Flashcards in Chapter 7 Deck (106):
Genetics is the study of?
Inheritance and inheritable traits as expressed in an organism's genetic material
The genome of a cell or virus is?
Its entire genetic complement, including both its genes-specific sequences of nucleotides that code for polypeptides or RNA molecules- and nucleotide sequences that connect genes to one another.
The genomes of cells and DNA viruses are composed solely of? RNA?
Molecules of deoxyribonucleic acid (DNA), whereas RNA viruses use ribonucleic acid instead.
Nucleic acids are polymers of basic building blocks called?
Each nucleotide is made up of?
Phosphate attached to a nucleoside, which is in turn made up of a pentose sugar (ribose in RNA & deoxyribose in DNA) attached to one of five nitrogenous bases (guanine, cytosine, thymine, adenine, or uracil)
The bases of nucleotides hydrogen-bond to one another in specific ways called?
Complementary base pairs (bp)
The complementary base pairs (bp) in DNA & RNA
The complementary bases thymine and adenine bond to one another with two hydrogen bonds, whereas in RNA uracil, not thymine, forms two hydrogen bonds with adenine. In both DNA and RNA, the complementary bases guanine and cytosine bond to one another with three hydrogen bonds
What forms the two backbones of a helical, double stranded DNA (dsDNA) molecule?
Deoxyribonucleotides are liked through their sugars and phosphates to form the two backbones
The carbon atoms of deoxyribose are numbered how?
1' (pronounced "one prime") through 5'.
One end of a DNA strand is called the?
5' end because it terminates in a phosphate group attached to a 5' carbon; the opposite (3') end terminates with a hydroxyl group bound to a 3' carbon of deoxyribose. The two strands are oriented in opposite directions to each other; one strand runs in a 3' to 5' direction, while the other runs in a 5' to 3' direction. The two strands are antiparallel. The base pairs extend into the middle of the molecule.
The structure of DNA helps explain its ability to act as genetic material. First, the linear sequence of nucleotides carries the instructions for the?
Synthesis of polypeptides and RNA molecules. Second the complementary structure of the two strands allows a cell to make exact copies to pass to its progeny.
The DNA of prokaryotic genomes is found in two structures
Chromosomes and plasmids
Prokaryotic cells, both bacterial and archeaeal, package the main portion of their DNA, along with associated molecules of protein and RNA, as one or two distinct?
Chromosomes. Prokaryotic cells have a single copy of each chromosome and are called haploid cells
A typical prokaryotic chromosome consists of a circular molecule of DNA localized in a region of the cytoplasm called the?
What are the base pairs for DNA and RNA?
DNA: A-T base pair, G-C base pair
DNA: A-U base pair, G-C base pair
What structures do DNA nucleotides and RNA nucleotides have in common?
Both DNA & RNA nucleotides are each composed of a pentose sugar, a phosphate, and a nitrogenous base
The enzyme gyrase further folds?
And supercoils the entire prokaryotic chromosome
In addition to chromosomes, many prokaryotic cells contain one or more plasmids, which are?
Small molecules of DNA that replicate independently of the chromosome
Each plasmid carries?
Information required for its own replication, and often for one or more cellular traits. Typically, genes carried on plasmids are not essential for normal metabolism, for growth, or for cellular reproduction but can confer advantages to the cells that carry them.
Carry instructions for conjugation, a process involved in transferring genes from one bacterial cell to anothher
Fertility (F) plasmids
Carry genes for resistance to one or more antimibrobial drugs or heavy metals. Certain cells can transfer resistance plasmids to other cells, which then acquire resistance to the same antimicrobial chemicals.
Resistance (R) plasmids
Carry genes for proteinaceous toxins called bacteriocins, which kill bacterial cells of the same or similar species that lack the plasmid. In this way a bacterium containing this plasmid can kill its competitors.
Carry instructions for structures, enzymes, or toxins that enable a bacterium to become pathogenic. For example, E. coli, a normal resident of the human gastrointestinal tract, causes diarrhea only when it carries plasmids that code for certain toxins
Eukaryotic genomes consist of both
Nuclear and extranuclear DNA
DNA replication is what type of process?
Anabolic polymerization process that allows a cell to pass copies of its genome to its descendants.
DNA nucleotides with 3 phosphate linked together by two high-energy bonds
The key to DNA replication is the?
complementary structure of the two strands: Adenine and guanine in one strand bond with thymine and cytosine in the other
DNA replication is a simple concept
A cell separates the two original strands and uses each as a template for the synthesis of a new complementary strand
DNA replication begins at a specific sequence of nucleotides called an?
Locally unzips the DNA molecule by breaking the hydrogen bonds between complementary nucleotide bases, which exposes the bases in a replication fork
Enzyme DNA helicase
Enzymes of DNA replication in order
1) DNA helicase- unzips DNA molecule by breaking hydrogen bonds between bases
2) DNA polymerase- binds to each strand. Catalyze synthesis of DNA by addition of new nucleotides
After the enzyme DNA helicase unzips the DNA strands what keeps the strands separated so they do not rejoin while replication proceeds?
Other protein molecules stabilize the separated single strands
After helices untwists and separates the strands, a molecule of an enzyme called DNA polymerase binds to what and does what?
Binds to each strand. It catalyzes synthesis of DNA by the addition of new nucleotides only to a hydroxyl group at the 3' end of a nucleic acid.
All DNA polymerase replicate DNA in?
Only one direction-5' to 3'
Usual enzyme of DNA replication in bacteria
DNA polymerase III
Because the two original (template) strands are antiparallel, cells synthesis new strand in two different ways. Explain
One new strand, called the leading strand, is synthesized continuously, 5' to 3', as a single long chain of nucleotides. The other new strand, called the lagging strand, is also synthesized 5' to 3' but in short segments that are later joined. The two processes occur simultaneously
Describe the synthesis of the leading strand: A cell synthesizes a leading strand toward the replication fork in a series of 5 steps
1) The enzyme primase synthesizes a short RNA molecule that is complementary to the template DNA strand. This RNA primer provides the 3' hydroxyl group required by DNA polymerase III.
2) Triphosphate deoxyribonucleotides form hydrogen bonds with their complements in the parental strand. Adenine nucleotides bind to thymine nucleotides, and guanine nucleotides bind to cytosine nucleotides
3) Using every in the high-energy bonds of the triphosphate deoxyribonucleotides, DNA polymerase III covalently joins them one at a time to the leading strand. DNA polymerase III can add about 500-1000 nucleotides per second to a new strand
4) DNA polymerase proofreads. About 1 out of 100,000 nucleotides is mismatched with its template. DNA polymerase III recognizes errors & removes incorrect nucleotides before proceeding with synthesis.
5) DNA polymerase I replaces the RNA primer with DNA
Proofreading exonuclease function
DNA polymerase III
Adds nucleotides only to the 3' end of the new strand, the enzyme moves away from the replication fork as it synthesizes a lagging strand
DNA polymerase III
The steps in the synthesis of the lagging strand
1) Nucleotides pair up with their complements in the template
2) DNA polymerase III joins neighboring nucleotides & proofreads.
3) DNA polymerase I replaces the RNA primers of Okazaki fragments with DNA & proofreads the short DNA segment it has synthesized
4) DNA ligase seal the gaps between adjacent Okazaki fragments to form a continuous DNA strand
All primers are replaced with?
DNA replication is bidrectional meaning
DNA synthesis proceeds in both directions from the origin
In bacteria, the process of replication proceeds from?
A single origin, so it involves two sets of enzymes, two replication forks, two leading strands, and two lagging strands
The unzipping and unwinding action of helicase introduces supercoils into the DNA molecule ahead of the replication forks. Excessive supercoiling creates tension on the DNA molecule and would stop DNA replication. What prevents this?
The enzymes gyrase and topoisomerase remove such supercoils by cutting the DNA, rotating the cut ends in the direction opposite the supercoiling, and then rejoining the cut ends
A cell transcribes RNA from a DNA gene & then translates polypeptides using the code carried by the RNA molecules. Polypeptides determines ?
Phenotype by acting as structural, enzymatic, & regulatory proteins
The actual set of genes in its genome
Physical features & functional traits of an organism, including characteristics such as structures, morphology, & metabolism
Purpose: To duplicate the cell's genome
Beginning point: Origin
Ending point: Origin or the end of a linear DNA molecule
Purpose: To synthesize RNA
Beginning point: Promoter
Ending point: Terminator
Purpose: To synthesize polypeptides
Beginning point: AUG start codon
Ending point: UAA, UAG, or UGA stop codons
Cells must continually synthesize proteins required for growth, reproduction, metabolism, and regulation. This synthesis requires that they accurately transfer the genetic information contained in DNA nucleotide sequences to the amino acid sequences of polypeptides. Cells do not transfer the info. directly, first they make an RNA copy of the gene, this is called transcription, during this the information is?
Copied as RNA nucleotide sequences; RNA molecules in ribosomes then synthesize polypeptides in a process called translation.
DNA is transcribed to RNA which is translated to form
Cells transcribe four main types of RNA from DNA
1) RNA primer
2) messenger RNA
3) ribosomal RNA
4) transfer RNA
Molecules for DNA polymerase to use during DNA replication
Molecules, which carry genetic information from chromosomes to ribosomes
Messenger RNA (mRNA)
Molecules which combine with ribosomal polypeptides to form ribosomes- the organelles that synthesize polypeptides
Ribosomal RNA (rRNA)
Molecules which deliver the correct amino acids to ribosomes based on the sequence of nucleotides in mRNA
Transfer RNA (tRNA)
Transcription occurs in the?
Nucleoid region of the cytoplasm in bacteria
Initiation of transcription: RNA polymerases bind to specific DNA nucleotide sequences called promoters, each of which is located
Near the beginning of a gene and serve to initiate transcription
Necessary for recognition of a promoter
One the RNA polymerase adheres to a promoter sequence, an RNA polymerase?
Unzips & unwinds the DNA molecule in the promoter region & then travels along the DNA, unzipping the double helix to form a bubble as it moves
What are promoters?
Specific DNA nucleotide sequences located near the beginning of a gene and serve to initiate transcription
Basic points of transcription
1) RNA polymerase bind to promoters
2) Adheres to promoter and unzips/unwinds DNA molecule & travels along DNA unzipping double helix
3) 10 nucleotides away triphosphate ribonucleotides align opposite their complements in the open DNA bubble
4) RNA polymerase links 2 adjacent ribonucleotide molecules w/energy from phosphate bonds of the first ribonucleotide
5) Enzyme moves down DNA strand, elongating RNA by repeating the process
How do cells provide some control over transcription?
Uses different sigma factors and different promoter sequences
Effects the amounts and kinds of polypeptides produced
Variations in sigma factors and promoters
How many DNA strands are transcribed?
RNA polymerase links nucleotides only to the?
3' end of the growing molecule
How does RNA polymerase differ from DNA polymerase
1) RNA polymerase unwinds & opens DNA by itself; helicase is not required
2) RNA polymerase does not need a primer
3) RNA polymerase transcribes only one of the DNA strands
4) RNA polymerase is slower than DNA polymerase III
5) RNA polymerase incorporates ribonucleotides instead of deoxyribonucleotides
6) Uracil nucleotides instead of thymine
7) Proofreading function of RNA polymerase is less efficient
What are gene mutations?
Changes in DNA
DNA will be transcribed to make?
DNA transcribed to make mRNA which will then make a protein
Mutations causes changes in?
DNA which will then cause changes in mRNA and then proteins
There are two ways to get mutations
1) Spontaneous mutations
2) Induced mutations
What is spontaneous mutations?
Something in the process of replicating the DNA goes wrong (common type is strand slippage)
A lot of mutations are caused by?
Our environment which are called induced mutations. (i.e. radiation, or cigarette which is a chemical that causes mutation)
What are point mutations?
Mutations just at one point
Spontaneous mutations can occur from
1) Base substitutions
2) Removal or addition of nucleotides
3) Transposable elements
Most common type of mutation is?
Base substitutions which results from mistakes during DNA synthesis
What are the 3 types of point mutation?
1) Silent mutations
2) Missense mutation
3) Nonsense mutation
Silent mutations results from
A nucleotide change that generates a codon which specifies the same amino acid
Missense mutation results from?
Amino acid substitution
Nonsense mutation results from?
Mutation that changes an amino acid codon to a stop codon
Point mutations are?
When one of our DNA bases (A,T,G,C) is replaced with another which leads to a change in one RNA nucleotide & ultimately a change in one amino acid
Frame shift mutations are?
Adding a base (A,T,G,C) to a sequence. This change leads to additional base in RNA. This mutation changes reading frame of RNA. RNA is read in groups of 3 (codons) when being translated to form protein. Since we added an extra base all the codons coming after the extra base will read differently. This is usually a bigger difference than point mutations.
Nonsense mutations are?
Any genetic mutation that leads to the RNA sequence becoming a stop codon instead
Missense mutations are?
Any genetic mutation that changes an amino acid from one to another
When the mutation doesn't affect protein at all since many different RNA codons can code for the same amino acid its possible that the mutation might not affect the protein at all.
Where the new amino acid is of the same type of the original
Conservative mutation (i.e. glutamate & aspartate which are both acidic amino acids so a mutation that swapped out an aspartate for a glutamate would be a conservative mutation)
One where the new amino acid is a different type of the original
Non-conservative mutation (i.e. serum amino acid, which is a small polar amino acid being replaced with phenalalamine which is a large non polar amino acid)
All mutations are classified by?
Their effects on protein or on DNA:
- DNA effects: point, frame-shift
- Protein effects: Missense, nonsense
Mutations originate at?
The DNA level, but show their effects at the protein level
Information in DNA is transmitted or copied onto? Process called?
RNA in a process called transcription. Then the information in RNA is used to make the corresponding polypeptide in a process called translation
Each ___ nucleotides on the DNA are going to code for one amino acid
3 On the RNA as well each 3 nucleotides will code for one amino acid and then in translation those amino acids are put together to form a polypeptide protein
Similarities of DNA & RNA
Both nucleic acids meaning they are made up of units called nucleotides. Each nucleotide has a sugar, phosphate group, and nitrogenous base
Differences between DNA & RNA
1) DNA is double stranded RNA is single stranded
2) Sugar in DNA-deoxyribose & RNA- ribose
3) DNA has thymine base & RNA has uracil base
4) DNA is more stable than RNA
RNA made during transcription
Job of mRNA
Go to the ribosome & the ribosome will put together the corresponding polypeptide chain
Where is mRNA made in eurkaryotic and prokaryotic cells
rRNA ribosomal RNA does what
Found in ribosome. Acts like an enzyme even though its a nucleic acid. Known as ribozyme meaning it has enzymatic function. Its the enzymatic activity of the rRNA in the ribosome that puts together the polypeptide
Transfer RNA has a 3 structure. Job is to carry amino acids and then to bring amino acids to the ribosome so that the ribosome can put together a polypeptide chain
The enzymes that put together RNA in eukaryotic cells
mRNA is put together by RNA polymerase to II
rRNA is put together by RNA polymerase I
tRNA is put together by RNA polymerase III
Synthesis of a protein from an mRNA template
Stages of translation
Translation initiation begins
When the small subunit of the ribosome attaches to the mentholated cap at the 5' end of mRNA and moves to the translation initiation site. tRNA is a key molecule that contains an anticodon that is complementary to the mRNA codon to which it binds
The first mRNA codon is typically
Attached to the end of the tRNA is and the basic steps of elongation
The corresponding amino acid (Met) which corresponds to the AUG codon (start codon) then the large subunit of the ribosome binds to create the peptidyl P site and aminoacyl A site. The first tRNA occupies the P site the second tRNA enters the A site and is complementary to the second mRNA codon. The (Met) is then transferred to the A site amino acid, the first tRNA exits, the ribosome moves along the mRNA & the next tRNA enters