CHAPTER 5 Flashcards
1
Q
Genetics
A
study of inheritable traits as expressed in an organism’s genetic material
2
Q
Genome
A
the entire genetic complement of an organism, includes its genes and nucleotide sequence.
3
Q
DNA Structure: Antiparallel
A
two complimentary strands of DNA form a double helix with each strand being parallel to each other but oriented in the opposite direction.
4
Q
RNA Structure: messenger RNA (mRNA)
A
contains the code to make polypeptides
5
Q
transfer RNA (tRNA)
A
attaches amino acids and brings them to ribosome during translation
6
Q
ribosomal RNA (rRNA)
A
helps form the ribosome and peptidyl transferase
7
Q
small Nuclear RNA (snRNA)
A
helps with splicing of eukaryotic mRNA during process
8
Q
regulatory RNA; antisense RNA (asRNA)
A
can bind to mRNA and prevent them from being translated
9
Q
micro-RNA (miRNA)
A
can bind to mRNA molecules to prevent them from being translated by recruiting enzymes that hydrolyze them
10
Q
small Interfering RNA (siRNA)
A
See miRNA
11
Q
Haploid
A
single chromosome copy
12
Q
The study of genes and how their expression produces traits in an organism and how they are inherited from one generation to the next is called?
A
genetics
13
Q
The entire genetic compliment of an organism (i.e., all the DNA found in an organism) is called
A
genome
14
Q
Nucleotides consist of what three components?
A
- Phosphate
- Pentose sugar
- Nitrogenous base
15
Q
Which two of the three components above contribute to the identity of nucleic acids?
A
Pentose sugar and nitrogenous base
16
Q
What are the five different nitrogenous bases for nucleotides?
A
Adenine (A), Thymine (T), Guanine (G), Cytosine (C), Uracil (U)
17
Q
What are four major differences between DNA and RNA?
A
DNA – contains deoxyribose sugar, double stranded, stable under alkaline conditions
RNA - ribose sugar, single stranded, not stable under alkaline conditions
They each perform different functions in the human body
18
Q
The two complimentary strands of DNA form a double helix with each strand being parallel to each other but oriented in the opposite direction. What is the term that describes this orientation?
A
antiparallel
19
Q
Add the complementary DNA nucleotides to the sequence of DNA
nucleotides shown below. Be sure to include the directionality of the
complimentary strand.
5’ GCTACGTAATCGGTACGT 3’
A
3’ CGATGCATTAGCCATGCA 5’
20
Q
What is the function of DNA?
A
Stores the genetic material of an organisms in special regions called genes
21
Q
What allows RNA to have many functional forms?
A
It can take many forms because it is single stranded
22
Q
What are the five main types of RNA and their basic shape and function?
A
23
Q
Which three types of RNA are directly involved in the process of translation for all cells?
A
24
Q
Add the complementary RNA nucleotides to the sequence of DNA nucleotides shown below. Be sure to include the directionality of the complimentary strand.
5’ GCTACGTAATCGGTACGT 3’
A
25
Answer the questions comparing bacterial and eukaryotic genomes
Circular or linear chromosomes?
Single or multiple chromosomes per cell?
Haploid or diploid?
Location of chromosomes in cell? Possess plasmids?
BACTERIAL
Circular Single
Haploid
Nucleoid of cytoplasm and in plasmids
Yes, in some cells
EUKARYOTE
Linear Multiple
Diploid
Nucleus in mitochondria chloroplast and plasmids in cytosol
In some fungi, algae, and protozoa
26
What are the four main types of bacterial plasmids and what type of genes they contain?
1. Fertility plasmids – sex pilius- allow for conjugation
2. Resistance plasmids – resistance for antibiotics
3. Bacteriocins plasmids – kill other bacteria
4. Virulence plasmids – increase pathogens
27
Why do cells need to replicate their genomes?
To prepare for the cell to divide
28
The process by which all chromosomes of a cell are copied identically just before the cell divides is called
DNA replication
29
Is the process of DNA replication catabolic or anabolic?
Anabolic
30
Is the process of DNA replication exactly the same in eukaryotes as it is in bacteria or is it somewhat different?
Different
31
DNA replication is considered a “semi-conservative process”. What does the term semi-conservative mean?
The daughter DNA molecules consist of one original strand and one new strand
32
What are the four main requirements for DNA replication to occur?
1. Double stranded parental DNA with origin of replication
2. Enzymes
3. Stabilizing proteins
4. Deoxyribonucleotides triphosphates (dNTPs)
5. RNA primer
33
Does extrachromosomal DNA (plasmid DNA) also undergo DNA replication? If so, does it replicated the same time as the chromosome or at different times?
Yes, it undergoes replication but independently
34
Parental DNA contain a special region or regions where the process of DNA replication begins. What are these regions called?
Origin of replication
35
What do deoxyribonucleoside triphosphates (dNTPs) consist of?
Deoxyribose, one of the four DNA nitrogenous bases, and three phosphates
36
dNTPs serve what two purposes during DNA replication?
They provide the nucleotide (monophosphate nucleotide) and are a source of high energy
37
What are the four dNTPs used during DNA replication?
dATP, dTTP, dGTP, dCTP
38
What are the five main enzymes needed for DNA replication and their function?
1. Topoisomerase (jyrase) – relives supercoiled DNA tension ahead of the replication fork so that DNA helicase can progress
2. DNA helicase – separates double stranded DNA by breaking the hydrogen bonds between complementary base pairs
3. Primase – creates the primer
4. DNA polymerase
39
What role do single stranded binding proteins play during DNA replication?
Binds to each separate DNA molecule to prevent the two strnds from coming back together so that each can act as a template
40
What are the three points of interest that are different than eukaryotic DNA replication:
1. Bacteria has 1 origin of replication
2. It only uses twi DNS polymerase (I &III). The DNA polymerase that adds al the new DNA nucleotides that form the new complimentary strand is DNA polymerase III and the one that the RNA primers with DNA nucleotides is DNA polymerase I.
3. Bacteria DNA replication uses a specific topoisomerase called DNA gyrase
41
DNA replication can be summarized into what three general steps? What happens during each step?
1. Initiation – involves the separation of the double stranded DNA by DNA helicase and the formation of the replication bubble.
2. Elongation – Involves the uniting of the two replication forks and the replacement of the RNA primers with DNA nucleotides.
3. Termination – involves the polymerization of DNA by the DNA polymerase enzyme
42
Use the space below to replicate the following double stranded molecule of DNA. Make sure you synthesize each new daughter strand at the correct starting end just like DNA polymerase does in cells.
5’ AATAGGTATTCGGTGCGA3’
3’ TTATCCATAAGCCACGCT 5’
43
Bacterial DNA is methylated at adenine nucleotides and occasionally cytosine nucleotides. What are three reasons for the bacterial cells to do this?
1. Initiation of DNA replication
2. Protection against viral infection
3. Repair DNA
44
What are the two main differences in eukaryotic DNA replication compared to bacterial DNA replication?
1. Eukaryotic chromosomes have thousands of origins of replication, bacterial chromosomes only have one
2. Bacterial DNA replication uses two DNA polymerase, eukaryotic DNA replication uses several
45
What is the difference between genotype and phenotype?
Genotype is a set of genes in the genome
Phenotype is the physical features and functional traits of the organism
46
What two processes are involved in protein synthesis and what specifically does each process produce?
Transcription – information in DNA is copied as RNA
Translation – polypeptides synthesized from RNA
47
What is the flow of genetic information required to make the various types of RNA and polypeptides (aka the central dogma of biology)?
DNA transcribed to RNA and RNA translated to form polypetides
48
What are the six main requirements for transcription to occur (note any requirement that is eukaryotic or bacterial specific)
DNA template strand containing gene
RNA polymerases (RNA polymerase II bacteria ; RNA polymerase I , II & III for eukaryotes
Sigma factors (bacteria only)
Transcription factors (eukaryotes only)
NTPs (ATP, UTP, CTP, GTP)
mRNA processing enzymes (eukaryotes only)
49
During transcription, is the entire genome transcribed? Or are only special regions called gene transcribed?
Transcription only occurs in specialized regions within the genome called genes.
50
What are the five main types of RNA and their basic shape and function?
-Messenger RNA (mRNA) -carries information from DNA to the ribosomes (site of protein synthesis) in the cell. The mRNA code sequences determine the amino acid sequence int eh protein that is produced.
-Transfer RNA (tRNA) – it is used to transfer specific amino acids to growing polypeptide chains at the ribosomal site of the protein synthesis during translation.
-Ribosomal RNA (rRNA) – it incorporates into the ribosome
-Small Nuclear RNA (snRNA) – eukaryotes
-Regulatory RNA Antisense RNA (asRNA) – bacteria
-Micro RNA (miRNA) – eukaryotes only – used to regulate gene activity ; they are tiny RNA molecules that regulate the expression of mRNA molecules
-Short interfering RNA (siRNA) – eukaryotes
51
Transcription can be summarized into what three general steps? What happens during each step?
Initiation, elongation and termination
52
Bacterial transcription uses all the general requirements. However, there are four unique attributes of bacterial transcription. What are those four differences?
Uses 1 RNA polymerase (RNA polymerase II) to transcribe all types of RNA
Sigma factors help RNA polymerase II bind to promoter
Termination process involves a terminator sequence
RNA transcription occurs in the nucleoid
53
Can more than one molecule of RNA polymerase transcribe a gene at a time?
No, only one molecule of RNA polymerase can transcribe a gene at a time.
54
What are the five unique attributes in eukaryotic transcription that are not found in bacterial transcription?
RNA transcription occurs in the nucleus
Transcription also occurs in mitochondria and chloroplast
There are 3 types of RNA polymerase : RNA polymerase I, II and III
Numerous transcription factors
mRNA processed before translation
55
What are the three processing steps eukaryotic mRNA must undergo before it can be translated and the purpose of each?
Capping – the 5’ end receives a cap made of modified guanine nucleotides
Polyadenylation – the 3’ end receives a poly A tail made of 50-250 adenine nucleotides
Splicing – introns are removed through RNA splicing
56
Below represents a small section of DNA containing a gene.
Transcribe that gene by adding the complementary RNA nucleotides.
5’ ATGACGTATTCGGATTGA 3’
3’ TACTGCATAAGCCTAACT 5’ – Template Strand
5’ AUGACGUAUUCGGAUUGA 3’
57
After a gene has been transcribed it can be translated into a polypeptide. The mRNA molecule is “read” in three nucleotide sequences which are called?
Protons
58
How many amino acids does a codon code for?
1
59
Use the codon table below to translate the following mRNA molecule
5’ AUGACGUAUUCGGAUUGA 3’
Start/met – Thr – Tyr – Ser – Asp - Stop
60
The purpose of translation is to make what type of molecules?
Polypeptides
61
Is the process of translation always occurring in all cells?
Yes
62
Is the process of translation catabolic or anabolic?
Anabolic
63
What are the six requirements for translation to occur?
mRNA molecule
charged tRNA
small and large ribosomal subunits initiation factors
GTP
Stop codon and release factors
64
Be able to draw a basic representation of a bacterial mRNA molecule and a mature eukaryotic mRNA molecule.
65
Be able to draw out a tRNA molecule and label the amino acid attachment site, and the anticodon.
66
Translation occurs on non-membranous organelles called?
Cytosolic ribosomes
67
Where are ribosomes found in bacterial cells? Where are they found in eukaryotic cells?
Cytosol of all cells and on the surface of the endoplasmic membrane of the eukaryotic cells
68
Be able to draw out a ribosome and label the small and large subunits, the A, P, and E sites, and the mRNA attachment site.
69
The process of translation can be summarized by what three general steps. What happens during each step?
Initiation – brings together mRNA, an initiator tRNA (met of fMet), and the 2 ribosomal subunits to form an initiation complex
Elongation – amino acids are added one by one to the growing polypetide chain, each addition involves
proteins called factors and occurs in three steps, translation proceeds along the mRNA in a 5’à3’ direction
Termination – occurs when a stop codon in the mRNA reaches the A site of the ribosome, a protein called the release factor promotes the hydrolysis of the bond between the polypeptide and the tRNA in the P site. This reaction releases the polypeptide, and the translation assembly comes apart.
70
Be able to draw or describe the initiation complex for translation
71
What three things occur during the elongation step of translation?
Codon recognition – the anticodon of incoming amino acid tRNA binds to codon of mRNA
Peptide bond formation – rRNA in the ribosomes catalyzes the formation of a peptide bond between the incoming amino acid in the A site and the amino growing polypeptide (transfer polypeptide chain in P site to new amino acid in A site)
Translocation – the P site tRNA moves to E site and is them released; A site tRNA moves to P site which makes A site available for new tRNA to bond
72
Does the ribosome translate the mRNA in the 5’ to 3’ or 3’ to 5’ direction?
5’ to 3’
73
The termination step of translation occurs when what has been reached on the mRNA molecule?
When a stop codon in the mRNA reaches the A site of the ribosome
74
Stop codons do not code for an amino acid, but instead codes for what molecule?
A protein called a release factor
75
Do bacteria have to process their mRNA prior to it being translated?
Bacterial mRNA does not have to undergo processing (no capping, poly A tail or intron removal) and does not need to be transported outside of the nucleus before it can be translated.
76
Why are bacteria able to undergo transcription and translation at the same time, but eukaryotes can’t?
Because mRNA does not need to be processed or transported outside of the nucleus
77
What are the three main differences in eukaryotic translation compared to bacterial translation
Initiation occurs when ribosomal subunits bind to 5’ guanine cap
First amino acid is methionine rather than f-methionine
Ribosomes can synthesize polypeptides into the cavity of the rough endoplasmic reticulum
78
Transcribe then translate the following gene:
3’ TACCCTCACGTAAAACAA 5’
5’ ATGGGAGTGCATTTTGTT 3’
79
Know the following concerning DNA replication, transcription, and translation:
a. The purpose of the process
b. The type of cells it occurs in
c. The cellular location
d. Where the process begins
e. The basic mechanism by which the process is carried out f. The major steps
g. The requirements for each process to occur
h. The products of each reaction
i. Is the process catabolic or anabolic?
80
Genes that are always being expressed are called?
Constitutive (aka housekeeping genes)
81
Genes that are only transcribed when the cell needs the product of that genes are called?
Non-constitutive (aka facultative genes)
82
Why do cells only transcribe genes when their products are actually needed by the cell?
Allows cell to conserve energy
83
What are the four main sites of regulation of gene expression? Which is the most highly regulated in both eukaryotes and prokaryotes.
DNA level – chromatin control (eukaryotes only)
Transcription – most heavily regulated site; inhibiting initiation or elongation steps
mRNA – negative feedback and regulatory RNA in bacteria ; regulation by alternative splicing, mRNA stability and regulatory RNA
Translation – blocking ribosome assembly, decrease rRNA production and availability, posttranslational modifications, degradation of proteins, feedback inhibition (eukaryotes and bacteria); inhibiting elongation factors (eukaryotes only)
84
Regulation of gene expression is overall similar in all cells, but there are some differences between bacterial and eukaryotic gene expression.
85
What are bacterial operons?
Consist of a promoter and a series of genes
86
Genes that have multiple RNA coding regions under the control of a single promoter are called?
operon
87
What are the four main parts of a bacterial operon?
Promoter
Operator
Terminator
Genes
88
What are the two types of bacterial operons and give the example we used for each.
Inducible operons – example lac (lactose) operon
Repressible operons - example trp (tryptophan) operon
89
Which of the two types of operons contain genes that code for enzymes that may be used in catabolic reactions?
Inducible
90
Which of the two types of operons contain genes that code for enzymes that may be used in anabolic reactions?
Repressible
91
Which of the two types of operons is off by default and requires an inducer molecule that removes a repressor from the operator so that RNA polymerase II has access to the promoter?
Inducible
92
Which of the two types of operons is on by default and requires the presence of a corepressor that can activate a repressor and cause it to block RNA polymerase II’s access to the promoter?
Repressible
93
Eukaryotes typically lack operons like we see in bacteria but have more levels of regulation overall than bacteria.
94
What is the definition of mutation?
Any change in the nucleotide sequence of an organism’s genome
95
What are the two broad types of mutations and the difference between each?
Point mutation – one base pair is affected, substitutions and frameshift mutations
Gross mutations – include inversions, duplications and transpositions
96
What are the three types of point mutations and the difference between each?
Substitutions Frameshift (insertion) Frameshift (deletion)
97
What are the three types of substitution point mutations and the difference between each?
Silent Mutation – no change in amino acid sequence of polypeptide (no phenotypic change)
Missense mutation – slightly different amino acid sequence of polypeptide (may have phenotypic change)
Nonsense mutation – polypeptide synthesis ceases (can be fatal)(negative phenotype)
98
What is the definition of a mutagen?
Any physical or chemical agent that can cause DNA to mutate
99
What is the main example of a physical mutagen and the differences between the two forms of this mutagen?
Ionizing and nonionizing radiation
100
What are the three main types of chemical mutagens and how does each cause mutations?
Nucleotide analogs – disrupts DNA and RNA replication
Nucleotide altering chemicals – results in base pair substitutions and missense mutaitons
Frameshift mutagens – results in nonsense mutaitons
101
Know that after mutations have occurred, bacteria and eukaryotes have repair enzymes that can recognize and cut out small sections mutated DNA and replace it with functional DNA nucleotides
102
What is a homologous sequence of DNA?
Example: crossing over of alleles during meiosis
103
What is crossing over of alleles?
Homologous sequence
104
What is meant by horizontal transfer of DNA?
Donor cell contributes part of genome to recipient cell
105
What are the three types of horizontal gene transfer in bacteria and the difference between each?
Transformation – free DNA int eh environment and competent recipient
Transduction – bacteriophage (infect bacterial cell)
Bacterial conjugation – cell to cell and F plasmid which is either in cytosol or incorporated into chromosomes of donor (Hfr) cell
106
vertical gene transfer
the transfer of DNA from parent cells to daughter cells through normal cell division
107
horizontal gene transfer
the transfer of foreign genes to cells via mechanisms other than vertical gene transfer
▪ transformation
▪ transduction
▪ bacterial conjugation
