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Flashcards in Chapter 6 Deck (79)

What is replication

DNA duplication


What is transcription

RNA is synthesized from DNA template. First step is gene expression and it can be regualted by transcription factors


What are transcription products

mRNA, tRNA, and rRNA


What is mRNA

Messenger RNA: encodes polypeptides


What is tRNA

Transfer RNA: plays role in protein synthesis


What is rRNA

Ribosomal RNA: makes up the ribosomes


What is translation

Inform in mRNA is used to build polypeptides on ribosomes, this can also be regulated


Describe a dsDNA strand

DNA strands are anti-parallel (5 to 3 is complement to 3 to 5), in a double helix and base pairing holds the two strands together.


In mRNA what is the codon do (triplet code)

In the mRNA, the codon (triplet code) is recognized by tRNA to translate a particular amino acid into the sequence.


Describe the ends of the amino acid sequence (protein). In what direction are protines synthesized by ribosomes

The protein strand begins with the N-terminus (-NH2) and ends with the C-terminus (-COOH). Proteins are synthesized from the N-terminus to C-terminus direction


What is the central dogma of molecular biology

DNA to RNA to Protein


How are genes transcribed in Eukaryotes

Each gene is transcribed individually. There are introns present and mRNA undergoes splicing


How are genes transcribed in Prokaryotes

Multiple genes are sometimes transcribed together, usually involved in the same pathway (operon), almost no introns or no RNA splicing


What is an operon

Operon are bacterial gene transcripts that contain more than one gene, encoding enzymes of a single biochemical pathway. Each gene on the mRNA will have its own start and stop codons to make separate proteins when it undergoes translation


What is the benefit of prokaryotes transcribing genes in the cytoplasm

Because it takes place in the cytoplasm, while the mRNA is being transcribed, ribosomes can attach to it and begin translation


What are the 3 components of nucleic acids

Sugar, Base, and Phosphate group


What are the possible sugars in nucleic acids

Deoxyribose and ribose


What are the possible bases in nucleic acids

Nitrogen bases: Cytosine, Thymine, Uracil, Adenine, and Guanine


What connects the sugars to one another

The phosphate, a phosphodiester bond


What are the complementary base pairs

A pairs with T/U and G pairs with C


What is on the 5' and 3' end of the DNA strand

5' end has a phosphate group and 3' end has a hydroxyl group


What is a genome

Entire complement of genes in cell or virus


What is a chromosome

Main genetic element in prokaryotes. Usually one circular chromosome per cell. They contain the essential "housekeeping genes"


What are housekeeping genes

They are essential genes that are needed for replicating DNA, transcribing genes, making ribosomes, all the fundamental metabolism needed for a cell to be alive


Aside form the chromosome what are other genetic elements in cells

Virus genomes, plasmids, and transposable elements


What are Plasmids

Self-replicating small circular DNA molecules that replicate separately from chromosome. Usually small, between 1-50 genes and usually contain nonessential genes but provide a special phenotype such as antibiotic resistance. Can have hundreds of plasmids in a cell


How are genes and operons distributed on DNA strands

They are distributed on both DNA strands (top and bottom) and factors determine which strand of the DNA will be transcribed to RNA


What are R plasmids

Resistance plasmids: confer resistance to antibiotics or other growth inhibitors or toxins. Many of them are conjugative, meaning that they can be transferred to other bacteria


How can plasmids be transferred to other genes

If a cell lyses and breaks open, the plasmid molecules are released to the environment and other cells can take it up in a process called transformations. Some plasmids are conjugated (when two cells touch a bridge can form between them) and a plasmid transfer can occur


Describe the genes of a conjugative plasmid

A conjugative plasmid would contain Tra genes, needed to help transfer it to another cell, and contain a OriT promoter as the origin of transfer.


What are the critical features of a plasmid

Replication functions (have an origin of replication and a gene for replication) and have a selective marker that provides resistance against something


What kind of plasmids are in pathogenic bacteria

Virulence characteristics are encoded in these plasmid genes


What are virulence characteristics

Enables pathogen to colonize host and cause the host damage which provides the bacteria with food, protection, and dispersal


What is Hemolysin

Causes the lysis of red blood cells and release nutrients from the cell


What is Enterotoxin

Causes diarrhea, once its exits the body it can disperse easily


What are bacteriocin

Genes encoding bacteriocins are often carried on plasmids. They encode for proteins that can inhibit or kill closely related bacteria species. Not an essential housekeeping gene but makes them better adapted to the environment


Where does DNA replication begin on bacterial chromosomes

Origin of replication (Ori). Bacterial chromosomes usually have just one Ori


In what direction does the DNA polymerase synthesis the new DNA strand.

In the 5' to 3' direction


What is the replication fork

The opening of the DNA strand as the leading strand goes into it


Describe the leading strand

The DNA polymerase can continuously lay down new base pairs in the 5' to 3' direction


Describe the lagging strand

The DNA polymerase has to discontinuously lay down new base pairs in the 5' to 3' direction, but overall the synthesis is in the 3' to 5' direction. Can only proceed once the leading strand has opened up room from the replication fork.


How often does DNA replication make mistakes

DNA replication is extremely accurate, DNA polymerase has a proofreading mechanism that ensures high fidelity. Mutation rates in cells are 10^-8 to 10^-11 errors per base.


What is PCR

PCR is polymerase chain reaction, basically DNA replication in a test tube. Otherwise known as DNA amplification, repeatedly replicates a strand of DNA over and over


What is needed for PCR

DNA template, 2 primers, DNA polymerase, and nucleotide triphosphates


In PCR what is the DNA template

The DNA strand to be copied


In PCR what are the two primers that you add

Used to start DNA synthesis, short DNA fragments that base-pair to a defined region that is to be amplified.


Why are primers needed

DNA polymerase needs to add new nucleotides to a 3' end of a piece of DNA that already exists so you need primers to start the synthesis.


In PCR what kind of DNA polymerase is used

Taq or Pfu polymerase is used because they are heat stable enzymes that can function at high temperatures


How does the PCR process work temperature wise

The temperature is increased to have the parental strands of DNA melt to form single strands, then the temperature is decreased to the DNA strands will re-anneal and the primers can re-attach


What happens with each cycle of the PCR

The copies of the target sequence doubles


What are promoters

Site of initiation of transcription and are located upstream of the open reading frame (ORF) start codon


What is the sigma factor

A protein subunit of RNA polymerase that recognizes the promoters on DNA


What are transcription terminators

Specific sites that stop transcription and are usually downstream of the ORF (after the coding for the stop codon in translation)


Describe the process of transcription

The sigma subunit interacts with the RNA polymerase to allow it to recognize the sequence at the promoter region. Afterwards the sigma factor will leave after its done its job. RNA polymerase begins transcription and the mRNA chain grows. It will copy everything from the promoter region until it huts the terminator sequence at which it will fall off and release the mRNA strand


What are the two highly conserved regions of promoters that sigma factors (proteins) recognize

-10 region and -35 region


What is the -10 promoter region

Located about 10 bases before the start of transcription (Prinbow box)


What is the -35 region

Located about 35 bases upstream (before) of the transcription start site


What are the two different methods of RNA synthesis termination that are dependent on specific DNA seqeunces

Intrinsic terminators and Rho-dependent termination


What are intrinsic terminators

Transcription is terminated without any additional factors. Sequences that the RNA polymerase can recognize by itself and terminates the trnascription


What is Rho-dependent termination

Rho protein recognizes specific DNA sequences and causes termination by interacting with RNA ploymerase


What is a unit of transcription

Region of chromosome bounded by sites where transcription is initiated and terminated. A gene or operon and included 5' to 3' untranslated region. In bacteria the Unit of transcription can have multiple ORFs. Each gene will have its own start and stop codons on the same mRNA (operon)


What happens to RNAs that are not translated

They are usually rRNA, tRNA, or regulatory small RNAs


What are the two things that gene expression requires to make a certain amount of bacteria

You can control how often your promoter is activated to make mRNA and you can control how long the mRNA exists in the cell before its degraded


What is the mRNA half life

The time mRNA exists in the cell before its degraded. In bacteria this half life is only a few minutes, bacteria can rapidly turn genes on and off. Allows regulation of gene expression


What is a polycistronic mRNA

In prokaryotes, it is an mRNA encoding a group of co-transcribed genes. A mRNA made from an operon


In relation to a polycistronic mRNA, what is an operon

A group of usually related genes that are cotranscribed on a polycistronic mRNA. Genes that are clustered together on the chromosome.


What is the benefit of polycistronic mRNA

Allows for coordinated expression of multiple genes that are all required for the same pathway. Can have one promoter regulate 3-4 different gene products for a pathway and coordinate the expression of the genes with just one promoter determining whether the gene is on or off


What are polypeptides

They are amino acids that are linked via peptide bonds


Describe translation

Depends on the genetic code of the mRNA, the tRNAs will read the triplet code (1 codon = 1 AA) and will bring the correct AA to the growing polypeptide chain. Translation occurs on the ribosomes


What is the basic structure of an amino acid

Has a central carbon that is bonded to a hydrogen, an amino group, a carboxylic acid group, and a amino acid side chain that determines its chemical characteristics. The amino and carboxylic acid group are involved in the peptide bond


Describe the Nonionizable polar amino acids

They tend to have OH and O groups on the side chain, they are polar and interact with water but do not have a charge


Describe the acid and basic ionizable amino acids

They have charged side groups (carboxylic groups, amino groups) and are very hydrophilic


Describe the nonpolar hydrophobic amino acids

Greasy, nonpolar, and noncharged side chains. A lot of hydrocarbons and carbon groups that are not charged. These are the amino acids that you would find in the middle of the membrane that has to interact with the hydrophobic fatty acid tails


What is the size of Eukaryotic ribosomes



What is the size of Prokaryotic ribosomes



What is the benefit to having different ribosomes

Many antibiotics work by inhibiting translation of bacterial ribosomes (70S) and these antibiotics don't affect eukaryotic ribosomes (80S)


What happens to the proteins that are made in the cytoplasm that need to be embedded in the membrane for transporters or need to be secreted.out of the cell

These proteins have special sequences that produce a strand of amino acids called the signal sequence (the signal sequence is made in the very beginning of the protein).


What is this signal sequence for special proteins

The signal sequence is recognized by SecA (cell's secretory system) and delviers it to a transport apparatus that lets the protein either leave the cell or deliver it to the membrane and insert it to become a transport


What if a protein does not have a signal sequence

If a protein does not have a signal sequence then they are just made in the cytoplasm and are NOT directed to the membrane to be secreted or inserted