Biochemistry - Chapter 14: Nucleic Acids & Protein Synthesis

unchanged

Living cells are able to produce nearly exact replicas of themselves through hundreds of generations. THis requires certain information to be passed ___________.

Nucleic Acids

A biomolecule involved in the transfer of genetic information from existing cells to new cells, are high molecular weight compounds with nearly __infinite varieties__ of possible structures. This enables them to represent a huge amount of information that can be transmitted sexually or asexually to reproduce an organism.

RNA

Found in the cytoplasm of living cells, unbranched polymers of linear molecules, contains A C G and U bases, the sugar component is D-ribose, and the phosphate is derived from phosphoric acid.

DNA

Found primarily in the nuclei of cells, polymers of linear molecules, contains A C G and T bases, the sugar component is D-deoxyribose, and the phosphate is derived from phosphoric acid.

Nucleotides

The monomers that make nucleic acids.

__Three Chemical Components:__

1) Nitrogenous Base

2) Sugar (Carbohydrate)

3) Phosphate

heterocyclic compounds

Each of the five bases found in nucleic acids are _______________________ that can be classified as a pyrimidine or a purine, the parent compounds from which the bases are derived.

Pyrimidine Bases

Uracil (U), Thymine (T), and Cytosine (C)

Purine Bases

Adenine (A) and Guanine (G)

beta

Both RNA and DNA have their anomeric carbon in the _____ position.

cellular pH

The phosphate in RNA and DNA is derived from phosphoric acid (H3PO4), which under __________ conditions exists in ionic form.

water

A nucleotide can be formed by the rx of the three components with two moles of _______ being removed.

1’, 5’

In a nucleotide, the base is always attached to the __ position of the sugar (anomeric carbon) and the phosphate is located at the __ position. The carbon atoms in the sugar are designated with a number followed by a prime to distinguish them from the atoms in the nitrogenous base.

100 million

DNA molecules are among the largest molecules known, they can contain between 1 and ___________ nucleotide units.

phosphodiester bonds

The linkages between the nucleotides that are joined together by the phosphate groups that connect the 5’ carbon of one nucleotide to the 3’ carbon of the next in the chain.

Nucleic Acid Backbone

The linkage of alternating phosphate and sugar units to which the bases are attached, constant throughout the entire nucleic acid molecule.

primary structure

One DNA molecule only differs from another only in the sequence of the bases along the backbone (____________________).

James Watson, Francis Crick

The secondary structure of DNA was proposed in 1953 by ________________ (American molecular biologist) and ________________ (English biologist). This was perhaps the greatest discovery of modern biology and it earned both of them the Noble Prize in Physiology & Medicine in 1962.

equal

The analysis of DNA from many different forms of life revealed an interesting pattern. The relative amounts of each base often varied from one organism to another, but in all DNA percentages of __adenine & thymine__ were always _______ to each other as were the percentages of __guanine & cytosine__.

20, 30

Human DNA contains __% guanine & cytosine, and __% adenine & thymine. This led Watson and Crick to conclude that DNA is composed of two strands entwined around each other in a double helix.

antiparallel

The two intertwined polynucleotide chains of the DNA double helix run in opposite (___________) directions. Each end of the double helix contains the 5’ end on one chain and the 3’ end of the other.

outside, inside

The sugar-phosphate backbone is on the ________ of the helix and the bases are on the ________. The chains are held together and stabilize the molecule through H-bonds between the bases that extend inward from the sugar-phosphate backbone.

spacing

The ________ in the interior of the double helix is such that adenine always H-bonds to thymine, and guanine always H-bonds to cytosine.

Complementary

The two DNA strands with these matched sequences are said to be ______________ (not identical) to each other.

genetic material

DNA is responsible for the storage and transmission of _______________ (one of the most essential functions of an organism).

Chromosome

Protein-coated strand of multi coiled DNA. A tightly packed bundle of DNA and protein that is involved in cell division (A normal human cell contains 46).

Histones

Each chromosome contains one molecule of DNA coiled tightly about proteins called _________.

Genes

Made up of individual sections of DNA, are the fundamental unit of heredity, and direct the synthesis of a specific protein.

* Viruses contain several hundred.
* Bacteria like E. Coli contain about 1,000.
* Human cells contain approximately 25,000.

Karyotype

Shows the 46 chromosomes of a human cell.

True

T or F: Watson and Crick’s model was the first to explain the transmission of heredity information (it explains how DNA is duplicated for the next generation).

Replication

The process by which an exact copy of DNA molecule is produced. Occurs when two strands of DNA separate and each serves as a template (pattern) for the construction of its own complement. It generates DNA double-stranded molecules that are exact replicas of the original DNA molecules.

Daughter molecules

The two ______________________ have exactly the same base sequences as the original parent DNA. EAch contains one strand of the parent and one new complementary strand.

Semiconservative Replication

Replication where one strand of the daughter DNA molecule comes from the parent DNA molecule and the other is a new complementary strand.

Steps of Replication

1) Unwinding the Double Helix

2) Synthesis of DNA Segments

3) Closing the Nicks

Unwinding the Double Helix

(Step of Replication) An enzyme called __helicase__ catalyzed the separation and unwinding of the nucleic acid strands at a specific point on the DNA helix. The hydrogen bonds are broken and the strand unwinds.

Replication Fork

The point of unwinding.

Synthesis of DNA Segments

(Step of Replication) Synthesis occurs on both nucleic acid strands that were separated. The process goes from 3’ to 5’ on the template and the new strand is synthesized from 5’ to 3’. One of the new strands synthesized proceeds towards the replication fork and the other proceeds away from it. The enzyme that synthesizes the new strand (add the correct nucleotides) is called __DNA polymerase__. The new strands are antiparallel. One of the strands grows smoothly towards the fork while the other is synthesized in fragments.

Okazaki Fragments

Discovered by Reiji Okazaki, the strand synthesized in segments.

Nicks

The gaps between Okazaki fragments.

Closing the Nicks

(Step of Replication) One daughter DNA strand is synthesized without any nicks, but the Okazaki fragments of the other strand must be joined together. The result is two DNA double-helical molecules that are identical to the original molecule.

Ligase

Enzyme catalyzing the connection of the Okazaki fragments.

Kary Mullis

(1983) Discovered a revolutionary laboratory technique called polymerase chain reaction (PCR).

eukaryotic cells

Through observations with electron microscopes, it has been found that replication in _________________ occurs simultaneously at many points along the original DNA molecule. This allows the molecules to be replicated rapidly.

PCR

Mimics the natural process of replication in that the helix unwinds and DNA polymerase makes a new copy.

Procedure:


1. Target DNA is added to a buffer solution containing DNA polymerase, the cofactor MgCl2, the four nucleotide building blocks, and primers.
2. The mixture is heated at 95C for 1-10 minutes to unravel (denature) the DNA into single strands.
3. The tube is cooled to 50-65C for 1-10 minutes and the primers hydrogen bond to the separated strands of DNA.
4. The tube is heated to 72C for 1-10 minutes where DNA polymerase make new DNA strands.

Primers

Short nucleotide segments that will bind to the separated DNA strands and serve as starting points for new chain growth.

doubles

Each PCR cycle _________ the amount of DNA, therefore 30 cycles theoretically amplifies the amount to 1 billion.

PCR Purposes

1. Detect mutations associated with genetic diseases.
2. Detect the presence of unwanted DNA from a pathogen (microorganism).
3. Utilize degraded DNA samples in forensics.
4. Analyze and examine ancient DNA.

single stranded, loops

RNA consists of nucleotides joined by 3’ → 5’ phosphodiester bonds (like DNA), the number of nucleotides range from __73__ to thousands, the secondary structure of RNA is ___________________, does not contain a base ratio of 1:1, but do contain regions of double-helical structure where they form _______ (\~50%).

nucleus, cytoplasm, mitochondria

RNA is distributed throughout cells so it can be found in many areas including the _________, ______________, and ________________.

Messenger RNA

RNA that functions as the carrier of genetic information from the DNA of the cell nucleus directly to the cytoplasm where it is used in protein synthesis.

The bases in the sequence are __complementary__ to the bases of one of the strands of nuclear DNA. Has a short lifespan (\~1 hour), then degrades into the nucleotide parts that make it up.

Transfer RNA

RNA that delivers individual amino acid molecules to the site of protein synthesis.

Smallest of all nucleic acids (73-93 nucleotides), cells contain at least one specific type for each of the 20 amino acids found in proteins, has regions of H-bonds between complementary bases and regions with no H-bonds called loops. Has anticodons and the site of amino acid attachment.

Ribosomal RNA

RNA that constitutes 65% of the material in ribosomes (other 35% is protein).

Constitutes 80-85% of the total RNA of the cell.

Anticodon

A three-base sequence in tRNA that is complementary to one of the codons of mRNA.

3’, ester bond

The ___ end of the tRNA molecule contains a hydroxy group which is the site of amino acid attachment. Each amino acid is joined to the 3’ end of its specific tRNA by an ____________ that forms between the carboxyl group of the amino acid and the 3’ hydroxy group of ribose.

Ribosomes

The organelles responsible for protein synthesis.

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.

genes, proteins

Segments of DNA called ______ direct the synthesis of specific proteins, there is a specific one for every protein in the body. __________ manufacture all the other substances essential for life (carbs, lipids, etc.) In higher organisms (eukaryotes) the DNA is in the nucleus and protein synthesis occurs in cytoplasm.

Transcription

The transfer of genetic information from a DNA molecule to a molecule of messenger RNA.

Translation

The conversion of the code carried by mRNA into the amino acid sequence of a protein.

RNA polymerase, ribonucleotides

_________________ catalyzes RNA synthesis. First, the DNA double helix unwinds at a point near the gene that is to be transcribed and only one strand is transcribed. ______________ are linked together along the unwound DNA strand in a sequence determined by complementary base pairing of the DNA strand base.

starting point, termination point

During RNA synthesis, the DNA strand always has one sequence of bases recognized by RNA polymerase as the ______________________ and catalyzes the synthesis of mRNA in the 5’ to 3’ direction. It continues until it reaches another sequence of bases that is the _____________________. Once the mRNA molecule has been synthesized, it moves away from the DNA template (which rewinds).

template

tRNA and rRNA are synthesized in the same way with DNA serving as a __________.

Prokaryotic Translation

Each gene exists as a continuous segment of a DNA molecule and transcription produces mRNA that undergoes translation into a protein almost immediately due to there being no nucleus.

Eukaryotic Translation

Genes are in segments that are “interrupted”by segments that do not code for proteins. Both introns and exons are then transcribed into mRNA that produces hnRNA that undergoes a series of enzyme-catalyzed rx. The introns get cut out and the exons are spliced together to make mRNA. The results only contain the sequence of bases that actually code for protein synthesis.

Introns

The DNA segments that carry no amino acid codes, they remain in the nucleus (junk DNA).

Exons

The DNA segments (genes) that code for proteins, they exit the nucleus.

Heterogeneous Nuclear RNA

(hnRNA) Has both introns and exons.

Codon

Triplet of RNA nucleotide bases that code for a specific amino acid.

amino acid

In the early 1960’s it was proposed that a combination of mRNA bases (A,U,C,G) code for each _____________.

Marshall Nirenberg

In 1961, __________________ and his coworkers began to break the genetic code by making a synthetic molecule of mRNA consisting of uracil bases (UUU) and they incubated the synthetic mRNA with ribosomes, amino acids, tRNAs, and enzymes. The resulting polypeptide only contained phenylalanine amino acids.

1967

Many experiments followed Marshall Nirenberg’s and by ______ the entire genetic code had been broken.

Degeneracy

The genetic code is universal in almost every organism. Most amino acids are represented by more than one codon this is called _______________.

Methionine, Tryptophan

Only ______________ and _______________ are coded by one codon.

True

T or F: No single codon represents more than one amino acid, each three-base codon represents one amino acid.

stop codons

Only 61 of the possible 64 base triplets code for amino acids, the remaining three (UAA, UAG, UGA) are _______________. They tell the protein-synthesizing process when the primary structure is complete and it is time to stop adding amino acids.

start codon

The only ______________ is AUG which codes for the amino acid methionine. But it only functions that way when it occurs as the first codon of a sequence.

Initiation of Polypeptide Chain

(Step of Translation & Protein Synthesis) N-formylmethionine, initiates the growing polypeptide chain as the __N-terminal__ amino acid, once the protein is synthesized, N-formylmethionine is __cleaved__ from the protein product. The initiation process begins when mRNA is aligned on the surface of the __small ribosomal subunit__. It is aligned in such a way that the start codon occupies the __P site__.

Next, tRNA molecule with its attached fMet binds to the codon through H-bonds. The resulting complex binds to the __large ribosomal subunit__ to form the __initiation complex.__

Elongation of the Chain

(Step of Translation & Protein Synthesis) The __A site__ is located on the mRNA-ribosome complex next to the P site, incoming tRNA carrying the next amino acid will bond here. Each tRNA molecule can try to fit into the A site, but only the one with the correct __anticodon__ will fit properly. Once at the A site the 2nd amino acid is linked to fMet by a __peptide bond__ whose formation is catalyzed by the enzyme __peptidyl transferase__.

Now, tRNA bound to the P site is empty and the polypeptide chain is attached to the tRNA bound at the A site. The whole ribosome moves one codon along the mRNA toward its __3’__ end. As the ribosome moves, the empty tRNA is released from the P site and tRNA on A moves to P. With A available, new tRNA comes in to form another peptide bond and repeat until a chain is formed.

Termination of Polypeptide Synthesis

(Step of Translation & Protein Synthesis) Chain elongation continues until the ribosome complex reaches a __stop codon__. At that point, a specific protein known as a __termination factor__ binds to the codon and stops the process. The empty ribosome disciates and can then bind to another strand of mRNA and begin the process again. Several ribosomes can move along a single strand of mRNA. Therefore several identical polypeptide chains can be synthesized almost simultaneously from a single mRNA. This increases __efficiency__ and __utilization__ of the mRNA.

Polyribosomes

A complex of mRNA and several ribosomes (also called polysomes).

methionine

The first amino acid involved in protein synthesis in prokaryotic cells is a derivative of _____________.

translocation

Movement of the ribosome along the mRNA.

secondary, tertiary

Growing polypeptide chains extend from the ribosomes into the cellular cytoplasm. They then spontaneously fold to assume their 3D _____________ and __________ structures.

10 billion

The DNA copying mechanism is not totally error free, it’s estimated that on average 1 out of every __________ bases of DNA is incorrect.

Mutation

Any change resulting in an incorrect base sequence on DNA.

Mutagens

Certain chemicals (nitrous acid, dimethyl sulfate, etc.) can also induce mutations by reacting with DNA.

inhibits

Transcription of mutated DNA leads to an incorrect mRNA molecule which then leads to an incorrect amino acid sequence for a protein, or ________ the protein to be synthesized at all.

environmental factors

Some mutations occur naturally during DNA replication, but others can be induced by _______________________ such as ionizing radiation.

False

T or F: All mutations are bad and lead to lethal genetic diseases such as sickle-cell anemia, PKU, hemophilia, muscular dystrophy, etc.

Recombinant DNA

DNA of an organism that contains genetic material from another organism.

Genetic Engineering

Application of DNA technology that allows segments of DNA from one organism to be introduced into the genetic material of another organism. Has produced major advances in the fields of human healthcare, biology, and AG.

human insulin

An early success of genetic engineering was the introduction of the gene for _________________ into the bacterium E. Coli.

Restriction Enzyme

Protective enzyme found in some bacteria that catalyzes the cleaving of specific types of DNA. Were discovered in the 1960’s and they are what make genetic engineering possible.

foreign DNA

Restriction enzymes are normally part of a mechanism that protects certain bacteria from invasion of _____________ (viral).

methyl, untouched

Some of the bases in the DNA of these bacteria have _________ groups attached. The methylated DNA is ____________ by the restriction enzyme.

Palindromes

Sites on DNA acted on by restriction enzymes or the section in which the two strands have the same sequence but run opposite. In language, it is any word or phrase that reads the same in either direction.

predictable

At least 100 restriction enzymes are known and each catalyzes DNA cleavage in a specific and ______________ way. These enzymes are the tools that allow genetic engineers to cut DNA into fragments of known size and sequence.

DNA ligases

_______________ are also important in that they can be used to put together DNA pieces cut by restriction enzymes.

Vector

DNA carrier required in the introduction of a new DNA segment (gene) into a bacterial cell.

Plasmid

A vector that is a circular piece of double-stranded DNA found in the cytoplasm of bacterial cells. Range in size from two thousand to hundreds of thousands of nucleotides.

antibodies, toxins

Plasmids function as accessories to chromosomes by carrying genes that inactivate ___________ and produce _________. They have an unusual ability to replicate __independently__ of chromosomal DNA.