the amino side.
List the nonpolar amino acids
Alanine, valine, isoleucine, leucine, glycine, phenylalanine, tryptophan, methionine, proline (AVLIG FWMP)
List the uncharged polar amino acids
cysteine, serine, threonine, tyrosine, asparagine, glutamine (CS TYNQ)
List the negatively charged (acidic) polar amino acids
aspartic acid and glutamic acid (DE)
List the positiviely charged (basic) polar amino acids
Lysine, Arginine, Histidine (KRH)
Glycine
nonpolar, R group is H
Alanine
nonpolar, R group is methyl
Phenylalanine
nonpolar, R group is CH2 and benzene
Methionine
nonpolar, R group has methyl and sulfur
Serine
uncharged, hydroxyl group attached to a CH2
Threonine
uncharged, hydroxyl and methyl
tyrosine
uncharged, benzene ring with a hydroxyl group
glutamine
uncharged, 2 carbons then amino group attached to a carbon
cysteine
SH group, uncharged
glutamic acid
polar negative acidic, same structure as glutamine but instead of amino group, O-
histidine
positive, basic, polar, pentane ring structure
Describe the 4 levels of protein structure
Primary structure- unique sequence of amino acids forming the polypeptide
Secondary structure- produced by twists and turns of amino acid chain
Tertiary structure- overall 3D shape, formed by folding of amino acid chain with its secondary structure
Quaternary structure- formed from more than 1 polypeptide chain
What is the importance of amino acid order? Give an example
Changing even one acid can completely alter the structure, function, and higher levels of structure; substitution of a single amino acid in hemoglobin creates sickle cell disease
Describe secondary structures
formed from primary structure, alpha helix is twisted into right hand spiral and beta sheet zigzags in flat plane. Amino acid chemical groups extend outward from the spiral, helices form rigid, rod-like structures, stabilized by regularly spaced H bonds. hydrogen bonds stabilize sheets too.
What is a random coil?
has an irregularly folded arrangement; they provide flexible sites that allow the secondary structures to fold back on themselves and can also act as hinges to move parts of proteins.
describe tertiary structure
gives a protein its overall conformation; influenced by secondary structures, disulfide linkages, and hydrogen bonds. attractions between polar and nonpolar groups, etc. Determines a protein’s function, and arrangement and distribution of chemical groups determines chemical activity and solubility
How do cysteine sulfide linkages form?
Oxidation of sulfhydryl groups
What groups influence structure?
Basic, acidic, hydrophilic/phobic, sulfur containing
What is protein denaturation?
Unfolding of proteins due to temp, ph, chemicals so that it loses structure and function. can be reversible for some proteins
What did christian anfisen’s experiment do?
He took native ribonuclease and added chemicals that broke the 4 disulfide linkages present, then taking away the chemicals and reacting with oxygen in air reformed them with 95% recovert
Chaperonins
guide proteins called chaperonins or chaperone proteins bind temporarily with new proteins and allow them to fold correctly. unfolded polypeptide enters chaperonin cylinder, then cap goes on top, creating an enclosure, then protein folds and cap comes off
Quaternary structure
two or more polypetide chains- H-bonds, polar and polar, and disulfide; chaperonins allow for individual associations of amino acids
Functional domains
Subdivisions of proteins; in proteins with multiple functions, individual functions are located in different domains, and domains with similar functions are found in different proteins.
What are motifs?
3D arrangement of amino acid chains within and between domains produces highly specialized regions called motifs which have similar structures/sequences among proteins.
Give an example of a protein with domains
DNA polymerase- has a dna polymerase site that assembles DNA and a site that corrects mistakes during assembly (exonuclease site)
List protein combinations
link with lipids to form lipoproteins, found in membranes; link with carbs to form glycoproteins, which function as enzymes, antibodies, reception and recognition molecules, and extracellular supports. Link with nucleic acids to form nucleoproteins, which form structures like chromosomes.
