Chapter 2 Flashcards
(129 cards)
1
Q
What are soma cells?
A
All cells have diploid DNA - 2 chromosome sets, different set from each parent.
2
Q
What are germline cells?
A
Gametes have haploid DNA; different from parent cells and each other.
3
Q
What is the difference between soma and germline cells in terms of Mitochondrial DNA?
A
Soma - small circular genome, variable copy number.
Germline - inherited via egg only, XY do not contribute.
4
Q
What is a genotype?
A
The genetic make-up of a cell or individual; refers to specific copy number and/or alleles of genes present.
5
Q
What is a phenotype?
A
A cell or individual’s observable measurable traits. Variation in genotype can lead to variation in phenotype.
6
Q
What is gene expression?
A
The turning on (alleles of) a gene to produce its product.
7
Q
What is gene expression pattern?
A
The particular set of (alleles of) genes that is turned on or off in a given context. Variation in gene expression patterns can also lead to variation in phenotype. DNA sequence variation is not necessary for this to occur, but often interacts with expression patterns.
8
Q
What do genes produce?
A
Only RNA and protein!
9
Q
Which is the “first” phenotype?
A
Amino Acid
10
Q
How does the central dogma relate to information flow?
A
Nucleic acid to protein; never vice versa. DNA-->DNA - General DNA-->RNA - General RNA-->protein - General RNA-->DNA - Special RNA-->RNA - Special DNA-->Protein - Special
Prions are near exception
11
Q
What are the three components of DNA?
A
- Nitrogenous bases (A,T,G,C)
- Deoxyribose sugar
- Phosphate
12
Q
What are two Purine bases?
A
Double-ring structures - adenine & guanine
13
Q
What are two Pyrimidine bases?
A
Single-ring - cytosine & thymine
14
Q
What are nucleotides?
A
Consists of assembled sugar + phosphate + nitrogenous base.
15
Q
How do the nucleotide pairs bond?
A
Through hydrogen bonding.
16
Q
What is Chargaff’s Rules?
A
In any organism (1) amount of purines = amount of pyrimidines; (2) amount of T=A, amount of G=C.
17
Q
Why are nitrogenous bases considered complementary?
A
Each DNA base only pairs with one other, A-T and G-C.
18
Q
How are nucleotides are assembled?
A
Nucleotides are assembled into DNA double helix. 2 side-by-side strands of assembled nucleotides with complementary base-pairing.
19
Q
What type of bonds hold the DNA structure together?
A
A-T = 2 bonds G-C= 3 bonds
20
Q
How is the backbone of DNA formed?
A
The backbone is formed by the alternating phosphate and sugars linked by phosphodiester bonds. Sugar phosphate backbones run in opposite directions, antiparallel.
21
Q
How is directionality determined?
A
Directionality is determined by carbon position of phosphate attachment. Carbons on ribose are numbered 1’ to 5’ starting at the point of base attachment. Look at the carbon position (3’ vs 5’) left on free end of strand if phosphate group is cleaved off.
22
Q
Why is directionality important?
A
Directionality is important for DNA replication and transcription.
23
Q
What is the human genome composed of?
A
20,000-22,000 protein coding genes; over 8000 RNAs. Genes are in an antiparallel complementary macromolecule. Complementary bases hydrogen bond; forming double-helix.
24
Q
Who proposed the double-helix model?
A
Watson and Crick. Rosalind Franklin did a lot of the work.
25
What is semi-conservative replication?
Daughter cells contain double helix, one strand is new, the other directly from parent cell.
26
How does DNA replication work?
Each strand of double helix serves as template for replication. Templates guide assembly of complementary bases - make copy of other strand.
27
What are helicases?
Unwind DNA to make single-stranded unzip the double helix. Enzyme
28
What are topoisomerases?
Prevent super-coiling of DNA when unwound. Enzyme
29
What are polymerases?
Synthesize new DNA or RNA. Enzyme
30
What are ligases?
Join pieces of DNA end to end. Enzyme
31
What is a replication fork?
The site at which double helix is unwound to expose templates for copying. Nucleotides brought to replication fork by enzyme group called DNA polymerases.
32
How are nucleotides added to the leading strand?
Nucleotides are added to growing strand at 3' end only.
33
What does antiparallel mean in regards to replication?
The antiparallel nature of DNA means that replication goes in opposite directions on each strand.
34
What is the leading strand?
The leading strand is elongated in direction of fork movement, continuous addition of nucleotides at the 3' end.
35
What is the lagging strand?
The lagging strand is elongated in opposite direction of fork movement, nucleotides added as discontinuous segments.
36
What begins synthesis for the lagging and leading strands?
Both leading & lagging strand synthesis require RNA primer to begin. Leading strand requires initial priming, lagging strand repeated priming between segments.
37
What Okazaki Fragements?
Okazaki Fragments are segments of DNA added to the lagging strand in eukaryotes average 1000-2000 bp.
38
What is fidelity?
Accuracy of DNA replication, adherence to base-pairing rules. DNA replication results in few mistakes; fidelity is high. DNA polymerases "proof read" as they replicate, excise mismatched base pairs. Other DNA repair mechanisms are also crucial.
39
What are ingredients for PCR?
Buffer, Taq polymerase, template DNA, Primer (DNAx2), Nucleotides (x4)
40
What does PCR do?
Polymerase Chain Reaction amplifies a specific DNA region. Produces millions of copies of the target region and makes DNA for further molecular work.
41
What is PCR commonly used for?
Identify alleles/genotypes to assess variability in a population.
Characterize mutations.
Create sequences for phylogenies to determine taxonomic relationships.
Conduct forensic investigations.
42
What are the steps involved in amplification of DNA in a thermal cycler?
Denature - double stranded DNA
Anneal - primers to single-stranded DNA
Extend - primers yielding new double stranded DNA
Cycling - Repeat steps 1-3 (20-40 times)
43
What is the role of the DNA template for PCR?
Provides the target site of interest for amplification.
44
What is the role of primers in PCR?
Primers are a known sequence, anneal to single-stranded DNA template at target site. Primers provide initiation site for addition of nucleotides.
45
What is the role of nucleotides in PCR?
A, G, T, and C are the building blocks for new DNA strands.
46
What is the role of the buffer in PCR?
Maintains optimal pH and [salt] for polymerase.
47
What is the role of Taq polymerase in PCR?
We use Taq polymerase as it is a thermally stable enzyme. Taq polymerase extends growing DNA strand complementary to DNA template.
48
What is the role of MgCl2 in PCR?
Provides ions needed for enzyme reaction, in the buffer.
49
What is a nucleosome?
8 histones = nucleosome (146bp). DNA wraps on histone proteins.
50
What forms the interphase chromatin fiber?
The DNA-histone complexes coil into super helix.
51
What is heterochromatin?
Dense;
52
What is euchromatin?
Loose; DNA wrapped around histone
53
What is a telomere?
Involved in aging of the cell.
54
What is a centromere?
Enable sorting during cell division.
55
How is DNA packed?
DNA is packaged into large structures called chromosomes. There are 23 pairs in most human tissue. 22 pairs are autosomes. 1 pair is sex chromosomes.
56
What are autosomes?
22 pairs in somatic cells; one set from each parent. 50 to 250Mb, pairs have same (or similar) gene content - homologous.
Numbered 1-22. Largest is 1, 21 is the smallest. 200-2000 protein genes on each.
57
What is the locus?
The position on chromosome, homologous in pairs, genes are the same (usually).
58
What are alleles?
Variants of genes, different forms, varying DNA sequence. Different info at same locus.
59
What does heterozygous mean?
2 different alleles at a given locus on homologous loci on autosomes.
60
What does homozygous mean?
2 identical alleles at a given locus on homologous loci on autosomes.
61
What are sex chromosomes?
Males have XY and Females have XX. X and Y are mostly nonhomologous - very different relationship than autosomes.
62
What is the PAR?
A pseudoautosomal region - homologous parts of X and Y that enable segregation during meiosis.
63
What is hemizygous?
Genes that are effectively present in single copy in males.
64
What is the difference between X and Y?
Size - X is 155 Mb pairs, Y is 60Mb pairs.
Genes - X is 1000, Y is 45.
Pseudogenes - X is few, Y is many.
Sex genes - X is none. SRY male
65
What is X inactivation?
X inactivation offsets the imbalance in gene dosage between males and females. Only one copy of X is transcriptionally active in somatic cells.
66
What is a Barr Body?
Inactivated X, genes in PAR escape shut down, as do some others (about 80% genes on chromosome shut down, 20% are active)
67
What is the All but One X implication?
X inactivation in each cell is random. Every female (46, xx) is mosaic of cell types. Each somatic cell has a 50% chance of the maternal or paternal X being inactivated. The expression of X-linked disorders/polymorphisms is variable in heterozygotes.
68
What is the exception about somatic cells?
All somatic cells have both autosomes & sex chromosomes, EXCEPT red blood cells because they have no nucleus.
69
Do germ cells have both autosomes and sex chromosomes?
Yes, all germ cells have both autosomes and sex chromosomes. The copy number changes during meiosis.
70
Are all the alleles of genes from all chromosomes expressed in all cell types?
Yes, sex chromosomes do a lot more than determine sex.
71
What are the components of genes?
DNA, promoter, RNA-coding sequence (protein), terminator.
| This is independent of the organism.
72
What is a gene?
A functional unit of heredity; contains info for one or more RNA or protein products. Info to build product. Genes are defined based on 5'-3' order of transcribed product. Coding strand (sense) matches RNA. Template strand (anti-sense) is opposite.
73
What are the three major DNA sequence components?
1. Coding region
2. Regulatory regions
3. Other regions
74
What is collinearity?
Direction relationship between order of info content in gene and corresponding transcribed RNA and translated amino acids.
75
What are the regions in a eukaryotic gene?
Promoter, 5'UTR, Start Codon, Exons, Introns, and Stop Codon
76
What does the promoter region do in an eukaryotic gene?
The promoter region turns on transcription. Usually at the beginning of the 5' strand.
77
What is the 5'UTR region in an eukaryotic gene?
The untranslated region, not part of the protein. This regulates transmission.
78
What is the start codon in an eukaryotic gene?
The beginning of a protein sequence.
79
What are exons?
An exon contains info that makes it to final RNA - usually amino acid sequence for protein. Exons in humans are short, 150-200nt;
80
What are introns?
Noncoding sequences, removed by splicing. Introns are longer than exons, range from 20nt to 11000 nt. Introns almost always begin with GT and end with AG - splice recognition.
81
What is a stop codon?
The stop codon ends translation.
82
What is a polyadenylation signal?
Combined with 3' UTR; signals poly-A tail addition to mRNA. This aids in stability. 3' UTR can influence gene expression post-transcription.
83
What is RNA splicing?
Removal of introns from transcribed DNA sequence. Introns are NOT present in mRNA.
84
What are tandem repeats?
Identical sequence elements in a row. A large portion of the genome is repetitive sequences of different varieties and sizes. Only minor % of genome is coding sequence.
85
What are STRs or microsatellites?
Short tandem repeats <10 nt core sequence, <1000 nt long. High mutation rate, variable among individuals - forensic markers. Found throughout genome, even within genes.
86
What are minisatellites (VNTR)?
10-60 nt core sequence, 1000 to >50,000 nt long. Very high mutation rate, original DNA fingerprint. Throughout genome, often flank genes (Regulatory?), not usually within genes.
87
What is satellite DNA?
60 to 200 nt core sequence, important structures - centromere, telomeres. Usually found concentrated at centromere and ends of chromosome arms.
88
What are CNVs?
Copy number variants are segments of chromosomes that repeat in different multiples among individuals. Throughout genome, polymorphism and disease causing regions.
89
How is RNA modified during/after transcription?
RNA is modified via capping, polyadenylation, splicing, and sequence editing.
90
What is the difference between RNA and DNA?
RNA has ribose as a 5-carbon sugar (OH group at 2' position). Primarily single-stranded, no double-helix structure; can "self" base-pair to form 3D structures.
RNA has nitrogenous pyrimidine base Uracil instead of Thymine. U pairs with A as in DNA transcription. Can also weakly pair with G to form 3D structures.
RNA can catalyze reactions. DNA cannot.
91
What are the 3 major steps in path from gene to protein?
1. Transcription - copy info in DNA into RNA intermediate
2. Splicing - process RNA intermediate into final form specifying order of amino acids.
3. Translation - use RNA as template to synthesize amino acid chain.
92
What are the 2 major categories of RNA?
1. Messenger - transfers info from DNA-based genes to cellular machinery for protein production (gene expression). mRNA intermediate between DNA and protein.
2. Functional - RNA itself is final product, contributes to process of info transfer.
93
What are other types of RNA?
1. tRNA - Transfer - involved in movement of amino acids in cytoplasm (P/E)
2. rRNA - ribosomal - major components of ribosome P/E
3. snRNA - small nuclear - part of spliceosome, molecular machine that processes primary RNA transcript. E only
4. miRNA - micro - regulate expression of other genes. E only
94
What is transcription?
Production of RNA strand with sequence that matches that of a DNA gene. Anti-sense strand used as template, RNA strand synthesized is complementary. RNA sequence matches DNA sequence of coding (sense) strand. Both DNA strands can be used as templates but in any one gene the same strand is always used.
95
Does RNA strand elongate in 5' to 3' direction?
Yes, same as DNA.
96
How are nucleotides added to RNA strand?
Nucleotides are added to growing RNA strand via base pair rules by RNA polymerase II. Multiple RNA polymerases work simultaneously - produce many copies of RNA transcript.
97
What are general transcription factors GTF?
Binding proteins that attract RNA polymerase, play role in initiating transcription.
98
What is the TATA BOX?
A common promoter sequence TATA, ~30bp upstream of start site. GTFs bind to TATA box and attract RNA polymerase.
99
What are three types of RNA polymerase?
1. Transcribes all rRNA genes.
2. Transcribes all protein coding genes.
3. All small functional RNAs.
100
What is primary transcript?
RNA strand produced - matches coding strand.
101
What is RNA splicing?
Most eukaryotic genes require processing to remove introns, this happens in the nucleus.
102
What is the spliceosome?
The spliceosome is made of several snRNP subunits. snRNP = small nuclear RNA + set of proteins.
The function is...
1. Bind intron sequence, recognize intro/exon boundaries.
2. Hold 1 transcript in correct position to join exons.
3. Catalyze reactions that remove introns, join exons.
103
What is alternative splicing?
Different proteins from same 1' transcript based on which regions are removed. Different combinations of exon result. Introns vary in size by species and between genes. RNA also processed through addition of cap at 5' end and poly-A tail at 3' end.
104
What is the first step from DNA to phenotype?
Transcription is the first step from DNA to phenotype produces RNA intermediate.
105
Why is RNA processed?
RNA is processed to remove introns, so primary transcript and mature mRNA are different.
106
Which type of RNA specifies the amino acid sequence produced by genes?
mRNA specifies amino acid sequence of polypeptide produced by gene.
107
Which allows more protein to be produced, DNA or RNA?
RNA intermediate allows much more protein to be produced than if DNA alone were used.
108
Can the primary transcript produce multiple polypeptides?
Primary transcript can be spliced in different ways to produce multiple polypeptides from the same gene.
109
What is colinearity?
The sequence of nucleotides in gene determines sequence of amino acids in protein (via
110
What is the genetic code?
Nucleotides form the genetic code. Relationship between codons and amino acids they indicate.
111
What is the central dogma?
Unidirectional information flow nucleic acids to protein, never reverse.
112
What is a codon?
A unit of genetic code; 3-nucleotide sequence ('word') specifying amino acid. Genetic code is in mRNA nucleotide sequence. Somehow needs to be converted to amino acids by cellular machinery.
113
What is translation?
The production of polypeptide with amino acid sequence specified by codon sequence of mRNA. Translation is done in cytoplasm, after transport from nucleus in eukaryotes.
114
What are the four features of the genetic code?
1. Non-overlapping - consecutive amino acids specified by consecutive codons.
2. Three bases make up each codon.
3. Code is read from fixed starting point to end of coding sequence (reading frame).
4. Code is degenerate - most amino acids specified by more than one codon.
115
What is tRNA?
tRNA is transfer RNA, an adapter molecule which brings amino acids to ribosome during translation.
116
What is the structure of tRNA?
Amino acid binding site and anticodon region complementary to mRNA. tRNAs have similar structure but differ in amino acid acceptor and anticodon sequence.
117
What pairs with the mRNA?
The anticodon loop.
118
What is the A site?
The A site binds incoming tRNA carrying next amino acid in sequence.
119
What is the P site?
The P site contains growing peptide chain, interacts with central portion of ribosome.
120
What is the E site?
The E site is the deacylated tRNA ready to be released from ribosome. The ribosome moves along mRNA strand in 5' to 3' direction, so A,P,E sites always changing.
121
Why is the genetic code degenerate?
The genetic code is degenerate because more than one codon specifies an amino acid (most). Further degenerate because of modified base pairing rules in codon-anticodon binding.
122
What is a wobble?
The relaxation of base pairing rules in codon-anticodon binding in translation. Allowing G to pair with U.
123
What is the Hayflick Limit?
The number of times a cell will divide before it stops and becomes senescent. Presumably governed by telomere length; shorten each cycle. Ranges but 40-60 divisions is general guideline. Cancer cells do not become senescent; telomere length can be restored.
124
What is ploidy (n) ?
The number of sets of homologous chromosomes in cells. Information content can differ among sets. Ploidy does not change during S phase or during mitosis, reduced by half in meiosis 1.
125
What is the DNA content (c) ?
The number of copies of the haploid genome in cells. No new information. Content doubled during S phase; reduced by half in mitosis and in both meiosis 1 and 2.
126
Where does Meiosis occur?
Takes place in germ cells only - often called meiocytes. Each meiocyte division yields 4 haploid daughter cells (gametes) in diploid life cycle. Reduction in ploidy.
Humans - meiosis in gonads, makes eggs and sperm.
Flowering plants - meiosis in anthers and ovaries, makes meiospores.
127
What are sister chromatids (SC)?
Identical copies of same chromosome, share a centromere. Have the same genes and alleles; identical copies (Exception - after crossing over).
128
What are homologous chromosomes (HC)?
Different copies of same chromosome, 1 from each parent. Same genes but different or same alleles. Not identical copies.
129
What is the difference between a gene and allele?
Gene - encodes for a product (RNA or protein); associated with a locus on a chromosome. Has basic components regulatory (promoter, UTRs) coding sequence (exons)
Allele - Variant version of gene; has different DNA sequence. Different DNA sequence = altered product/phenotype.
