BGEN 3022 Midterm Exam with complete
solutions 2024/2025
genome - ANSWER-complete DNA sequence of a cell or organism
- 2 in humans: nuclear, mitochondrial
mitochondrial genome - ANSWER-- Very small (16.6kb long)
- No histones
- Highly redundant
- Compact (no 'extra' DNA)
- DS ring
- Each mito has multiple copies of the mtDNA genome
- 2 rRNA, 22tRNA, 13 oxidative phosphorylation proteins
- High mutation rate (10x nuclear)
- inherited from mother
major difference between nuclear and mitochondrial genome content - ANSWER-
nuclear genome has much more extra space (non-protein coding sequences)
human nuclear genome content - ANSWER-1% of DNA encodes proteins
4% DNA encodes "non-coding" RNAs
95% transposable element repeats, heterochromatin, "other" sequences
2 types of RNA - ANSWER-- classical (- mRNA, rRNA, tRNA)
- non-coding (- lncRNAs, mRNAS, snoRNA, scaRNAs, snRNAs, piRNAs, exRNAs,
siRNAs)
,lncRNA - ANSWER-long non-coding RNA
- can adopt complex secondary and tertiary folding structures
- i.e., XIST
miRNAs - ANSWER-micro RNAS
- important regulators of gene expression
o negative regulators via translational repression or mRNA degradation
o Bind complementary 3'UTRs of target mRNAs
- >1000 in human genome
- Small genes (22nt long)
- Infrequently mutated
- Revealed through C. elegans mutations (lin-4, let-7)
o Identified only in large scale screens via phenotypes
- Mutations Linked to certain human disease
o Hearing loss, keratoconus, cancer, obesity
§ Same inheritance patterns as mutations in protein-encoding genes
snRNA - ANSWER-small nuclear RNA
- Diverse family involved in splicing events
snoRNAs - ANSWER-small nucleolar RNA
- Guide processing of mainly rRNAs (>400)
gene families - ANSWER-multiple copies of closely related genes that arose from
a single ancestral gene
- Members = paralogues
- Often found in clusters on Xm
- Arise through duplication events
5 mechanism of duplication - ANSWER-- unequal recombination
- chromosomal translocation
- DNA polymerase slippage
- transposable elements
,- whole genome duplication
unequal recombination - ANSWER-repetitive sequences/confusion during
recombination leads to unequal crossing over
- primary mechanism of duplication
- net gain AND loss of DNA
- involves small OR large regions
- helps explains clusters at same chromosomal location
DNA polymerase slippage - ANSWER-reattachment following slippage causes
misalignment/bubble
- Occurs in sections of repeated patterns of bases
- Causes small duplications, insertions, deletions
- One of the main causes of DNA variants/mutations
chromosomal translocation - ANSWER-exchange of DNA between different
chromosomes
- Can be reciprocal or unidirectional
- Results in duplications in other chromosomal locations
transposable elements - ANSWER-jumping genes"
-Retrotransposons(copy + paste) and DNA transposons (cut + paste)
retrotranposition - ANSWER-class 1
= copy + paste
- Duplicate original gene
- Use RNA intermediate
- Encode reverse transcriptase enzyme (RNA->DNA) i.e., retrovirus
- 40% human genome
- Transposed sequences typically not functional as they lack regulatory
sequences
- No introns
- Usually result in pseudogenes (resemble functional but are not)
, DNA Transposition - ANSWER-class 2
= cut + paste
- Move original gene (no duplicate)
- Mobile DNA elements (2% human genome)
- No RNA intermediate
- Encode transposase enzymes needed to excise and re-insert
- Can carry other sequences
- Recognized by inverted repeats that flank them
- Can result in functional genes
whole genome duplication - ANSWER-- results from chromosomal nondisjunction
- 2 rounds of duplication in early vertebrate development
- Polyploidy = extra copies of Xm
Effects of duplication on genes - ANSWER-produce copy number variations
- redundancy
- specialization
- degradation
redundancy - ANSWER-2 genes with same function
loss of either = little-no effect
loss of both = significant effect
- degradation of one copy can occur in the absence of selection
o result in pseudogene
specialization - ANSWER-mutative alteration in activity /expression of duplicated
gene creates novel function
- Reduces redundancy
- May be alterations to coding sequence or to transcriptional regulatory
sequences
- "new" genes unique function may be important
solutions 2024/2025
genome - ANSWER-complete DNA sequence of a cell or organism
- 2 in humans: nuclear, mitochondrial
mitochondrial genome - ANSWER-- Very small (16.6kb long)
- No histones
- Highly redundant
- Compact (no 'extra' DNA)
- DS ring
- Each mito has multiple copies of the mtDNA genome
- 2 rRNA, 22tRNA, 13 oxidative phosphorylation proteins
- High mutation rate (10x nuclear)
- inherited from mother
major difference between nuclear and mitochondrial genome content - ANSWER-
nuclear genome has much more extra space (non-protein coding sequences)
human nuclear genome content - ANSWER-1% of DNA encodes proteins
4% DNA encodes "non-coding" RNAs
95% transposable element repeats, heterochromatin, "other" sequences
2 types of RNA - ANSWER-- classical (- mRNA, rRNA, tRNA)
- non-coding (- lncRNAs, mRNAS, snoRNA, scaRNAs, snRNAs, piRNAs, exRNAs,
siRNAs)
,lncRNA - ANSWER-long non-coding RNA
- can adopt complex secondary and tertiary folding structures
- i.e., XIST
miRNAs - ANSWER-micro RNAS
- important regulators of gene expression
o negative regulators via translational repression or mRNA degradation
o Bind complementary 3'UTRs of target mRNAs
- >1000 in human genome
- Small genes (22nt long)
- Infrequently mutated
- Revealed through C. elegans mutations (lin-4, let-7)
o Identified only in large scale screens via phenotypes
- Mutations Linked to certain human disease
o Hearing loss, keratoconus, cancer, obesity
§ Same inheritance patterns as mutations in protein-encoding genes
snRNA - ANSWER-small nuclear RNA
- Diverse family involved in splicing events
snoRNAs - ANSWER-small nucleolar RNA
- Guide processing of mainly rRNAs (>400)
gene families - ANSWER-multiple copies of closely related genes that arose from
a single ancestral gene
- Members = paralogues
- Often found in clusters on Xm
- Arise through duplication events
5 mechanism of duplication - ANSWER-- unequal recombination
- chromosomal translocation
- DNA polymerase slippage
- transposable elements
,- whole genome duplication
unequal recombination - ANSWER-repetitive sequences/confusion during
recombination leads to unequal crossing over
- primary mechanism of duplication
- net gain AND loss of DNA
- involves small OR large regions
- helps explains clusters at same chromosomal location
DNA polymerase slippage - ANSWER-reattachment following slippage causes
misalignment/bubble
- Occurs in sections of repeated patterns of bases
- Causes small duplications, insertions, deletions
- One of the main causes of DNA variants/mutations
chromosomal translocation - ANSWER-exchange of DNA between different
chromosomes
- Can be reciprocal or unidirectional
- Results in duplications in other chromosomal locations
transposable elements - ANSWER-jumping genes"
-Retrotransposons(copy + paste) and DNA transposons (cut + paste)
retrotranposition - ANSWER-class 1
= copy + paste
- Duplicate original gene
- Use RNA intermediate
- Encode reverse transcriptase enzyme (RNA->DNA) i.e., retrovirus
- 40% human genome
- Transposed sequences typically not functional as they lack regulatory
sequences
- No introns
- Usually result in pseudogenes (resemble functional but are not)
, DNA Transposition - ANSWER-class 2
= cut + paste
- Move original gene (no duplicate)
- Mobile DNA elements (2% human genome)
- No RNA intermediate
- Encode transposase enzymes needed to excise and re-insert
- Can carry other sequences
- Recognized by inverted repeats that flank them
- Can result in functional genes
whole genome duplication - ANSWER-- results from chromosomal nondisjunction
- 2 rounds of duplication in early vertebrate development
- Polyploidy = extra copies of Xm
Effects of duplication on genes - ANSWER-produce copy number variations
- redundancy
- specialization
- degradation
redundancy - ANSWER-2 genes with same function
loss of either = little-no effect
loss of both = significant effect
- degradation of one copy can occur in the absence of selection
o result in pseudogene
specialization - ANSWER-mutative alteration in activity /expression of duplicated
gene creates novel function
- Reduces redundancy
- May be alterations to coding sequence or to transcriptional regulatory
sequences
- "new" genes unique function may be important
