Chapter 4 Flashcards
(101 cards)
1
Q
what are the three key processes of macromolecular synthesis?
A
DNA replication
Transcription
Translation
2
Q
What is a Gene?
A
A unit of heredity specifying a particular protein or polypeptide chain or a tRNA or rRNA located on the chromosome or other large molecules Known as genetic elements
3
Q
What are Genetic Elements?
A
A Structure that carries Genetic information, such as a chromosome, plasmid, or a virus genome.
4
Q
Where is genetic information embedded?
A
In DNA & RNA
5
Q
What is Deoxyribonucleic Acid (DNA)?
A
a polymer of nucleotides connected via phosphate deoxyribose sugar backbone; the genetic material of cells and some viruses (the blueprint)
6
Q
What is RNA?
A
a polymer of nucleotides connected via a phosphate-ribose backbone; involved in protein synthesis and coverts DNA into a defined amino acid sequence.
7
Q
What are informational macromolecules?
A
any large polymeric molecule that carries genetic information, including DNA &RNA
8
Q
What are nucleotides?
A
A monomeric unit of nucleic acid consisting of a sugar a nitrogen base and a phosphate
9
Q
What are purines?
A
Adenine and Guanine, which contain 2 fused herocyclic rings.
10
Q
What is Pyramidine?
A
bases of nucleic acids that contain one ring : cytosine,thymine, and uracil (RNA)
11
Q
What is a nucleoside and what is it used for?
A
Is a nucleotide minus the phosphate which then function in energy conservation,redox reactions,and carriers of sugar
12
Q
What is a phosphate bond?
A
a type of covalent bond linking nucleotides together in a polynucleotide.
13
Q
What is primary structure
A
the precise sequence of monomeric units (nucleotides) in an informational macromolecule such as a polypeptide or nucleic acid
14
Q
What are the specific base pairing in both DNA and RNA?
A
DNA; A-T & G-C in RNA; A-U and G-C
15
Q
What are the three main types of RNA?
A
tRNA,rRNA, and mRNA
16
Q
What is a mRNA?
A
a small RNA molecule that contains the genetic information to encode one pr more polypeptides by caring genetic information form DNA to the ribose.
17
Q
What is tRNA?
A
an RNA molecule used in translation that posses an anticodon at one end and a corresponding amino acid on the other end. Converts the nucleic sequence of RNA to a defined sequence of amino acids in proteins.
18
Q
What is rRNA?
A
the types of RNA found in the ribosome, some participate in protein synthesis.
19
Q
What are the molecular processes of genetic information?
A
Replication
Transcription
and Translation
20
Q
What is DNA replication?
A
the synthesis of DNA using DNA as a template producing 2 copies and is carried out by DNA polymerase.
21
Q
What is Transcription?
A
the synthesis of an RNA molecule complementary to one of the two strands of a double-standed DNAmolecule and is carried out by RNA polymerase
22
Q
What is Translation?
A
synthesis of a protein using the genetic information in mRNA called translocation.
23
Q
What is one difference in the transcription of genes in prokaryotes and eukaryotes?
A
in eukaryotes each gene is transcribed yield a single mRNA and prokaryotes a single mRNA can yield many genes
24
Q
What is a codon?
A
a sequence of 3 bases in a messenger RNA that encodes a specific amino acid
25
What are the characteristics of DNA
DNA is a double-stranded helix that is complementary and antiparallel and are supercoiled by enzymes called topoismerases, such as DNA gyrase
26
What is antiparallel in reference to?
In reference to the double stranded nucleic acids which the two strands run in opposite direcrtions from the 5-3 to the 3-5
27
How are supercoils inserted into DNA and what are the two types?
Supercoils are inserted by topermerase enzymes and have to 2 types Negative, DNA twisted in the opposite sense and is under wound;and positive where it is twisted in the right direction and is overly wound.
28
What is DNA Gyrase
an enzyme found in most prokaryotes that introduces negative supercoiling in DNA.
29
What are Chromosomes
a genetic element carrying genes essential to cellular functioning; in which prokaryotes have a single chromosome containing circular DNA and Eukaryotes having multiple DNA chromosomes each containing linear DNA.
30
What is a Plasmid
an extrachromosomal genetic element that is not essential for growth and has no extracellular form
31
What are transposable elements?
segments of DNA that move from one site on a a DNA molecule to another, and either on the same molecule or different molecules and plays an important role in genetic variation.
32
what is an operon?
One or more genes transcribed into a single RNA under the control of a single regulatory site.
33
What is special about R plasmids?
carry genes that profoundly influence the physiology of the cell the R plasmids confer the resistance to antibiotics or other growth inhibitors.
34
what 2 major characteristics of the virulence of the pathogens are often plasmid encoded
1) the ability of the pathogen to attach to and colonize specific host tissue.
2) the production of toxins, enzymes and other molecules that can cause damage to the host.
35
What are Bacteriocins?
agents produced by certain bacteria that inhibit or kill closely related species.
36
What does it mean for DNA to be semiconservative?
DNA synthesis yielding a new double helices consisting of one parental and one progeny strand.
37
What is DNA polymerase?
An enzyme that synthesizes a new strand of DNA in the 5'-3' direction using an antiparallel strand as a template.
38
what is a primer?
a short length of DNA or RNA used to initiate synthesis of a new DNA strand, usually consisting of RNA
39
where does dan synthesis begin?
At the site of origin
40
DNA synthesis begins at the site of origin and is unwound by helicase which is then stabilized by single binding proteins,where the DNA synthesis occurs continuously on the lagging strand and on fragments on the leading strand resulting in Okazaki fragments. (T/F)
FALSE!
41
What is the replication fork?
The site on the chromosome where DNA replication occurs and where the enzymes replicating the DNA are bound to the untwisted single stranded DNA.
42
The single stranded region is immediately covered with single stranded DNA and prevent the helix from reforming. Unwinding of the double helix by helicase generates positive supercoiling ahead of the advancing fork,to counteract DNA gyros travels along the DNA ahead of the replication inserting negative supercoils to cancel each other out (T/F)
True
43
What is the leading strand
The new strand of DNA that is synthesized continuously during DNA replication.
44
What is the Lagging strand
the new DNA strand that is synthesized in short pieces during DNA replication and then are joined together later.
45
On the lagging strand RNA primers must be synthesized y primase multiple times to provide free 3'-OH groups for DNA polymerase 3 also known as the Okazaki fragments. (T/F)
True
46
What is DNA ligase?
An enzyme that seals nicks in the backbone of DNA as well as participates in DNA repair and genetic molecular cloning.
47
in organisms with circular DNA replication is
bidirectional from the origin of replication
48
Replication proteins aggregate to form a large replication complex known as the replisome. The lagging strand does not loop out to allow the replisome to move smoothly along both strands literally pulls the DNA template as replication occurs. (T/F)
False
49
Which enzymes preform the function of proofreading the DNA
pol 3 a separate subunit DnaQ and pol 1 preform proofreading functions.
50
What enzyme removes the primer from both the leading and lagging strand.
DNA pol 1
51
where does replication end?
at the terminus of replication;Ter sites-DNA sequences recognized by a protein called Tus, which functions to block the progress of the replication forks
52
What are the key in the difference from RNA and DNA?
1) RNA contains ribose instead of deoxyribose
2) RNA contains uracil instead of thymine
3) except in certain viruses, RNA is not double stranded
53
What is the Secondary Structure?
the initial pattern of folding a polypeptide or a polynucleotide, usually the result of hydrogen bonding, whose biological function depends on the final 3-D structure of the protein.
54
Transcription is catalyzed by what enzyme?
RNA Polymerase
55
What is RNA Polymerase?
An enzyme that synthesizes RNAin the 5'-3' direction using an antiparallel 3'-5' direction using an antiparallel 3'-5' DNA strand as a template.
56
RNA transcription is often as little as a single gene. which does not allow the cell to transcribe genes at different frequencies depending on the need for the cells proteins, in which genes cannot be regulated. (T/F)
Flase
57
In Bacteria promoters are recognized by the sigma factors that allow joint regulation of large families of genes in response to growth conditions. As well as Transcription by RNA polymerase continue until specific sites called transcription terminators are reached. (T/F)
True
58
What are promoters?
The site on DNA where the RNA polymerase binds and begins transcription.
59
What is Termination
stopping the elongation of an RNA molecule at a specific site
60
What is the other mechanism for transcription termination and how does it accomplish it?
Rho, because Rho does not bind to RNA polymerase or DNA and once it has paused at an Rho-dependent termination site Rho causes both the RNA and RNA polymerase to be released from DNA thus terminating transcription.
61
In prokaryotes, most messenger RNA have a short half-life because they are degraded by enzymes called what? And can it degrade tRNA or rRNA?
ribonucleases, and cannot degrade tRNA or rRNA because of their secondary structure which prevents them from degradation.
62
RNA polymerase proceed through such clusters and transcribes these entire groups into single long mRNA molecules, such groups that are cotranscribed are called what?
polycistronic mRNA
63
What is RNA processing?
The conversion of a precursor RNA to its mature form.
64
What are exons?
The coding sequence in a split gene.Contrast with introns the inverting noncoding regions.
65
What are introns?
The intervening non coding sequence in a split gene.Contrast with exons, the coding sequence.
66
What is a Primary Transcript?
An unprocessed RNA molecule that is the direct product of transcription.
67
In Eukaryotes the process by which introns are removed and exons are joined is called what?
splicing
68
What is a spliceosome?
A complex of ribonucleoprotiens that catalyze the removal of introns from RNA primary transcripts.
69
How does the spliceosome function?
the proteins of the spliceosome cut out the intron and join the flanking exons together to form a contiguous protein-coding sequence in the mature mRNA.
70
What are the two other steps in the processing of mRNA in eukaryotes that are unique to its domain?
capping and the poly (A) tail
71
What is capping?
capping is the addition of methylated guanine nucleotide at the 5'-phosphate end of the mRNA,and added in reverse to the rest of the mRNA molecule and is needed to initiate translation.
72
what is the poly (A) tail
the trimming of the 3' end of the primary transcript and adding 100-200 adenylate residues, where the poly(A)tail stabilizes mRNA and must be removed before the mRNA can be degraded.
73
What are proteins and what are the 2 major classes of proteins?
A polymeric molecule consisting of one or more polypeptides. And the 2 major classes are catalytic proteins (enzymes) and structural proteins.
74
What are Enzymes?
A catalyst, usually composed of proteins, that promotes specific reactions or group of reactions that occur in the cell.
75
Structural proteins are integral parts of the the major structures of the cells: membrane, wall ribosomes and so on. While regulatory proteins control most of the cell processes by a variety of mechanisms, including binding to DNA and affecting transcription. (T/F)
True
76
What are Amino Acids?
One of the 22 monomers that make up the proteins; chemically, two-carbon carboxylic acids containing an amino group and a characteristic substituent on the alpha carbon.
77
What are peptide bonds?
A type of covalent bond joining amino acids in a polypeptide.
78
What is a polypeptide?
Several amino acids linked together by peptide bonds
79
What are Enantiomers?
One form of a molecule that is the mirror image of another form of the same molecule. And are designated in either D (found in cell wall) or L (cellular proteins) depending on how it rotates
80
Cells cannot be interconverted (T/F)
False can be by enzymes known as racemases.
81
What is the Genetic Code?
The correspondence between nucleic acid sequence and amino acid sequence of proteins.
82
What is an anticodon?
A sequence of three bases in transfer RNA that base -pairs with a codon during protein synthesis
83
What is Wobble?
In reference to protein synthesis, a less rigid form of base pairing allowed only in codon-anticodin pairing.
84
What is codon Bias?
The nonrandom usage of multiple codons encoding the same amino acid. Also called codon usage.
85
What are Open reading frames (OFRs)?
A sequence of DNA or RNA that could be translated to give a polypeptide. Where they are used to identify protein-encoding genes.
86
What is a start codon?
A special codon, usually AUG, that signals the start of a protein.
87
How is the correct reading frame ensured?
Reading frame fidelity (accuracy) is governed by interactions between mRNA and rRNA within the ribosome.
88
What are stop codons?
A codon that signals the end of a protein. These include UAA,UAG, and UGA. also known as nonsense codons
89
What is aminoacyl-tRNA synthestase?
An enzyme that catalyzes the attachment of the correct amino acid to the correct tRNA. If wrong amino is inserted it results in a faulty protein.
90
What are ribosomes?
A structure composed of RNAs and proteins upon which new proteins are made. (site of protein synthesis)
91
What is the peptide (P) site and E site
the p site is where the growing polypeptide chain is held by the previous tRNA. and the e site is where tRNA is released from the ribosome.
92
How is protein synthesis terminated?
When the ribosome reaches a stop codon on the sequence, where release factors recognize the stop codon and cleave the attached polypeptide from tRNA, releasing the final product.
93
How does rRNA play a role in protein synthesis?
rRNA plays a role in the initiation process through base pairing with the RBS on the mRNA,in ribosome subunit association, positioning tRNA in the A&P sites on the ribosome, the actual formation of peptide bonds is catalyzed by rRNA. Thus besides its role in the structural backbone of the ribosome, it also plays a major catalytic role in the translocation process.
94
what is a tmRNA and how does it work on trapped ribosomes?
bacterial cells have tmRNA, when tmRNA collides with a stalled ribosome, it binds alongside a defective mRNA and protein synthesis can proceed since tmRNA has both a short stretch of RNA and alanine, therefore degrading the protein.
95
What generates the secondary structure of a protein?
Hydrogen bonding between the oxygen and nitrogen atoms of two peptide bonds, generates the structure
96
Polypeptides contain regions of alpha helix but not beta-sheet secondary structures, in which the type of folding and its location in the molecule being determined by the primary structure and the hydrogen bonding opportunities (T/F)
False as they contain both beta sheets and the alpha helix
97
What is the tertiary structure?
the final folded structure of a polypeptide that has previously attained the secondary structure. In which depend largely on the hydrophobic interactions and generates the 3-D shape of each polypeptide chain.
98
what is the quaternary structure?
in proteins, the number and arrangement of individual polypeptides in the final protein molecule.
99
What is denaturation?
the irreversible destruction of a macromolecule by using heat or chemicals to break the H bonding of the protein reducing it to its primary structure. May refold back into the tertiary structure depending on the level of denaturation.
100
What are Chaperonins (molecular chaperone)?
A protein that helps other proteins fold or refold from a partly denatured state.
101
What is a signal sequence?
A special N-terminal sequence of approximately 20 amino acids that signals that a protein should be exported across the cytoplasmic membrane that are recognized by signal recognition particles (SRP)s.
