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BIMM 120 > Chapter 6 > Flashcards

Chapter 6 Flashcards

1
Q

What is replication

A

DNA duplication

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2
Q

What is transcription

A

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

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3
Q

What are transcription products

A

mRNA, tRNA, and rRNA

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4
Q

What is mRNA

A

Messenger RNA: encodes polypeptides

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5
Q

What is tRNA

A

Transfer RNA: plays role in protein synthesis

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6
Q

What is rRNA

A

Ribosomal RNA: makes up the ribosomes

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7
Q

What is translation

A

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

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8
Q

Describe a dsDNA strand

A

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.

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9
Q

In mRNA what is the codon do (triplet code)

A

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

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10
Q

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

A

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

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11
Q

What is the central dogma of molecular biology

A

DNA to RNA to Protein

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12
Q

How are genes transcribed in Eukaryotes

A

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

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13
Q

How are genes transcribed in Prokaryotes

A

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

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14
Q

What is an operon

A

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

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15
Q

What is the benefit of prokaryotes transcribing genes in the cytoplasm

A

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

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16
Q

What are the 3 components of nucleic acids

A

Sugar, Base, and Phosphate group

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17
Q

What are the possible sugars in nucleic acids

A

Deoxyribose and ribose

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18
Q

What are the possible bases in nucleic acids

A

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

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19
Q

What connects the sugars to one another

A

The phosphate, a phosphodiester bond

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20
Q

What are the complementary base pairs

A

A pairs with T/U and G pairs with C

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21
Q

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

A

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

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22
Q

What is a genome

A

Entire complement of genes in cell or virus

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23
Q

What is a chromosome

A

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

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24
Q

What are housekeeping genes

A

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

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25
Q

Aside form the chromosome what are other genetic elements in cells

A

Virus genomes, plasmids, and transposable elements

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26
Q

What are Plasmids

A

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

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27
Q

How are genes and operons distributed on DNA strands

A

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

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28
Q

What are R plasmids

A

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

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29
Q

How can plasmids be transferred to other genes

A

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

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30
Q

Describe the genes of a conjugative plasmid

A

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.

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31
Q

What are the critical features of a plasmid

A

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

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32
Q

What kind of plasmids are in pathogenic bacteria

A

Virulence characteristics are encoded in these plasmid genes

33
Q

What are virulence characteristics

A

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

34
Q

What is Hemolysin

A

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

35
Q

What is Enterotoxin

A

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

36
Q

What are bacteriocin

A

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

37
Q

Where does DNA replication begin on bacterial chromosomes

A

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

38
Q

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

A

In the 5’ to 3’ direction

39
Q

What is the replication fork

A

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

40
Q

Describe the leading strand

A

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

41
Q

Describe the lagging strand

A

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.

42
Q

How often does DNA replication make mistakes

A

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.

43
Q

What is PCR

A

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

44
Q

What is needed for PCR

A

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

45
Q

In PCR what is the DNA template

A

The DNA strand to be copied

46
Q

In PCR what are the two primers that you add

A

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

47
Q

Why are primers needed

A

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.

48
Q

In PCR what kind of DNA polymerase is used

A

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

49
Q

How does the PCR process work temperature wise

A

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

50
Q

What happens with each cycle of the PCR

A

The copies of the target sequence doubles

51
Q

What are promoters

A

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

52
Q

What is the sigma factor

A

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

53
Q

What are transcription terminators

A

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

54
Q

Describe the process of transcription

A

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

55
Q

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

A

-10 region and -35 region

56
Q

What is the -10 promoter region

A

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

57
Q

What is the -35 region

A

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

58
Q

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

A

Intrinsic terminators and Rho-dependent termination

59
Q

What are intrinsic terminators

A

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

60
Q

What is Rho-dependent termination

A

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

61
Q

What is a unit of transcription

A

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)

62
Q

What happens to RNAs that are not translated

A

They are usually rRNA, tRNA, or regulatory small RNAs

63
Q

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

A

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

64
Q

What is the mRNA half life

A

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

65
Q

What is a polycistronic mRNA

A

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

66
Q

In relation to a polycistronic mRNA, what is an operon

A

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

67
Q

What is the benefit of polycistronic mRNA

A

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

68
Q

What are polypeptides

A

They are amino acids that are linked via peptide bonds

69
Q

Describe translation

A

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

70
Q

What is the basic structure of an amino acid

A

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

71
Q

Describe the Nonionizable polar amino acids

A

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

72
Q

Describe the acid and basic ionizable amino acids

A

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

73
Q

Describe the nonpolar hydrophobic amino acids

A

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

74
Q

What is the size of Eukaryotic ribosomes

A

80S

75
Q

What is the size of Prokaryotic ribosomes

A

70S

76
Q

What is the benefit to having different ribosomes

A

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

77
Q

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

A

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).

78
Q

What is this signal sequence for special proteins

A

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

79
Q

What if a protein does not have a signal sequence

A

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

BIMM 120 (17 decks)

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