Midterm 1 study material Flashcards
Define Histone vs Nucleosome
Histones are proteins that serve as the core around which DNA wraps in eukaryotic cells. They play a critical role in organizing and compacting DNA into chromatin. Histones also help regulate gene expression by controlling the accessibility of DNA to transcription factors. There are five main types of histones: H1, H2A, H2B, H3, and H4.
A nucleosome is the basic structural unit of chromatin. It consists of a segment of DNA (about 147 base pairs) wrapped around a core of eight histone proteins (two each of H2A, H2B, H3, and H4). The nucleosome acts like a “spool” that helps compact DNA into a more manageable structure within the nucleus. The H1 histone, called the linker histone, binds outside the nucleosome to help further fold the DNA.
When we have a chromosome, we know we have DNA wrapped around histones to make nucleosome complexes, but then when we convert it back to regular double stranded DNA, then::
1) WHY do we do this?
2) What happens to the nucleosomes?
(1) We unwind chromosomes back into regular double-stranded DNA to enable critical cellular processes such as gene expression, DNA replication, and DNA repair. This unwinding allows transcription factors and RNA polymerase to access the DNA, facilitating the transcription of genes into RNA for protein synthesis. Additionally, during the S phase of the cell cycle, the DNA needs to be unwound for replication before cell division, and any damage to the DNA can be repaired more effectively when it is accessible.
2) When chromosomes are unwound into double-stranded DNA, the nucleosomes disassemble, allowing the histone proteins to detach from the DNA. This disassembly makes the DNA accessible for processes like transcription and replication. After these processes are complete, the nucleosomes can reassemble around the DNA, reforming chromatin to restore the compact structure necessary for proper organization and regulation within the nucleus.
Explain alternative splice sites.
Alternative splice sites enable a gene to produce multiple mRNA variants by allowing different exons to be included or excluded during the splicing process. This occurs because the splicing machinery can recognize various splice sites within the pre-mRNA transcript, which can be influenced by regulatory proteins and signals.
The how involves the spliceosome—a complex of proteins and RNA that carries out splicing. The spliceosome assembles on the pre-mRNA and can interact with different splice sites, resulting in various combinations of exons being joined together. This process is often influenced by factors such as sequence elements in the pre-mRNA, signaling pathways, and the specific needs of the cell.
The why relates to the need for functional diversity in proteins. By producing different splice isoforms, a single gene can contribute to various cellular functions, adapting to changes in developmental stages, tissue types, or environmental conditions. This ability to generate diverse proteins from a limited number of genes enhances the complexity and adaptability of biological systems.
What is Transcription vs Translation?
Transcription is the process by which a gene’s DNA sequence is copied into messenger RNA (mRNA) in the nucleus.
Translation is the process of converting the mRNA sequence into a protein.
Exon vs Intron?
Exon is the coding region of DNA.
Intron is the NON-CODING region that will be spliced out. (cut out).
True or false:
Duplicated genes are more common in higher eukaryotes?
True!
True or False:
Lower Eukaryotes have a higher density of protein-coding genes WITHOUT introns.
true!
What is an Alu site?
An Alu site is a short, repetitive DNA sequence found throughout the human genome and is part of the Alu element family, the most common transposable elements. These sequences don’t have a clear, purposeful function and are often considered “genetic accidents” because they can randomly copy and insert themselves into different parts of the genome. While most of the time they don’t cause harm, they can sometimes affect gene regulation, contribute to evolution, or in rare cases, cause mutations that lead to genetic disorders.
What is a Pseudogene?
A pseudogene is a segment of DNA that resembles a functional gene but has lost its ability to code for a protein due to accumulated mutations. These mutations can disrupt important parts of the gene, such as the coding sequence or regulatory regions, preventing proper transcription or translation. Pseudogenes often arise from gene duplication, where one copy becomes inactive, or from a gene being copied back into the genome without the necessary regulatory elements. Although generally non-functional, some pseudogenes may still play a role in regulating gene expression.
Define Gene Families.
Gene families are groups of related genes that share a common evolutionary origin, typically arising from gene duplication events. Members of a gene family often have similar sequences and may perform related functions, but they can also evolve to take on different roles in the organism. These families are important for understanding genetic diversity, evolutionary biology, and the functional complexity of genomes.
Why do higher eukaryotes have higher amounts of duplicated genes?
Duplicated gene amounts are higher in eukaryotes primarily due to their more complex genomes and cellular structures. Eukaryotic organisms often undergo gene duplication during cell division, which can lead to multiple copies of the same gene.
(ONE of the reasons can be crossing over, since unequal crossing over can make duplicate genes.)
WHat is a prion?
A prion is a misfolded protein that can cause other normal proteins to misfold in a similar way, leading to disease. Unlike viruses or bacteria, prions contain no genetic material (DNA or RNA) and are solely composed of proteins. When prions accumulate in brain tissue, they disrupt normal cellular functions, leading to neurodegenerative diseases like Creutzfeldt-Jakob disease in humans, mad cow disease in cattle, and scrapie in sheep. Prions are unique because they can spread and cause disease purely through protein misfolding, rather than through genetic information.
What does endoplasmic reticulum do?
The endoplasmic reticulum (ER) is an organelle in cells that plays a key role in producing, processing, and transporting proteins and lipids. There are two types of ER:
Rough ER is studded with ribosomes, which help synthesize proteins that are either secreted from the cell or inserted into membranes.
Smooth ER lacks ribosomes and is involved in lipid synthesis, detoxification, and calcium storage.
Both types work together to ensure proper folding, modification, and transport of molecules essential for cell function.
What is Rosalind Franklin’s “Photo 51”
Rosalind Franklin’s “Photo 51” is an X-ray diffraction image of DNA, taken in 1952. This photograph was crucial in revealing the double-helix structure of DNA. Franklin’s expertise in X-ray crystallography allowed her to capture this highly detailed image, which showed the distinctive helical pattern of DNA. Photo 51 provided key evidence that James Watson and Francis Crick used, without Franklin’s direct involvement, to build their model of DNA, which ultimately earned them the Nobel Prize. Franklin’s contributions were essential to understanding DNA’s structure, though her role was underappreciated at the time.
What is a Nucleosome?
A nucleosome is the basic unit of DNA packaging in eukaryotic cells. It consists of a segment of DNA wrapped around a core of eight histone proteins.
