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What are the primary functions of proteins?
Amino acids are composed of _____, _____, and _____.
Amino acids are composed of an amino group, a carboxyl group, and a side chain.
What is a zwitterion?
Compounds that have a positive charge on one atom and a negative charge on another.
What is meant by the isoelectric point?
A pH at which a samle of amino acids or protein has an equal number of positive and negative charges.
Which amino acid forms a disulfide bond?
- Reduced to Cysteine
- Oxidized to Cystine (the dimer of cysteine)
Write the equation for the reaction of an amino acid with
1. a strong acid and
2. a strong base.
1. The reaction in a strong acid involves taking a proton (the --COO- becomes --COOH)
2. The reaction in a strong base involves giving a proton (the --NH3+ becomes --NH2)
Show how dipeptides are formed. What is the N-terminus? What is the C-terminus? Where is the peptide bond?
Dipeptides are formed when two amino acids combine.
The N-terminus is the end of the peptide that has a free alpha-amino group (H3+
The C-terminus is the end of the peptide that has a free alpha-carboxyl group (--COO-
The peptide bond is where the --COO-
group of one amino acid combines with the --NH3
group of another (removing the O and an H)
What are the properties of proteins?
- The backbone exhibits tautomerism.
- They act as buffers (zwitterion characteristics)
- Proteins are "generally" water soluble
What is the primary structure of a protein?
The linear sequence of amino acids is the primary structure of the protein.
The primary structure is largely responsible for the eventual higher-order structures of proteins.
Describe the four conformations related to the secondary structure of a protein.
Alpha-helix: A secondary structure where the protein folds into a coil held together by hydrogen bonds parallel to the axis of the coil.
Beta-pleated sheet: A secondary protein structure in which the backbone of two protein chains in the same or different molcules is held together by hydrogen bonds.
Extended helix of collagen: Gly-X-Y e.g. every third amino acid in the chain is glycine which has the shortest side chain (--H) of all amino acids and results in a triple helix.
Random Coil: those protein conformations that do not exhibit a repeated pattern
Describe the five main interactions that stabilize the tertiary structure of a protein.
1. Covalent bonds: Most commonly the disulfide (S-S) bond.
2. Hydrogen Bonding: between backbone --C=O and --N-H groups. (OH-OH)
3. Salt Bridges: Occur between acidic amino acids and a basic amino acid side chain. Held together by ion-ion attraction. (+3HN-COO-)
4. Hydrophobic Interactions: Nonpolar groups preferring to interact with each other when in aqueous solutions. The result is a series of hydrophobic interactions.
5. Metal Ion Coordination: Two side chains with the same charge link via a metal ion. (-OOC--Mg2+--COO-)
What is meant by the quaternary structure of a protein?
The highest level of protein organization is the quaternary structure, which applies to proteins with more than one polypeptide chain.
Quaternary structure determines how the different subunits of the protein fit into an organized whole.
What are integral membrane proteins?
An integral membrane protein (IMP) is a protein molecule (or assembly of proteins) that is permanently attached to the biological membrane.
What is meant by denaturation of a protein? How can proteins be denatured?
Any physical or chemical agent that destroys the stabilizing structures of a protein changes the conformation of the protein. This process is denaturation.
Denaturation The loss of the secondary, tertiary, and quaternary structures of a protein by a chemical or physical agent that leaves the primary structure intact.
Proteins can be denatured using heat, 6 M urea, detergents, acids and bases, salts, reducing agents, heavy metals, and alcohol. Anything that may affect the bonds that uphold the tertiary structure...
What is the function(s) of enzymes?
Enzymes cause reactions to take place faster by lowering the activation energy.
As catalysts, enzymes are remarkable in two respects:
1. They are extremely effective, increasing reaction rates by anywhere from 109 to 1020 times.
2. Most of them are extremely specific.
Enzymes are generally composed of _____.
Give the type of reaction that the following classes of enzymes catalyze: oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases.
- Oxidorecuctases A+ + B <--> A + B+
- Transferases A- B + C <--> A + B - C
- Hydrolases A - B + H2O <--> A - H + BOH
- Lyases Ax-By <--> A=B + X-Y
- Isomerases Ax-By <--> Ay-Bx
- Ligases A + B <--> AB
What is the influence of a) substrate concentration, b) enzyme concentration, c) temperature, and d) pH on enzyme activity?
- a) Substrate concentration
- Saturation Curve. The rate does not increase continuously because a point is reached after which the rate stays the same even if we increase the substrate concentration further. At the saturation point, substrate molecules are bound to all available active sites of the enzymes.
- b) Enzyme ConcentrationThe rate increases linearly because the molar concentration of enzyme is almost always much lower than that of substrate.
- c) TemperatureMost enzymes have an optimal temperature of 37 degrees C. If we start below this temp and increase the temp the reaction rate will increase. However, if we get too hot we may alter the enzyme surface and the reaction rate will decrease.
- d) pHThe curve is the same as with temps. There is an optimal pH (7.3 for humans). Too high or low decreases the reaction rate however within the narrow range of optinum increases...
Know the vocabulary....
- Active site
- Competitive inhibitor
- Noncompetitive inhibitor
- Negative modulation
- Positive modulation
- Regulatory site
Describe the lock and key model vs the induced fit model for enzymes.
Lock-and-key model - A model explaining the specificity of enzyme action by comparing the active site to a lock and the substrate to a key.
Induced-fit model - A model explaining the specificity of enzyme action by comparing the active site to a glove and the substrate to a hand. (The glove changes shape as the hand enters).
Draw a reaction energy diagram and label the reactants, products, transition state, activation energy, and deltaH.
What is meant by feedback control?
Feedback control is an enzyme regulation process in which formation of a product inhibits an earlier reaction in the sequence.
Need X so make X and now don't need X so stop making X until we need X again.
Nucleotides are composed of _____.
Purine or Pyrimidine Base + Sugar + Phosphate
The complimentary base pairs in DNA are _____ and in RNA they are _____.
The complimentary base pairs in DNA are G-C and A-T and in RNA they are G-C and A-U
The DNA and RNA bases that can be classified as purines are _____ and those that are pyrimidines are _____.
- Purines are Adenine (A) and Guanine (G)
- Pyrimidines are Cytosine (C), Thymine (T), and Uracil (U)
The sugar in DNA is _____ and the sugar in RNA is _____.
- The sugar component of DNA is 2-deoxy-D-ribose
- The sugar component of RNA is D-ribose
What is the difference among nucleoside, nucleotide, and nucleic acid?
- A nucleoside -- Base + Sugar
- A nucleotide -- Base + Sugar + Phosphate
- A nucleic acid -- A chain of nucleotides
What is the primary, secondary, and higher order structure of DNA?
The primary structure of DNA is the sequence of nucleotides that can include the Backbone of the molecule and the bases that are the side-chain groups.
The secondary structure of DNA is the double helix
The higher-order structures of DNA is the coiling etc that establish the condensed chromatin within the body that enables a meter of DNA to fit in the nucleous of a cell.
What is the function of tRNA, rRNA, mRNA, snRNA, miRNA, siRNA?
Transfer RNA - Transports amino acids to site of protein synthesis
Ribosomal RNA - Combines with proteins to form ribosomes, the site of protein synthesis
Messenger RNA - Directs amino acid sequence of proteins
Small nuclear RNA - Processes initial mRNA to its mature form in eukaryotes
Micro RNA - Affects gene expression; important in growth and development
Small interfering RNA - Affects gene expression; used by scientists to knock out a gene being studied.
What are genes?
The unit of heredity; a DNA segment that codes for one protein or one type of RNA.
What is the function of exons? Introns?
Exon Nucleotide sequence in DNA or mRNA that codes for a protein
Intron A nucleotide sequence in DNA or mRNA that does not code for a protein.
How does DNA replicate?
The DNA replication occurs in several distinct steps.
The superstructures of chromosomes are initially loosened by acetylation of histones.
Topoisomerases relax the higher structures.
Helicases at the replication fork separate the two strands of DNA.
RNA primers and primases are needed to start the synthesis of daughter strands. The leading strand is synthesized continuously be DNA polymerase. The lagging strand is synthesized discontinuously as Okazaki fragments.
DNA ligase seals the nicks and the Okazaki fragments.
What is the meaning of these terms as related to DNA/RNA?
- Leading Strand
- Lagging strand
- Origin of replication
- Replication fork
How is DNA repaired?
An important DNA repair mechanism is BER, or single base excision repair which is also the most common.
A second repair mechanism, known as NER for nucleotide excision repair removes not a single mismatched base but rather whole nucleotides.
Explain the two primary ways in which DNA is amplified.
1. Cloning - Allow a rapidly growing organism, like bacteria, to replicate DNA.
2. Polymerase chain reaction (PCR) - The use of two primers that are complementary to the ends of the gene or to the bordering DNA. Through heating and cooling, using these primers to create millions of copies of the original DNA strand...
What is meant by the central dogma?
A doctrine stating the basic directionality of heredity when DNA leads to RNA, which leads to protein. This doctrine is true in almost all life forms except certain viruses.
What is meant by gene expression?
The activation of a gene to produce a specific protein. It involves both transcription and translation.
Gene expression is the turning on or activation of a gene.
Describe the basic process of transcription and translation.
Transcription is the process in which information encoded in a DNA molecule is copied into an mRNA molecule.
The mRNA carries the copy to the site of protein synthesis where Translation takes place.
Translation is the process in which information encoded in an mRNA molecule is used to assemble a specific protein.
How does DNA get transcribed into RNA?
In transcription, the information is copied from DNA onto mRNA by complementary base pairing. There are also start and stop signals.
The enzyme that synthesizes RNA is called RNA polymerase.
In eukaryotes, three kinds of polymerase are used for the different types of RNA (Pol I, II, and III).
What is the role of the polymerases (I, II, III) in transcription?
In eukaryotes, three kinds of polymerases catalyze transcription. RNA polymerase I (pol I) catalyzes the formation of most of the rRNA; Pol II catalyzes mRNA formation; and Pol III catalyzes tRNA formation as well as one ribosomal subunit and other small regulatory RNA types, like snRNA.
What is meant by the template strand of DNA?
The strand of DNA that serves as the template during RNA synthesis.
What is the role of a promotor? Termination sequence?
Promotor an upstream DNA sequence that is used for RNA polymerase recognition and binding to DNA. "The start signal"
Termination sequence a sequence of DNA that tells the RNA polymerase to terminate synthesis. "The Stop transcription"
What is a codon? Anticodon?
Codon A three-nucleotide sequence on mRNA that specifies a particular amino acid.
Anticodon A sequence of three nucleotides on tRNA, also called a codon recognition site, complementary to the codon in mRNA.
What is meant by the genetic code?
The sequence of triplets of nucleotides (codons) that determines the sequence of amino acids in a protein.
The genetic code is almost uniersal.
How do mutations occur?
Ionizing radiation (X rays, ultraviolet light, gamma rays) can cause mutations. Furthermore, a large number of organic compounds can induce mutations by reacting with DNA. Such compounds are called mutagens.
Explain recombinant DNA technique.
DNAs from two sources that have been combined into one molecule.