What functional groups do all amino acids share?
amino and carboxyl (which is acidic)
What part of the amino acid is different from one to the next?
The side chain or R group
What functional groups would you find in the side chains of polar amino acids?
a hydroxyl (OH), a sulfhydryl (SH), or a combination of carbonyl (=O) and uncharged amino (NH2)
What functional groups would you find in the side chains of acidic amino acids? What charge do they carry?
A carboxyl group (COO-), which is negatively charged
What functional groups would you find in the side chains of a basic amino acids? What charge do they carry?
A charged amino group (NH+, NH2+, NH3+)
What functional groups would you find in the side chain of nonpolar amino acids?
You might see methyl (CH3) but none of the other functional groups. Nonpolar side chains are mainly composed of carbon-hydrogen bonds that are nonpolar.
How would you use a pipe-cleaner to model the four levels of protein structure?
The pipe-cleaner itself represents the primary structure or chain of amino acids.
Taking a portion of the pipe cleaner and making a spiral to represent an alpha helix or zig-zagging it to make a beta pleated sheet would represent the secondary structures.
Bending the entire pipe-cleaner over itself to connect distant points on the pipe-cleaner represents the interactions between side chains that results in the tertiary structure
Adding another folded pipe-cleaner would represent the joining of two different polypeptides to represent quaternary structure.
Describe each level of protein structure
Primary structure is a specific sequence of amino acids held together by peptide bonds
Secondary structures are areas of folding that occur due to hydrogen bonding between amino and carboxyl groups to form alpha helix and/or beta pleated sheets
Tertiary structure is the final 3D shape of the polypeptide after side chain interactions have formed
Quaternary structure is multiple polypeptides held together by side chain interactions between the polypeptides
What types of bonds hold together each level of protein structure?
Primary- covalent peptide bonds
Secondary- hydrogen bonds
Tertiary- various types depending on side chains. Nonpolar sidechains form hydrophobic interactions, polar sidechains form hydrogen bonds with each other and water molecules on the outside, acidic and basic sidechain for ionic bonds, cysteine sidechains can form covalent disulfide bridges
Quaternary- similar to tertiary but between sidechains on the different polypeptide chains
What type of side chains clump together away from water?
Nonpolar/hydrophobic
What type of side chains form hydrogen bonds?
polar
What type of side chains form ionic bonds with each other?
basic and acidic
What type of side chains form disulfide covalent bonds?
cysteine side chains
A side chain contains a hydroxyl group (OH). Is it polar, nonpolar, acidic, or basic? What type of bonds will it form during protein folding?
polar: hydrogen bonds
A side chain contains only carbon and hydrogen. Is it polar, nonpolar, acidic, or basic? What type of bonds will it form during protein folding?
nonpolar: hydrophobic interactions (clump with other nonpolar sidechains away from water)
A side chain contains a carboxyl group (COO-). Is it polar, nonpolar, acidic, or basic? What type of bonds will it form during protein folding?
acidic: it will form ionic bonds with basic side chains or other + charged molecules
A side chain contains a charged amino group (NH3+). Is it polar, nonpolar, acidic, or basic? What type of bonds will it form during protein folding?
basic: it will form ionic bonds with acidic side chains or other negatively charged molecules
A side chain contains a sulfhydryl group (SH). Is it polar, nonpolar, acidic, or basic? What type of bonds will it form during protein folding?
polar- it will form covalent disulfide bridges with another cysteine side chain
What type of side chains tend to be toward the interior of a protein’s tertiary and quaternary structure? Which types tend to be towards the exterior?
nonpolar side chains are hydrophobic and tend to be clumped in the middle of a protein
polar, acidic, and basic side chains are hydrophilic and tend to be oriented towards the outside of a protein
What happens when a protein denatures?
The protein unravels/unfolds because hydrogen and ionic bonds are disrupted
What intracellular conditions can cause a protein to denature?
- high temperatures
- high or low pH
- high or low salinity
Which level of protein structure is not affected by denaturation?
primary because it is held together by covalent bonds and not hydrogen or ionic bonds
Explain how a mutation in DNA can cause a protein’s function to change.
The sequence of bases in a gene determine the sequence of amino acids at the primary level. If the order of amino acids is changed, the side chains may interact differently and/or take up more or less space in the protein. This may cause the protein to fold into a different shape and keep the protein from interacting with other molecules in the same way.
What is the function of enzymes?
Perform chemical reactions- an enzyme generally performs either a type of dehydration synthesis or hydrolysis reaction
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11.1 Genotype, Phenotype, Punnett Squares27
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10.3/10.4 Meiosis and Errors26
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10.2 Mitosis and Differentiation23
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10.1 Cell Cycle25
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9.2 Membrane Transport23
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9.1 Cell Structure and Function33
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8.4 Translation and Mutations34
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8.3 Transcription and Central Dogma30
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8.2 DNA Replication26
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8.1 DNA39
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7.3 Cellular Respiration25
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7.2 Metabolism22
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7.1 Enzyme Structure and Function20
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6.3 Protein Structure and function29
