Exam II Flashcards
Nucleic Acids
polymers specialized for the storage, transmission, and use of genetic information. There are two types of Nucleic acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). They are polymers composed of monomers called nucleotides
• DNA
encodes hereditary information. DNA and the proteins encoded by DNA determine metabolic functions
RNA
intermediates, the information encoded in DNA is used to specify the amino acid sequences of proteins
Distinguishing RNA from RNA
Sugar: Ribose, Bases: adenine, cytosine, guanine, uracil, Strands: Single
Distinguishing RNA from DNA
Sugar: Deoxyribose, Bases: Adenine, Cytosine, Guanine, Thymine, Stands: Double
• Nucleotides consist of three components
• Nucleosides
Molecules consisting of a pentose sugar and a nitrogenous base-but no phosphate group
• The base 0f nucleic acids take one of two chemical forms:
a six membered single-ring structure called a pyrimidine, or a fused double-ring structure called a purine.
• Purine
Fused double-ring structure form of a nucleic acid. Adenine and Guanine.
• Pyrimidine
– a six membered single-ring structure form of a nucleic acid. Cytosine, Thymine, and Uracil
• During formation of a nucleic acid
new nucleotides are added to an existing chain one at a time.
• Phosphodiester Linkage
The resulting bond of a condensation reaction done by the hydroxyl group when creating a nucleic acid. This linkage reaction always occurs between the phosphate on the new nucleotide (5’) and the carbon at the 3’ position on the last sugar.
• Nucleic acids group in the 5’ to 3’ direction
• The pentose sugar and phosphate provide what in the nucleotides
• The pentose sugar and phosphate provide the hydroxyl functional groups for the linkage of one nucleotide to the next. This is done through condensation reaction, and the resulting bond Is called a phosphodiester linkage.
• Oligonucleotides
include RNA molecules that function as primers to begin the duplication of DNA; RNA molecules that regular the expression of genes; and synthetic DNA molecules used for amplifying and analyzing other, lo0nger nucleotide sequences
• Polynucleotide
more commonly referred to as nucleic acids, include DNA and most RNA. Polynucleotides can be very long, and indeed are the longest polymers in the living world. Some DNA molecules in humans contain hundreds of millions of nucleotides
Why is DNA less flexible than RNA?
• The lack of a hydroxyl group at the 2’ position in DNA makes its structure less flexible than that of RNA, which, unlike DNA, can form variety of structures
• Complementary base pairing
In DNA, A-T, C-G. In RNA, A-U, C-G. Base pairs are held together primarily by hydrogen bonds.
• The hydrogen bond attraction is not as strong as a covalent bond. The base pairs are relatively easy to break with a modest input of energy. The breaking and making of hydrogen bonds in nucleic acids is vital to their role in living systems
• RNA
– Rna is a single strand, however, many single stranded RNA molecules fold up in 3d structures, because of hydrogen bonding between the ribonucleotides in separate portions of the molecules. This results in a 3d surface for the bonding and recognition of other molecules. This folding occurs by complementary based pairing, and the structure is thus determine by the particular order of bases in the RNA molecule
• DNA
DNA is usually double stranded; that is, it consists of two separate poly nucleotide strands of the same length. DNA is remarkably uniform. The sugar phosphate groups form the sides of the ladder, and the bases with their hydrogen bonds form the runs on the inside. DNA carries genetic information in its sequence of base pairs rather than in its 3d structure. The key differences among dna molecules are manifest in their different nucleotide base sequences.
- DNA is a purely informational molecule. The information encoded in the sequence of basses carried in its strands.
- DNA replication
- RNA
some DNA sequences can be copied into RNA, in a process called transcription. The nucleotide sequence in the RNA can be used then to specify a sequence of amino acids in a polypeptide chain. This process is called translation.
- Gene expression
the overall process of transcription and translation
Replication, transcription, translation
In what order is DNA replicated and transcribed
- DNA republication and transcription depend on the base pairing properties of nucleic acids.
o 5’-TCAGCA-3’
o 3’-AGTCGT-5’ - Transcription of the lower strange will result in a single strand of RNA with the sequence 5’-UCAGCA-3’
- DNA republication usually involves the entire DNA molecule. Since DNA holds essential information, it must be replicated completely so that each new cell or new organism receives a complete set of DNA from its part
- Genome
- Genes
the sequences of DNA that encode specific proteins and are transcribed into RNA
- In humans, the gene that only encodes the major protein in hair (keratin) is expressed only in skin cells. The genetic information in the keratin-encoding gene is transcribed into RNA and then translated into a keratin polypeptide
- Enzymes
are catalytic proteins that speed up biochemical reactions
- Defensive proteins
such as antibodies recognize and respond to substances or particles that invade the organism from the environment
- Hormonal and regulatory proteins
- Storage proteins
store chemical building blocks-amino acids-for later use.
- Structural proteins
such as collagen provide physical stability movement
- Transport proteins
such as hemoglobin carry substances within the organism
- Genetic regulatory proteins
regulate when, how, and to what extent a gene is expressed
Amino acids are the building blocks of proteins
- Amino acids
all contain two functional groups: the nitrogen containing amino group and the carboxylic acid group.
- Only 20 amino acids occur extensively in the proteins in all organisms
- R Group
- Blue group
Five amino acids have electrically charged side chains (+1 or -1), attract water, and attract oppositely charged ions
- Purple group
five amino acids have polar side chains and ten to form hydrogen bonds with water and other polar or charge substances. These amino acids are also hydrophilic
- Green group
Seven amino acids have side chains that are nonpolar hydrocarbons or very slightly modificed hydrocarbons. In the watery environment of the cell, these hydrophic side chains may cluster together in the interior of the proein. These amino acids are hydrophic
- Orange group
– three amino acids –cysteine, glycine, and prline – are special cases, although the side chains of the later two generally are hydrophix
o The cystein side chain, which has a terminal –SH group, can react with another cyseine side chain to form a covalent bond called a disulfide brige. Disulfide bridges help determine how a polypeptide chain folds.
o The glycine side chain consists of a single hydrogen atomn and is small enough to fit into tight corners in the interior of a protein molecule, where a larger side chain cold not fit
o Proline possesses a modified amino group that lacks a hygrogen and insidead forms a covalent bond with the hydrocarbon side chain, resulting in a ring structure. This limits both its hydrogen bonding ability and its ability to rotate. Thus proline often functions to stablize bends or loops in proteins
- Peptides
amino acids can form short polymers of 20 or fewer amino acids. These include some hormones and other molecules involved in signaling from one part of an organism to another.
- Polypeptides
- Polymerization
takes place in ther amino to carboxyl direction
- Proteins and peptides form via
a seuqnetial addition of new amino acid to the end of existing chains. The amino group of the new amino acid reacts with the carboyxl group of the amino acid at the end of the chain. This condensation reaction forms a peptide linkage.
- Primary structure
the primary structure of a protein is established by covalnt bonds, but higher levels of structure are determined largely by weaker forces such as hydrogen bons and hydrophobic and hydrophilic interations
- Secondary structure
a proteins secondary structure consists of regular, repeated spaatial patterns in different regions of a polypeptide chain. There are two basic types of secondary structure, both determined by hydrogen bonding between the amino acid that make up the primary structure
o The alpha helix - a right handed coil that turns in the same direction as a standard wood screw. The R groups extend outward from the peptide backbone of the helix. The coiling results from hydrogen bonds that form between the N-H group on one amino acid and the C=O group on another within the same turn of the helix.
o The beta pleared sheet – formed from two or more polypeptide chains that are extended and aligned. The sheet is stablized by hydrogen bonds between the N-H groups and C=O groups on the two chains. A beta pleated cheet may form between separate polypeptide chains or between different regions of a single polypeptide chains that is bent back on itself.
- Tertiary structure
- Tertiary structure R group reactions
Disulfide bridges can form between specific cysteine side chains, holding a folded polypeptide together. Hydrogen bonds between side chains also stablize folds in proteins. Hydrophobic side chains can aggregate together in the interior of a protein, away from water, folding the polypeptide in the process. Van der Waals internations can stablize close associations between hydrophobic side chains. Ionic interations can form between positively and negativwely charged side chains, forming salt bridges between amino acids. Inonic bonds can alos be buried deep wiuthin a protein, away from water.
- Denatured
Both secondary and tertiary structure derive from primary structure. If a protein is heated slowly, the heat will disrupt only the weaker interactions, causing the secondary and tertiary structure to break down. The protein is then said to be denatured.
- In many ases the protein can return to its normal teriary structure when it cools, demonstrating that all the information needed to specify its unique shape is contained in its primary structure.
- Quarternary structure
– many functional proteins contain two or more polypeptide chain, called subunits, each folded into its unique teriary structure. The protein’s quarternary structure results from the ways in which these subunits bind together and interact.
- Various conditions can alter the weak, noncovalent interactions:
o Increases in temp causes more rapid molevular movements and thus can break hydrogen bonds and hydrophic interactions
o Alterations in the concentration og H+ can change the patterns of ionization fo the exposed carboyxl and amino groups, thus disrupting the pattern of ionic attractions and repulsions
o High concentrations fo polar substances such as urea can disrupt the hydrogen bonding that is crucial to protein structure
o Nonpolar substances may also denature a protein in cases where hydrophic groups are essential for maintaing the protein’s structure.
- Catalysts
– substances that speed up reactions without themselves being permanently altered. A catalyst does not cause a reaction to occur that would not proceed without it, but it increases the rate of the reaction. No catalyst makes a reaction occur that cannot otherwise occur.
- A bio catalyst provides a molecular structure that binds the reactants and can participate in the reaction itself. This participation does not permanently change the enxyme. At the end of the reaction, the catalyst is unchanged and available to catalyze additional similar reactants
To speed up a reaction, an energy barrier must be overcome
Enzymes bind specific reactants at their active sites
- Catalysts increase the rates of chemical reactions.
- Most nonbiological catalysts are nonspecific. For example, powdered platinum catalyzes virtually any reactant in which molecular hydrogen is a reactant.
- Most biological reactants are highly specific.
- Substrated 0 reactants in an enxyme catalyzed reactions.
- Active site
substrate molecules bindg to a particular site on the enzyme.
- The specificty of an enzyme results from the exact 3d shape and chemical properties of its active site. Only a narrow range of substrates, with specific shapes, functional groups, and chemical properties, can fit properly and bind to the active site.
- Enzyme-substrate comlex
– the binding of a substrate to the active site of an enzyme produces an ES complex that is held together byu one or more means, such as h bonding, electrical attraction, or temporary covalent bonding.
- The ES copmlex gives rise to product and free enzyme.
- During and after the formation of the ES copmlex, chemical interactions occur. These interactions contribute directly to the breaking of old bonds and the formation of new ones. IUn catalyzing a reaction, an enxyme may use on or more mechanisms
o Inducing strain – once the substrate has bound to the active site, the enzyme causes the bonds in the substrate to stretch, putting it in an unstable transition state.
o Substrate orientation – When free in solutions, substrates are moving from place to place randomly while at the same time vibrating, rotationg, and tumbling. The enzyme lowers the activation energy needed to start the reaction, by bringing together specific atoms so that bonds can form
o Adding chemical groups – The side chains of an enzyme’s amino acids may be directly involved in the reation.
o Most for enzymes and substrates the relationship is more like a baseball and a catcher’s mitt: the substrate first binds and then the active site changes slightly to make the binding tight.
o The rest of the macromolecule has at least three roles:
It provides a framework so the amino acids of the active site are properly positioned in relation to the substrate
It participates in the changes in protein shape and structure that result in induce fit
I provides binding sites for regulatory molecules.
Noneprotein partners
Some enzymes require ions or other molecules to function
- Cofactors
inorganic ions such as copper, zinc, and iron that bind to certain enzymes.
Coenzyme
- Prosthetic groups
Rate of Reaction
- For a given concentration of enzyme, the rate of the enzyme-catalyzed reaction initially increases as the substrate concentration increases from zero but then it leveles off. Why? Because the concentration of an enzyme is usually much lower than that of its substrate and does not change as substrate concentration changes. When all the enzyme molecules are bound to substrate molecules, the enzyme is working at its maximum rate. Under these conditions the active sites are said to be saturated
Enzymes can be regulated by inhibitors
- Various chemical inhibitors can bind to enzymes, slowing down the rats of the reactions they catalyze.
- Naturally occuring inhibitors regulate metaboloism
- Irreversible inhibition
if an inhibitor covalently binds to an amiono acid side chain at the active site of an enxyme, the enxyme is permanently inactivated because it cannot interact with its substrate. The irreversible inhibition of enzymes is of partical use to humans, but this form of regulatiojn is not common in the cell because the enzyme is permnanently inactivated and cannot be recyled
Reversible inhibition
– an inhibitor is similar enough toa particular enzyme’s natural substrate that it can bind noncovalently to the active site, yet different enough that no chemical reaction occurs. This is analogous to a key that inserts into a lock but does not turn it. When such a molecule is bound to the enzyme, the natural substrate cannot enter the active site and the enzyme is unable to function
o Competitive inhibitor – competes with the natural substrate for the active site.
o Iin this case, the inhibition is reversble. When the concentration of the competitive inhibitor is reduced, the active site is less likely to be occupied by the inhibitor
- Noncompetitive inhibitor
An allosteric enzyme is regulated via changes in its shape
- The change in enzyme shape that is due to noncompetitive inhibitor binding is an example of allostery
- Allosteric regulation
occurs when a non substrate molecule binds or modifies a site other than the active site of an enzyme, inducing the enzyme to change its shape. The change in shape laters the chemical attraction of the active site for the substrate, and so the rate of the reaction is change. Allosteric regulation can result in the activation of a formerly inactive enzyme, or the inactivation of an enzyme.
o Covalent modification
- An enzyme can have more than one allosteric site and these may be modified by eithe covalent or noncovalent bonding
o Covalent modification – an amino acid reisdue can be covalently modified by the addition of phosphate. If this occurs in a hydrophic region fo the enzyme, it makes that region hyfrophilic, because phosphate carries a negative charge. The porotein twists, and this can expose or hide trhe active site.
o Noncovalent binding
- An enzyme can have more than one allosteric site and these may be modified by eithe covalent or noncovalent bonding
A regulatory molecule may bind noncovalently to an allosteric site, causing the enzyme to change shape. This can either activate or inhibit the enzyme’s function.
- Internal Membrane
Some groups of bacteria-including cyanobacteria- carry out photosynthesis: they use energy from the sun to convert carbon dioxide and water into carbohydrates. These bacteria have an internal membrane system that contains molecules needed for photosynthesis.
