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Colin MOD > Ch. 1 - The Cell as a Unit of Health and Disease > Flashcards

Ch. 1 - The Cell as a Unit of Health and Disease Flashcards

1
Q

What are the Classes of Non-Protein Coding sequences ?

A
  • Promoter and Enhancer regions
  • Non-coding regulatory RNAs
  • Mobile Genetic Elements (transposons, aka Jumping genes)
  • Special Structural Regions
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2
Q

What are Promoter and Enhancer regions of DNA?

A

Regions of DNA that provide binding sites for transcription factors.

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3
Q

What are Noncoding Regulatory RNAs?

A

Segments of DNA are transcribed into RNAs that are never Translated into proteins

These RNA help regulate gene expression trhough various mechanisms

Examples:

  • Micro RNAs
  • Long Noncoding RNAs WHICH ARE USED FOR X INACTIVATION
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4
Q

Aside from promoters and enhancers, what else are DNA binding site sequences used for?

A

There are DNA binding sites for factors that organize and maintain higher order chromatin structures

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5
Q

What are mobile genetic elements?

A

AKA Jumping Genes

These segments can move around the genome

They are implicated in gene regulation and chromatin organization

Function not well established

EXAMPLE: Transposons

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6
Q

What are special structural regions of DNA?

A

Telomeres (tips of chromosomes)

Centromeres (chromosome tethers)

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7
Q

What segments of DNA are most involved with polymorphisms/gene variations associated with disease?

A

Non-Protein coding regions

This indicates that gene regulation may be more important in disease causation than structural changes in specific proteins

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8
Q

What are the two most common forms of DNA variation in the human genome?

A

Single-Nucleotide Polymorphisms (SNPs)

Copy Number Variations (CNVs)

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9
Q

What are SNPs?

A

Single Nucleotide Polymorphisms

Variations at SINGLE nucleotide positions

  • Almost always Biallelic (only two options exist: A or T)
  • Only 1% of SNPs occur in coding regions (as expected by statistics; coding regions make up 1.5% of genome)
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10
Q

What are CNVs?

A

Copy Number Variants

Consist of 1000 to Millions of base pairs

Can be biallelic (only two options exist, A or T) or very complex rearrangements of genomic material

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11
Q

What is epigenetics?

A

Heritable changes in gene expression that are not caused by alterations in DNA sequence

Epigenetic alterations are reversible and are amenable to therapeutic intervention

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12
Q

What is a nucleosome?

A

DNA segments (147 base pairs) long that are wrapped around a histone protein

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13
Q

What is histone?

A

Protein octamer composed of 4 pair of subunits - H2A, H2B, H3, and H4

Histone molecules are positively charged

Negatively charged DNA strands wrap 1.8 times around each histone molecule forming a beads-n-a-string structure called “Chromatin”

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14
Q

What is Euchromatin and Heterochromatin?

A

Euchromatin - tightly condensed chromatin DNA that is not being actively transcribed
- Inactive DNA

Heterochromatin - loosely packed chromatin DNA that is being actively transcribed
- Active DNA

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15
Q

What are chromatin remodeling complexes?

A

Reposition nucleosomes on DNA, exposing or obscuring gene regulatory elements such as promoters

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16
Q

What are Chromatin Writer Complexes?

A

Carry out histone modifications called “Marks”

Some examples of these modifications include methylation, acetylation, and phosphorylation of specific amino acid residues on the histones

Euchromatin (actively transcribed DNA) are associated with Histone Marks that make DNA accessible to RNA Polymerases

Heterochromatin (inactivated DNA) are associated with Histone Marks that enable compaction of DNA, making it inaccessible to RNA Polymerases

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17
Q

What are Chromatin Erasers?

A

Histone Marks are reversible due to the actions of Chromatin Erasers (remove the Marks from the Histone molecules)

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18
Q

What are Chromatin Readers?

A

Proteins that “Read” marks by binding to patterns of Marks and regulate gene expression

19
Q

What is Histone Methylation?

A

Specific Chromatin Writers methylate (add methyl group) to Lysine and Arginine residues on Histone molecules

Methylation of Lysine residues can either promote transcriptional activity or repress it depending on the residue that gets methylated

20
Q

What is Histone Acetylation?

A

Histone Acetyl Trasnferases (HAT) molecules acetylate (add acetyl groups) to Lysine residues.

Acetylation of Lysine generally causes chromatin to open up and increase transcription activity

This process is reversed by Histone Deacetylases (HDAC), causing chromatin condensation and decrease in transcription activity

21
Q

What is Histone Phosphorylation?

A

Serine residues on Histone molecules are phosphorylated (phosphoryl group is added)

Depending on the residue the phosphoryl group is added to, it can either open up the DNA and increase transcription activity, or it can condense the DNA and decrease transcription activity

22
Q

What is DNA Methylation?

A

Methyl groups are added to DNA gene regulatory elements

Methylation of DNA typically results in transcriptional silencing

DNA Methylation is tightly regulated by methyltransferases, demethylating enxymes, and methylated-DNA-binding proteins

23
Q

What are Chromatin Organizing Factors?

A

Believed to bind to noncoding regions and control long-range looping of DNA

Important in regulating spatial relationships between gene enhancers and promoters that control gene expression

24
Q

What are miRNAs?

A

Micro RNA

Do no encode protein, they function primarily to modulate the translation of target mRNAs into their corresponding proteins

Post-translational silencing of gene expression by miRNA is a fundamental and well-conserved mechanism of gene regulation present in all eukaryotes (plants and animals)

22 nucleotides on average in length

25
Q

Describe the process of miRNA trasncription

A

miRNA genes are transcribed, producing a primary miRNA (pri-miRNA)

pri-miRNA is progressivley processed through various steps, including trimming by the enzyme DICER, produces mature single-stranded miRNAs of 21 to 30 nucleotides in length.

26
Q

How does miRNA, once transcribed, cause post-transcriptional silencing?

A

The mature single-stranded miRNA associate with RNA-induced Silencing Complex (RISC)

The miRNA-RISC either form a perfect match or imperfect match

A perfect match miRNA-RISC causes the target mRNA to be cleaved, ultimately silencing the gene

An imperfect match miRNA-RISC binds to target mRNA and represses tranlsational, ultimately silencing the gene

27
Q

What specifically is the target of miRNA?

A

All mRNAs contain a so-caled “seed sequence” in their 3’ untranslated region (UTR) that determines the specificity of miRNA binding and gene silencing (post-translational silencing)

28
Q

What are siRNAs?

A

Small Interfering RNAs (siRNAs) are short RNA sequences that can be introduced experimentally into cells.

They are miRNAs that are made in the laboratory

siRNAs serve as substrates for DICER and interact with the RISC complex in a manner analogous to miRNAs

They are useful to knockdown target genes in the lab and as a potential therapeutic strategy (i.e. knockdown oncogenes)

29
Q

What are lncRNAs?

A

Long Noncoding RNA

There are 10-20 fold more lncRNAs than mRNAs

lncRNAs modulate gene expression in many ways

They can bind regions of chromatin, restricting RNA polymerase access to coding genes within the region.

Example: XIST

Many enhancers are sites of lncRNA synthesis, and these lncRNA appear to often increase transcription from gene promoters through a variety of mechanisms

30
Q

What is XIST?

A

Transcribed from the X chromosome, XIST is an lncRNA that plays a role in physiologic X chromosome inactivation in females.

The gene responsible for XIST is able to avoid inactivation.

31
Q

What is the function of the Rough Endoplasmic Reticulum?

A

Rough ER synthesizes new proteins destined for the plasma membrane or secreted proteins using membrane embedded ribosomes

These proteins are assembled in the Golgi apparatus

Proteins intended for the cytosol are sythesized by free ribosomes in the cytosol

32
Q

What is the function of the Smooth Endoplasmic Reticulum?

A

Smooth ER are abundant in cells that produce lots of Steroid Hormones and Lipoproteins like the gonads and liver – lipids

Smooth ER also used for modification of hydrophobic compounds (i.e. drugs) into water-soluble molecules for excretion
- Conjugation - liver

33
Q

What is the function of Lysosomes?

A

Lysosomes are intracellular organelles that contain degradative enzymes that permit the digestion of a wide range of macromolecules including proteins, polysaccharides, lipids, and nucleic acids

34
Q

What is the function of Proteasomes?

A

Proteasomes are a specialized kind of grinder that selectively chews up denatured proteins

Release peptides in the process

In some cases the peptides generated canbe presented in the context of Class I Major Histocompatibility (MHC) Molecules
- Antigen presentation in the context of intracellular pathogens (i.e., virally infected cells) required proteasomes and MHC Class I molecules

35
Q

What are Peroxisomes?

A

**A small organelle that plays a specialized role in the breakdown of fatty acids, generating hydrogen peroxide in this process.

36
Q

What are endosomal vesicles?

A

Structures that shuttle internalized material to the appropriate intracellular sites

Or they direct newly synthesized materials to the cell surface or targeted organelle/

37
Q

What is the cytoskeleton?

A

Structural proteins responsible for many functions

  • Cell movement of organelles and proteins
  • Movement of cell in its environment
  • Maintain basic cellular shape and intracellular organization (which are vital to maintaining cell polarity)
38
Q

What are mitochondria?

A

Powerhouse of the cell

Most ATP that powers teh cell is made through oxidative phosphorylation in the mitochondria

They also serve as an important source of metabolic intermediates that are needed for anabolic metabolism

They are sites of syntehsis of certain macromolecules (e.g., heme)

They contain important sensors of cell damage that can initiate and regulate the process of programmed cell death

39
Q

What is Phosphatidylinositol (PTI)?

A

PTI is membrane lipid that occupies mostly the inner membrane (cytosolic) leaflet

Can be phosphorylated to serve as an electrostatic scaffold for intracellular proteins

Can be hydrolyzed by phospholipase C to generate second messengers in the cytosol like IP3 and DAG

40
Q

What is Phosphatidylserine?

A

A membrane lipid that is normally restricted to the inner (cytosolic) leaflet where it confers a negative charge involved in electrostatic protein interactions

**When it flips to the extracellular surface (which happens in cells undergoing apoptosis (programmed cell death), it becomes an “eat me” signal for phagocytes

**It also serves as a cofactor for Platelets when clotting blood

41
Q

What are Glycolipids and Sphingomyelin?

A

Membrane bound molecuels that are preferentially expressed on the extracellular surface.

Glyoclipids are important in cell-cell and cell-matrix interactions (including inflammatory cell recruitment and sperm-egg interactions)

42
Q

What is Phosphatidylethanolamine?

A

Phosphatidylethanolamine is a membrane lipid found mostly on the inner leaflet of the cell membrane

43
Q

What are Lipid Rafts?

A

Aggregates of proteins and cholesterol that have similar solubilities

Allows collections of proteins to come together for cell signaling

Nonrandom distribution of lipids and membrane proteins effects cell-cell and cell-matrix interactions, intracellular signaling, and generation of specialized membrane regions involved in the secretory or endocytic pathways

44
Q

What are the 4 general arrangements of proteins associated with the plasma membrane?

A

Most proteins are integral or transmembrane proteins

  • They have one or more hydrophobic alpha helical segment that traverse the lipid bilayer
  • They have positively charged aminoacids in their cytoplasmic domains, which anchor the proteins to the negatively charged head groups of membrane phospholipids.

Proteins may be synthesized in the cytosol and postranslationally attached to prenyl groups (e.g. farnesyl, related to cholesterol) or fatty acids that insert into the CYTOSOLIC SIDE of the plasma membrane

Insertion into the membrane may occur through glycosylphosphatidylinositol (GPI) anchors on the EXTRACELLULAR SURFACE surface of the membrane

Peripheral membrane proteins may noncovalently associate with true transmembrane proteins

Colin MOD (5 decks)

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