Test 3 Flashcards
(114 cards)
1
Q
What are the three ways a chromosome can be distinguished (besides synaptic structure)? Describe them
A
Size- (Chromosome #1 is the largest)
Staining- Each chromosome has characteristic banding patterns
Centromere location
Metacentric → located in exact middle
Telocentric → located at one end or the other
Acrocentric → located between middle and end long and short arm
2
Q
Describe the two types of deletions
A
Breakage and Rejoining- A portion of the chromosome falls out and the chromosome incorrectly repairs itself without that piece
Crossing over between repetitive DNA- The chromosome twists around and one part improperly connects with another part, causing a loop to fall off
3
Q
How can deletions be detected?
A
Smaller size, missing bands, changed centromere location, and synaptic structure (extra ‘deletion’ loop on one side)
4
Q
What are the genetic consequences of a deletion?
A
Depends on genes in deleted region
5
Q
How does an inversion happen?
A
A portion of the chromosome falls out and the chromosome incorrectly repairs itself by switching the portion around or a segment of DNA loops around and fuses in place
6
Q
What are the two types of inversions? Describe them.
A
Pericentric inversion includes the centromere, Paracentric inversion does not include the centromere
7
Q
What does an inversion result in?
A
Dicentric bridge (para) or other synaptic structure (peri) both produce
->
2 unbalanced gametes (inviable), 1 normal gamete, 1 inversion gamete
8
Q
How can inversion be detected?
A
Partially inverted banding patterns, change in centromere location (if pericentric and asymmetric), synaptic structure
both pericentric and paracentric have inversion loops, only para has dicentric bridge
9
Q
What are the genetic consequences of an inversion?
A
NO problems with dosage (same numbers of gene copies). Reduced fertility (due to CO in the inverted synapse, unbalanced gametes). The inversion is inherited by some progeny
10
Q
How does a translocation occur?
A
Two chromosomes break apart and join their separate parts together, changing the order (not necessarily a duplication)
11
Q
How can a translocation be detected?
A
Change in size, change in banding pattern (partially switched with other segment), change in centromere location, synaptic structures (T shaped thing)
12
Q
Define Aneuploidy
A
Change in Chromosome number
13
Q
Define Turner’s SYNDROME
How often does it occur?
A
XO (one X chromosome and no other sex chromosomes)
Phenotypically female with no Barr bodies
1/5000 female births or 1/10000 total births
All autosomal monosomic (2n-1) are lethal, Turner’s Syndrome is the only viable human monosomic
14
Q
Define Klinefelter’s SYNDROME
A
Trisomic with extra X chromosome (XXY)
Phenotypically male with Barr bodies
15
Q
Define Trisomy X
A
Trisomic with 3 X chromosomes (XXX) Phenotypically female with two Barr bodies
No symptoms, can only detect by karyotyping
16
Q
XYY Genotype, or Jacob’s Syndrome
A
Trisomic with extra Y (XYY) Phenotypically male
No symptoms, can only detect by karyotyping
17
Q
Trisomy 21 or Down’s Syndrome
A
High variable expressivity
Chromosome 21 is the smallest chromosome with the fewest genes, so it has the lowest probability of dosage effects.
18
Q
Trisomy 13/18 or Patau/Edward’s Syndrome
A
Lifespan of only a few years
19
Q
Remaining Trisomies (not 13/18/21)
A
Spontaneous abortion. All trisomies occur with equal frequency, prevalence is due to severity
20
Q
How does Aneuploidy originate? (general)
A
The failure of the homolog or chromatid segregation during meiosis. ANAPHASE (Nondisjunction)
21
Q
How does aneuploidy differ depending on when it occurs (Meiosis I or II)?
A
Occurs during Meiosis I → Produces n+1 and n-1 gametes (2 of each)
Occurs during Meiosis II → Mix of gametes (2 normal, one -1 one +1)
22
Q
Define Polyploidy
A
Changes in numbers of chromosome sets
23
Q
Origin of (fertile) polyploidy in plants Creation of an octoploid
A
Spindle failure in mitosis of one cell -> mosaic plant (4n and 2n) -> 2n pollen/egg selfing -> 4n zygote or tetraploid
Spindle failure in tetraploid → (8n and 4n) → 4n pollen/egg → 8n zygote or octoploid
24
Q
When does spindle failure occur? (polyploidy)
A
During anaphase, when the kinetochore divides but no separation of chromatids occurs
25
What does the nuclear envelope do different in the creation of Polyploidy?
During telophase the nuclear envelope forms around a single chromosome cluster (rather than two, one on each end)
26
How is a sterile triploid created?
4n plant + 2n plant -> 3n zygote -> sterile 3n plant (cannot divide to make sperm or egg)
The abundance of triploids will depend on the relative frequencies of diploids and tetraploids
27
How is a hexaploid created?
Spindle failure in triploid -> 6n and 3n -> 3n pollen/egg -> 6n zygote or hexaploid
28
How are pentaploids and septaploids created?
Pentaploid: From hexaploid(3n) and tetraploid(2n) or diploid(n) and octoploid(4n)
29
Define Autopolyploidy
Extra sets of chromosomes from the same original species via somatic doubling
30
Define Allopolyploidy
Extra sets of chromosomes from different but related species
31
Describe how cross pollination between two 2n plants can produce a hybrid plant and a fertile derivative
```
Cross Pollination (between two 2n plants) → na + nb zygote → na + nb plant
*Sterile due to issues pairing up in production of sperm/egg
```
na + nb plant → Spindle Failure (Somatic doubling) → → → 2na + 2nb plant
Species A + Species B → Sterile Cross-Hybrid (na + nb) → Fertile Derivative (2na + 2nb)
32
What three things are chromosomes made up of?
Chromatin, protein, and DNA
33
Describe Griffith's experiment
S strain kills mouse, R strain does not, heat killed S strain does not.
R strain plus heat killed S strain does, and results in live S strain cells
34
Describe Avery, McLeod, and McCarty's experiment
Destroyed either polysaccharides, lipids, RNA, protein, and DNA one at a time to see which one would result in the mouse living and no live S strain recovered
35
What are the two types of Nucleotides? Describe them.
Purines and Pyrimidines
Purines (Adenine and Guanine): Six membered ring connected to a five membered ring
Pyrimidines (Cytosine, Thymine, Uracil): Five membered ring
36
Describe the location (which carbon) of the significant parts of each nucleotide
Both have a deoxyribose sugar with a phosphate at the 5*, an OH at the 3*, H at the 2* (deoxy), and their nitrogenous base on at 1*
37
Describe Chargaff's Rule
Molar ratio of Adenine to Thymine is 1:1
Molar ratio of Guanine to Cytosine is 1:1
38
Describe the structure of DNA. (units, stands, groves, appearance)
Nucleoside monophosphate units. Each strand is complementary and anti-parallel. Has major and minor grooves, forms a right-handed double helix
39
What holds the nitrogenous bases from one strand to those of another?
Hydrogen bonds
40
What holds the Nucleoside monophosphate units of one strand together?
Phosphodiester linkages
41
What does it mean when you say DNA replication is Semi-conservative
When one piece of DNA replicates, one strand on each of the two new pieces is new and one is from the old template strand
42
DNA REPLICATION
Where does initiation of DNA replication occur? (Pro v Euk)
Origin of replication (OriC)
Eukaryotes have multiple, Prokaryotes have one
43
DNA REPLICATION
What do Initiator Proteins do?
Separate the strands of DNA by breaking hydrogen bonds (can recognize major groove)
44
DNA REPLICATION
What does helicase do? (Initiation)
Initation- Loaded on DNA, not yet active
45
DNA REPLICATION
What does Primase do? Why?
Synthesizes primer.
DNA polymerase cannot create DNA from free nucleotides, it requires a template.
Primers are short sections of RNA that are complementary to the DNA template and antiparallel.
Primase creates primers on both strands of DNA.
46
DNA REPLICATION
What does DNA polymerase III do? (Initiation)
loaded on DNA, not yet active (two at each fork)
47
DNA REPLICATION
What does Helicase do?(Elongation)
unwind duplex bidirectionally away from the origin
48
DNA REPLICATION
What does DNA polymerase III do? (Elongation)
Adds single dNTPs (nucleotides triphosphate) to the 3* OH of a pre-existing polynucleotide
49
DNA REPLICATION
What is used to power the formation of the new phosphodiester bond?
Cleavage of phosphates from incoming NTPs is used to power the formation of the new phosphodiester bond
50
DNA REPLICATION
Which direction does DNA polymerase III add on new nucleotides?
Can only synthesize in the 5* to 3* direction
51
DNA REPLICATION
Describe the Leading strand
Leading Strand (2 total, 1 per fork)
Follows the fork on that strand that goes from 3* to 5* (5* end is same direction as expanding fork)
Keeps right up next to the fork because new strand grows from 5* to 3* (antiparallel to template)
52
DNA REPLICATION
Describe the Lagging Strand
```
Lagging Strand (2 total, 1
per fork)
```
Follows the fork on the strand that goes from 5* to 3* (3* end is same direction as expanding fork)
Gap between fork and new strand because it grows in 5* to 3* sections to keep up with the 3* end of the template
53
DNA REPLICATION
How is the lagging strand synthesized?
Discontinuously. Each new 5* to 3* piece is an Okazaki fragment.
The lagging strand requires new primers to be added each time a new fragment is created. Each fragment is not linked to each other, because the new DNA cannot bind to the RNA primer
54
DNA REPLICATION
How is the primer removed up until the final linkage? (include orientation)
DNA polymerase I works at the 3* OH end of each Okazki fragment to break the phosphodiester bond from one RNA nucleotide to another and replace them with a deoxyribonucleotide (5* to 3* endonuclease and polymerase activity)
This continues to replace a NMP with a dNMP until the primer is gone
**Cannot create the final bond between the last nucleotide that replaced the end of the primer and the start of the new fragment
55
DNA REPLICATION
How is the final linkage created between the 3* OH of one Okazaki fragment and the 5* phosphate of the next ?
DNA ligase must create that final linkage between the 3* OH of one Okazaki fragment and the 5* phosphate of the next using ATP energy
-DNA polymerases uses energy from dNTP, but no new nucleotide is added
56
DNA REPLICATION
How many origins of replication are there in eukaryotes? Prokaryotes?
Multiple in eukaryotes, one in prokaryotes
57
DNA REPLICATION
How is each new nucleotide added on by DNA polymerase?
trial and error (sampling soup). Seeing which incoming nucleotides can hydrogen bond
58
DNA REPLICATION
How does proofreading occur with DNA synthesis?
Mismatched nucleotide pairs create a distortion in the DNA helix that prompts the DNA polymerase to stop and reverse to remove the last few nucleotides it added (3* to 5* endonuclease activity) before continuing its polymerase activity
59
DNA REPLICATION
How does termination occur in bacteria? What is used?
In bacteria, the two new strands will be two loops that are chain-linked to each other
The enzyme topoisomerase II converts them into two separate loops
60
DNA REPLICATION
How does termination occur in eukaryotes?
In eukaryotes, their linear chromosomes mean that the very end of each DNA molecule has a gap about the size of the primer that was removed from the lagging strand (cannot replace primer without fragment on other side)
61
DNA REPLICATION
What is the function of telomerase? Why?
Telomerase is an enzyme that adds many repeated segments of DNA to the end of the 3* segment (5* to 3*)
DNA polymerase can then add DNA beyond the end of the strand, and Ligase will complete its last linkage. The repair polymerase will remove the primer.
62
What is the overall pathway from DNA to phenotype?
DNA -(transcription)-> RNA -(processing)->( mature RNA) -> (translation) -> (protein: primary structure) -> (protein shape) -> (protein function) -> (phenotype)
63
How is DNA processing different between Prokaryotes and Eukaryotes?
Prokaryotes have coupled transcription/translation
Eukaryotic mRNA is processed in the nucleus before transported to the cytoplasm
64
Describe the structure of RNA. How is it different than DNA? Which nucleotide is replaced? What about the overall molecule shape/length?
1* C has the sugar, 5* C has the Phosphate, like DNA.
Unlike DNA contains an extra oxygen on the 2* C
Uracil replaces Thymine
Molecules are single stranded and gene length
65
TRANSCRIPTION
Describe Initiation
Promoter is -10 to -35 consensus sequence
The sigma subunit of RNA polymerase matches the consensus sequence and binds to the promoter
Does not need initiator proteins, primers, or helicases
66
TRANSCRIPTION
Describe Elongation
The sigma subunit leaves and another core protein of the RNA polymerase can begin transcribing.
Nucleotide triphosphate are brought in to start making the RNA - The first one keeps all of its phosphates while the others donate to form phosphodiester bond.
RNA Polymerase can use either strand as a template, but polymerase activity always goes 5* -> 3*
67
TRANSCRIPTION
Describe Termination
(prokaryotes)
2 Subtypes
TTS (Transcription termination signals) are sequences that cause termination
Intrinsic: Sequence that causes the end of RNA to have many C/G's followed by U’s -> strong bonds break weak bonds and cause the RNA to fall off and the end to bind to itself (match C+G)
Rho-dependent Termination: Requires a rho binding site on the RNA, Rho is an ATPase that takes the energy from ATP to wind up the RNA and pry it off of the template
68
TRANSCRIPTION
When can initiation begin again after termination?
As soon as the promoter region is free
69
TRANSCRIPTION
Compare the RNA transcript to the non-template strand
The RNA transcript is complementary to its template strand, so it looks like the non-template strand (without extra portions like the promoter and regulatory sequences)
70
Describe RNA processing in Prokaryotes
mRNA is translated as it is transcribed, so no processing takes place
71
What four things compose "RNA Processing" in Eukaryotes?
5* Cap, 3* polyadenylation, Intron Removal, Alternative Splicing
72
Describe the 5* RNA Cap
The extra phosphates from the end nucleotide are removed and replaced with a triphosphate methylated guanosine
73
Describe 3* polyadenylation of RNA (eukaryotes)
Eukaryotes do not have transcription termination signal, but a polyadenylation signal that cuts off the end of the mRNA and halts transcription
Another enzyme will add a bunch of A’s (not encoded on template)
74
Describe Intron Removal (eukaryotes)
Prokaryotes do not have any introns. The exons encode for protein.
Small nuclear RNAs (snRNAs) associate with small nuclear proteins to form the SPLICEOSOME, which removes the introns
75
Describe Alternative Splicing (eukaryotes)
Can produce many different RNA molecules from the same gene by removing different introns
76
How many different Amino Acids are there?
20
77
What makes up an amino acid?
An amino group (NH2), a carboxyl group (C(-OH)=O)), and one of 20 different R groups
78
What are the four categories of Amino Acids?
Nonpolar, Polar uncharged, Polar Positive Charge (basic), Polar Negative Charge (acidic)
79
What is the arrangement of a protein? How are the bonds/linkages created?
Peptide bond Amino end (NH3) - carbon with R group - carboxyl end (CN=O) peptide bond
Pepide bond / Amide linkages are created by a dehydration reaction
80
Describe Primary Structure (proteins)
The amino acids that make it up
81
Describe Secondary Structure (proteins)
Hydrogen bond between backbone components (amide/=O) creates 𝞪 helices and pleated sheets
82
Describe Tertiary Structure (proteins)
Folding of protein created by interactions between R groups in the same polypeptide chain
Ionic, covalent, and hydrogen bonds
83
Describe Quaternary Structure (proteins)
Protein compounds created by multiple proteins
| Formed by interactions between R groups of different polypeptide chains
84
Describe the components of a Prokaryotic Ribosome
Large subunit composed of a 23S and a 5S rRNA and 31 proteins. Small subunit composed of 16S rRNA and 21 proteins
85
Describe the components of a Eukaryotic Ribosome
Large subunit composed of 28S, 5.8S, and 5S rRNA and 49 proteins. Small subunit composed of 18S rRNA and 33 proteins.
86
What are the functional sites of a ribosome?
Acyl site, Peptidyl site, Exit site
mRNA binding groove
Peptidyl transferase site
87
Where is the mRNA binding groove on a ribosome?
Located under A and P sites of a ribosome
88
What is the structure of a Transfer RNA (tRNA)?
Amino acid attachment site or acceptor stem
Stems produced by hydrogen bonding and two loops
Anticodon loop
89
What does the anticodon loop do on a tRNA?
Base-pairs with codon on mRNA
90
Describe the formation of a "charged" tRNA.
"charged" means addition of an amino acid.
A specific amino acid pairs with a specific tRNA using a specific ATP-powered enzyme to produce a specific ‘charged’ tRNA
91
TRANSLATION
Describe how a ribosome is added to mRNA. (Initiation)
The three initiation factors help add the small ribosomal subunit and the fmet-tRNAmet to the mRNA template
met-tRNAmet is added to the P site
The large subunit is then added, and the initiation factors disassociate
92
Describe the two types of duplications
Two chromosomes break apart and join their separate parts together, leading one to have a deletion and the other a duplication
A segment of DNA pairs with its partner on the other strand, causing a deletion and duplication
93
How can duplications be detected?
Larger size
Duplicated bands
Changed centromere location
Synaptic structure
The additional segment of DNA can be tandem (head to tail, facing the same direction) or reverse
Tandem will have one extra loop, reverse will have an extra loop and a small section base-paired to itself
94
What are the genetic consequences of a duplication?
Depends on the genes in the duplicated region
Too many doses of certain genes can be detrimental
No genetic consequences if the duplicated genes are nonfunctional recessives
95
What are the possible synaptic structures formed by duplications?
The additional segment of DNA can be tandem (ABAB) or reverse (ABBA)
Tandem will have one extra loop containing the duplicated section, reverse will have an extra loop (non-duplicated) and a small section base-paired to itself (duplicated)
96
We will need to be able to draw and label T1/T2 and N1/N2 for viable translocation heterozygotes (translocated chromatid 1/2, normal)
N’s are across from N’s and T’s are across from T’s, rows go 1 → 2
A T with an N will result in duplications/deletions
A T with a T or an N with an N are complete and viable
97
What are the genetic consequences of translocations?
no problem with dosage same numbers of gene copies
reduced fertility (50%) due to segregation of homologs unbalanced gametes
98
TRANSLATION
How is the first codon added in the initiation of transcription? (prokar)
AUG is the mRNA start codon, but it is not the first three nucleotides of the mRNA
The small ribosomal subunit has rRNA (16S) components that basepair to the mRNA to make sure it is aligned in the correct reading frame called the Shine-Dalgarno sequence
99
TRANSLATION
How is the second codon added during the elongation phase of transcription?
The first amino acid/tRNA after the fmet-tRNAMET binds to the A site with help from 3 elongation factors
Peptidyl transferase moves the amino acid from fmet to the tRNA and forms a peptide bond
Another elongation factor uses GTP to move both tRNAs to the left
A new tRNA then binds to the A site and the fmet-tRNAMET that was in the E site leaves
100
TRANSLATION
Describe the orientation of the growing polypeptide chain
The amino acids are attached to their tRNA at their carboxylic acid end
The formation of the peptide bond between the amino group and the carboxylic acid group causes one of the amino acids to release from their tRNA
mRNA is translated in the 5* to 3* direction growing the polypeptide chain from the carboxyl end
101
TRANSLATION
Describe termination
There is no tRNA for the stop codon, instead three release factors (one of which resembles a tRNA) enter the A site and cause a water molecule to be added to the end of the peptide, allowing it to be released
Without the polypeptide, all components disassemble
102
Define promoter, +1 nucleotide, 5* UTR, and 3* UTR
Promoter - Where transcription is initiated
+1 Nucleotide - The first nucleotide that is transcribed into DNA
5* UTR - DNA between the +1 nucleotide and the Shine-Dalgarno is called the 5* UnTranslated Region
3* UTR - DNA between the stop codon and the tts is called the 3* UnTranslated Region
103
What are the components of a protein coding gene (include both pro and euk parts)?
Promoter -> +1 Nucleotide -> 5* UTR -> Shine-Dalgarno -> Start Codon -> Exons/Introns -> Stop Codon -> 3* UTR -> tts
104
Define codon
three nucleotide code words on mRNA that translate to amino acids by way of the tRNAs
105
How did we know that three nucleotides code for an amino acid? How many codons code for amino acids vs stops?
Three nucleotides per amino acid produces 64 different codons
61 of those code for amino acids, 3 of those code for “stop”s
106
How are codons "redundant"? What is the other term for this trait?
there is more than one codon for a given amino acid (also called wobble)
107
How are codons unambiguous?
only one amino acid for a given codon
108
Define mutation
changes in DNA information
109
Define point mutation. What does that include?
single base changes, includes switching one letter for another and insertions/deletions of a single base
110
Define synonymous in regards to single DNA base replacements
Produce the same amino acid with no effect on function
111
Define missense conservative in regards to single DNA base replacements
Produces a similar amino acid that may not affect function
New amino acid has same or similar properties (ex: polarity, charge)
112
Define missense nonconservative in regards to single DNA base replacements
Produces a dissimilar amino acid that may alter function
113
Define non-sense in regards to single DNA base replacements
Produces a stop codon that destroys function
114
Define frameshifts in regards to insertions or deletions of bases
Produces a new polypeptide that has an altered function, realigns whole sequence
