Chapter 21: Nucleic Acids and Protein Synthesis

Synthesis of mRNA

1. DNA strand unwind, exposing sequence to be transcribed. 2. mRNA (tRNA & rRNA) forms on DNA template. 3. DNA strands rewinds. 4. Synthesized mRNA.

RNA Synthesis

1. The DNA double helix begins to unwind at a point near the gene that is to be transcribed.

Replication steps

1. Unwinding of the double helix. 2. Synthesis of DNA segments. 3. Closing the nicks.

Initiation of the polypeptide chain.

1. mRNA aligns on a small ribosomal subunit so that AUG, the initiating codon, is at the ribosomal P site. 2. A tRNA with an attached N-formylmethionine forms hydrogen bonds with the codon. 3. A large ribosomal subunit binds to the small subunit and completes the initiation complex.

Total number of codons

64 only 61 represent amino acids

Okazaki fragments

A DNA fragment produced during replication as a result of strand growth in a direction away from the replication fork. The DNA fragments separated by the nicks.

Nucleic acid

A biomolecule involved in the transfer of genetic information from existing cells to new cells.

Ribonucleic acid (RNA)

A nucleic acid found mainly in the cytoplasm of cells.

Deoxyribonucleic acid (DNA)

A nucleic acid found primarily in the nuclei of cells

Replication fork

A point where the double helix of a DNA molecule unwinds during replication. The point where unwinding takes place.

Semiconservative replication

A replication process that produces DNA molecules containing one strand from the parent and a new strand that is complementary to the strand from the parent.

Initiation complex

A resulting complex binds to the large ribosomal subunit to form a unit.

Exons

A segment of a eukaryotic DNA molecule that is coded for amino acids.

Introns

A segment of an eukaryotic DNA molecule that carries no codes for amino acids.

Codon

A sequence of three nucleotide bases that represents a code word on mRNA molecules.

Ribosome

A subcellular particle that serves as the site of protein synthesis in all organisms. The sites of protein synthesis.

Anticodon

A three-base sequence in tRNA that is complementary to one of the codons in mRNA. Enables the tRNA to bind to the mRNA during protein synthesis.

Chromosome

A tightly packed bundle of DNA and protein that is involved in cell division. A human cell normally contains 46 structural units.

Start Codon

AUG also codes for Methionine Initiation codon only when it occurs as the first codon of a sequence. fMet

Bases found in both RNA and DNA

Adenine (A), guanine (G), and cytosine (C)

Gene

An individual section of a chromosomal DNA molecule that is the fundamental unit of heredity. The fundamental units of heredity. Each one directs the synthesis of a specific protein.

Purine

Bases: 1. Adenine (A) 2. Guanine (G)

Pyrimidine

Bases: 1. Uracil (U) 2. Thymine (T) 3. Cytosine (C)

Two Hydrogen bonds

Between adenine (A) and thymine (T) there are how many hydrogen bonds are there.

3' end of tRNA

Binds to an amino acid and transports it to the site of protein synthesis.

DNA ligase

Catalyzes the nicks on DNA replication.

RNA polymerase

Catalyzes the synthesis of RNA.

Methionine, initiation

Codons: 1 AUG

Tryptophan

Codons: 1 UGG

Lysine

Codons: 2 AAA, AAG

Asparagine

Codons: 2 AAC, AAU

Glutamine

Codons: 2 CAA, CAG

Histidine

Codons: 2 CAC, CAU

Glutamic acid

Codons: 2 GAA, GAG

Aspartic acid

Codons: 2 GAC, GAU

Tyrosine

Codons: 2 UAC, UAU

Cysteine

Codons: 2 UGC, UGU

Phenylalanine

Codons: 2 UUC, UUU

Isoleucine

Codons: 3 AUA, AUC, AUU

Threonine

Codons: 4 ACA, ACG, ACG, ACU

Proline

Codons: 4 CCA, CCC, CCG, CCU

Alanine

Codons: 4 GCA, GCC, GCG, GCU

Glycine

Codons: 4 GGA, GGC, GGG, GGU

Valine

Codons: 4 GUA, GUC, GUG, GUU

Arginine

Codons: 6 AGA, AGG, CGA, CGC, CGG, CGU

Leucine

Codons: 6 CUA, CUC, CUG, CUU, UUA, UUG

Serine

Codons: 6 UCA, UCC, UCG, UCU, AGC, AGU

Stop signals

Codons:3 UAG, UAA, UGA

Nucleotide positions

The base is always attached to the 1' position of the sugar, and the phosphate is generally located at the 5' position.

Amino acids

The building block of proteins.

Genetic code

The communicative relationship between mRNA nucleotides and amino acids.

Translation

The conversion of the code carried by messenger RNA into an amino acid sequence of a protein. From mRNA to tRNA. Convert to another language.

Nicks

The gaps or breaks between segments in the daughter strand.

Phosphodiester bonds

The linkages of nucleotides joined together in nucleic acids by phosphate groups that connect the 5' carbon of one nucleotide to the 3' carbon on the next. The result is a chain of alternating phosphate and sugar units to which the bases are attached.

Replication

The process by which an exact copy of a DNA molecule is produced. Occurs when two strands of DNA separate and each serves as a template for the construction of its own complement. Means to copy or to repeat.

Synthesis of DNA segments

The process proceeds from the 3' end towards the 5' end of the exposed strand (the template). Because the two strands are antiparallel, the synthesis of new nucleic acid strands proceeds toward the replication fork on one exposed strand and away from the replication fork on the other stand. New (daughter) DNA strands form as nucleotides. As the synthesis proceeds, a second replication fork is created when a new section of DNA unwinds. A new segment of ths strand begins growing from the new fork but is not initially bound to the segment that grew from the first fork. Thus, as the parent DNA progessively unwinds, this daughter strand is synthesized as a series of fragments that are bound together in step 3.

Nucleotide

The repeating structural unit or monomer of polymeric nucleic acids. Are composed of three simpler components: a heterocyclic base, a sugar, and a phosphate. (Pyrimidines and purines, Ribose or 2-deoxyribose, and phosphate.)

Nucleic acid backbone

The sugar-phosphate chain that is common to all nucleic acids. It is constant throughout the entire DNA molecule.

Polymerase chain reaction (PCR)

The technique mimics the natural process of replication, in which the DNA double helix unwinds. Became a standard research technique for detecting all manner of mutations associated with genetic disease. Can be used to detect the presence of unwanted DNA, as in the case of a bacterial or viral infection. Offers a fast and simple alternative. Has permitted DNA to be amplified from some unusual sources, such as extinct mammals, Egyptian mummies, and ancient insects trapped in amber.

Transcription

The transfer of genetic information from a DNA molecule to a molecule of messenger RNA. Transferring the necessary information from a DNA molecule onto a molecule of messenger RNA. Rewrite

Central dogma of molecular biology

The well-established process by which genetic information stored in DNA molecules is expressed in the structure of synthesized proteins.

Phosphate

Third component of nucleotides. Derived from phosphoric acid (H₃PO₄), which under the cellular pH conditions exists in ionic form.

Bases only found in DNA

Thymine (T)

Rewrite

Transcription

Convert to different language

Translation

Complementary DNA strands

Two strands of DNA in a double-helical form such that adenine and guanine of one strand are matched and hydrogen bonded to thymine and cytosine, respectively, of the second strand.

Bases only found in RNA

Uracil (U)

DNA sugar component

ᴅ-deoxyribose Occurs in the β-configuration.

RNA sugar component

ᴅ-ribose Occurs in the β-configuration,

Most degenerate codons

Leucine, serine, and arginine. Each one represent six codons.

Represented by single codon

Methionine and tryptophan

Degeneracy

Most of the amino acids are represented by more than one codon.

Closing the nicks

One daughter DNA strand is synthesized without any nicks, but the Okazaki fragments of the other strand must be joined together. An enzyme called DNA ligase catalyzes this final step of DNA replication. The result is two DNA double-helical molecules that are identical.

P site

Peptidyl site

Heterocyclic compounds

Pyrimidine or a purine.

Heterogeneous nuclear RNA (hnRNA)

RNA produced when both introns and exons of eukaryotic cellular DNA are transcribed.

Messenger RNA (mRNA)

RNA that carries genetic information from the DNA in the cell nucleus to the site of protein synthesis in the cytoplasm. Has a short lifetime - usually less than an hour. Synthesized as needed and then rapidly degraded to the constituent nucleotides.

Ribosomal RNA (rRNA)

RNA that constitutes about 65% of the material in ribosomes, the sites of protein synthesis. Constitutes 80-85% of the total RNA of the cell.

Transfer RNA (tRNA)

RNA that delivers individual amino acid molecules to the site of protein synthesis. Has regions where there is hydrogen bonding between complementary bases, and regions where there is no hydrogen bonding. Two regions that have important functions during protein synthesis: anticodon and the 3' end.

Repeat or copy

Replicate

Unwinding of the double helix

Replication begins when the enzyme helicase catalyzes the separation and unwinding of the nucleic acid strands at a specific point along the DNA helix. In this process, hydrogen bonds between complementary base pairs are broken, and the bases that were formerly in the center of the helix are exposed.

Nucleic acid categories

Ribonucleic acid and deoxyribonucleic acid. Both are polymers, consisting of long, linear molecules.

Secondary Structure of DNA

DNA double helix Adenine - Thymine (Uracil) Guanine - Cytosine Run in opposite (antiparallel) directions. Each end of the double helix contains the 5' end of one chain and the 3' end of the other. Sugar-phosphate backbone is on the outside of the helix, and the bases point inward. Stable by hydrogen bonding between the bases.

DNA polymerase

DNA strands form as nucleotides, complementary to those on the exposed strand, and are linked together under the influence of this enzyme.

Genes in prokaryotic cells

Exist as a continuous segment of DNA molecule.

Genes in eukaryotic cells

Exist as segments of DNA that are "interrupted" by segments that do not code for amino acids.

Drosophila

Fruit fly. Has the replication of the largest chromosome which would take more than 16 days if there were only one origin for replication for an estimate. Research results indicate that the actual replication is accomplished in less than 3 minutes because it takes place simultaneously at more than 6000 replication forks per DNA molecule.

Accepted dogma (principle)

Genetic information contained in DNA molecules is transferred to RNA molecules.

Three Hydrogen bonds

How many hydrogen bonds are between guanine (G) and cytosine (C)?

Stages of protein synthesis

Initiation of the polypeptide chain. Elongation of the chain. Termination of the completed polypeptide chain.

RNA

Is a long, unbranched polymer consisting of nucleotides joined by 3' → 5' phosphodiester bonds. Like DNA. Number of nucleotides in it differs from that of DNA in two ways: 1. The sugar unit is ribose rather than dexoyribose. 2. It contains the base uracil (U) instead of thymine (T). The secondary structure are single-stranded, except in some viruses. Three types: messenger, ribosomal, and transfer.

DNA molecules

Is among the largest molecules known. Contain between 1 and 100 million nucleotide units.

DNA

Is responsible for one of the most essential functions of living organisms, the storage and transmission of hereditary information.