Basic Molecules
I. Proteins
A. Subunits
1. Made up of a linear chain of amino acids linked together by peptide bonds
2. Of all amino acids, glycine is the simplest
H
O+| H |
H-N - C - C = O
|
H
3. Amino acids are able to ionize in aqueous solutions
a) primary amine group can take on a positive charge
b) carboxylic acid group can take on a negative charge
4. Some of the side groups on the alpha carbon are also charged in aqueous solution
B. Peptide bond
1. The structure of the bond is shown
H
R
O-
|
| |
N-C-C=O
H
|
|
+| H |
H-N - C - C = O
second
amino acid
|
H
glycine
|
H
2. Proteins are built up by forming peptide bonds between numerous amino acids
3. Amino acids are known by three-letter codes and single-letter codes
C. Higher levels of structure
1. Above the primary level, proteins adopt complex secondary configurations
2. Alpha helix and beta-pleated sheet are the most common motifs
3. Collections of motifs are common, for example, helix-loop-helix (HLH)
4. Examples are known from x-ray solutions of protein 3-dimensional structures
5. Tertiary-level structure is made by clipping the linear sequence or S-S bonding
D. In addition to single proteins, assemblages of proteins or polypeptides also do work
1. Proteins join through lock-and-key mechanisms making dimers or multimers
2. Two like molecules make up a homodimer; two unlike make up a heterodimer
II. Lipids
A. Contain one or more long hydrocarbon chains, sometimes covalently linked to glycerol
B. In a phospholipid, the 3-carbon glycerol covalently bonds phosphate at carbon 3 (C3)
1. One or both C1 and C2 have a hydrocarbon chain making the molecule amphipathic
2. A polar or charged group, such as choline, may also attach to the phosphate group
3. Phospholipid charged groups and polar groups interact with water
4. Their hydrocarbon chains undergo self-association in the core of membranes
C. In mono-, di-, or tri-glycerides, one or more hydrocarbons are linked to carbons 1-3
III. Nucleic acids
A. DNA has unique properties as a biomaterial (DNA is an information warehouse.)
1. Two long linear molecules of DNA make up a double helix by self-association
2. Repeating sugar-phosphate-sugar-phosphate linkages make a rigid backbone
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3. Relatively few types of chemical moieties (A, G, C, T) are found linked to sugar
4. Hydrogen bonding occurs between purine (A, G) and pyrimidine (C, T) type bases
5. Aggregate strength of the many hydrogen bonds makes the double helix very stable
B. Properties and functions of RNA
1. RNA contains more moieties (nitrogenous residues) due to having modified bases
2. Large portions of RNA structure can be found in single-stranded form
3. Stable three-dimensional projections of RNA can form in a strand by base pairing
4. Two major RNA classes exist in cells, one long-lasting and the other short-lived
Basic Processes
I. Replication
A. Double-stranded (ds) DNA is the starting material and dsDNA is produced
1. Process takes place in a replication bubble with a replication fork at each end
2. Two methods of DNA polymerase moving along the template
a) one is called leading strand synthesis
b) second is called lagging strand synthesis
3. Many other molecules are required for DNA synthesis including:
a) primase to synthesize a primer of RNA
b) helicase to unwind the DNA double helix
c) single-strand binding protein (also called helix destabilizing protein)
d) DNA polymerase is held onto the single strand of template by a clamp
B. The sequence of each daughter strand is dictated by the bases in template strand
II. Transcription
A. One strand of ds DNA is the starting material, and each coding unit corresponds to a gene
1. A single-stranded RNA is produced
2. RNA polymerase only moves in one direction on each gene
3. Polymerase is directed to a site on DNA where it should start by one or more
promoters
4. Many other molecules are required including:
a) sigma factor in bacteria or, in eukaryotes, other regulatory factors
b) these often fall off when polymerase starts progressing along template strand
c) "processivity" is aided by some proteins in eukaryotes (TFIIF, TFIIJ)
B. Three types of RNA polymerase transcribe three different types of genes
1. Polymerase I transcribes the ribosomal DNA (which encodes most rRNAs)
a) this process runs repetitively
b) 13 kilobases (45 Svedberg units) of RNA are the first product, but it is
rapidly broken down into smaller sequences of RNA.
2. Polymerase II transcribes single-copy genes
a) the process of Pol II transcription is highly regulated by proteins
b) also, enhancers upstream, downstream, or even inside introns regulate it
c) RNAs made by Pol II are called messenger RNAs, and their size is variable
3. Polymerase III transcribes the small RNAs making up the tRNAs and a single one
of the rRNA strands
III. Translation
A. There are five main steps in the process of making a protein (called translation)
1. tRNA is “charged” with an amino acid by a tRNA-aminoacyl synthetase. There
are 20 of these enzymes, and each recognizes a separate tRNA.
2. “Charged” tRNA binds to a protein, IF2, and the complex is attached to the
ribosome small subunit in this form
3. mRNA also loads onto the small subunit, which then combines with the large
4. Anticodon sequence of tRNA is fitted to a codon in the mRNA and amino acid
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incorporated into the nascent polypeptide chain by peptide bond formation
5. tRNA enters a site called A, and after peptide bond formation, is cycled to site P
a) specificity for the amino acid resides in the anticodon matching, and not in the
amino acid itself (i.e., there is no proofreading of the amino acid sequence)
b) synthesis is terminated when the last (stop) codon is read.
c) the last tRNA is hydrolyzed at A site, rather than forming a peptide bond,
with the result that the polypeptide ends in a carboxylic acid group.
B. Proteins that remain in cytoplasm or are destined for specific compartments below are
made on cytoplasmic ribosomes
1. Specific targeting signals exist for nucleoplasm, mitochondria, and chloroplast
2. Some cytoplasmic proteins have lipids added to them after translation and can
bind loosely to membranes
3. Polypeptides that are routed to Golgi, lysosomes, secretory vacuoles, or plasma
membrane (PM) are segregated at the ER
a) mRNA encodes a signal peptide, causing protein to be co-translationally
segregated
b) Signal recognition particle (SRP) temporarily halts translation until
ribosome becomes anchored on the surface of endoplasmic reticulum (ER)
c) SRP is displaced and synthesis resumes through a pore in ER membrane
d) signal peptide is cleaved off by signal peptidase after protein enters the ER
C. Polypeptides that are co-translationally segregated into ER can have one of these fates
1. Secreted (an example used in class was insulin secretion from the pancreas)
2. Routed to the plasma membrane (examples used in class: dystroglycan, CFTR)
3. May become membrane-bound proteins in Golgi, lysosome or secretory vacuoles
4. Or be one of about 40 proteins that are routed to lysosome (hydrolytic enzymes)
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