3_Cell Bio I

Question 1

how much of the genome binds proteins/ or affects gene expression?

(how large is the genome itself?)

Answer 1

80% of the genome either binds proteins, or affects gene expression;

human genome: 6.4 x 10^9 bases

20,000 genes encode proteins

Question 2

difference b/w heterochromatin and euchromatin?

Answer 2

heterochromatin: transcriptionally INACTIVE

euchromatin: transcriptionally active; dispersed; “loosely packed”

Question 3

review structure of DNA

Answer 3

• “beads-on-a-string” form of chromatin;
• nucleosome: inc. 200 nucleotide pairs of DNA; core histone and linker DNA

Question 4

nuclease vs. exonuclease functions

Answer 4

• nuclease: capable of cleaving the phosphodiester bonds between nucleotides of nucleic acids.
• exonuclease: removes successive nucleotides from the end of a polynucleotide molecule.

Question 5

what allows DNA double-helix to dissociate from histone core?

Answer 5

high concentration of salt

Question 6

which parts of the DNA are NON-CODING?

Answer 6

• Enhancer regions
• Promoter region (binding sites for transcription factors)
• Binding sites for proteins that maintain protein structure
• Noncoding regulatory RNAs
• Transposons (mobile genetic elements)
• Specialized structural regions (telomeres, centromeres)
• Role of 5-methylcytosine in silencing of gene expression

Question 7

process from DNA –> protein

Answer 7

1. DNA undergoes TRANSCRIPTION to form
2. pre-mRNA –> undergoes SPLICING to remove introns (noncoding)–>
3. mRNA which contains 5’-UTR and coding region (exons), and 3’-UTR –>
4. undergoes TRANSLATION –> form protein

Question 8

DNA polymorphisms:

define, types

Answer 8

• def: DNA variations; sequence difference compared to reference standard (of 1-2% of population)
  
  • can be assoc. w/ risk factors for disease
• types:
  
  • SINGLE NUCLEOTIDE POLYMORPHISM (SNP): 1% in coding regions; wide variability among populations
  • COPY NUMBER VARIATIONS (CNVs): 50% in coding regions; 5-24 x 10^6 base pair difference b/w individuals

Question 9

what are the two categories for non-coding RNAs?

Answer 9

• micro-RNAs (miRNAs)
• long noncoding RNA (lncRNA)

Question 10

micro-RNAs (miRNAs)

define, fxn, characteristics

Answer 10

• def: non-coding RNA
• fxn: involved in post-transcriptional SILENCING of expressed genes
• KC:
  
  • processing –> RNA-induced Silencing Complex
  • presence of constant “seed sequence” in 3’-UTR
  • about 1,000 genes for miRNAs per genome
  • experimental use in “knockouts” of gene expression

Question 11

long noncoding RNA (lncRNA:

define, fxn, characteristics

Answer 11

• def: non-coding RNA; large number, at least 1 order of magnitude greater than coding RNAs
• fxn:
  
  • modulation of gene expression,
  • involved in increased transcription;
  • role in gene silencing on X chromosome
• kc: presence in telomeres at ends of chromosomes

Question 12

which modified base is associated w/ silencing of gene expression?

Answer 12

in situ;

5-methylcytosine

• (a methylated form of cytosine –>involved in regulation of gene transcription;*
• When cytosine is methylated, the DNA maintains the same sequence, but the expression of methylated genes can be altered)*

Question 13

histones:

structure; fxn; modification; other names

Answer 13

• structure: low molecular weight proteins w/ nucleosomal DNA wrapped around it
• fxn: regulation of gene expression
• mod: by methylation, acetylation, phosphorylation
• aka:
  
  • chromatin “writers”, “erasers”, “readers”

Question 14

what are the various housekeeping fxns of the cell?

Answer 14

• acquire nutrients
• communication (intra- and inter-cellularly)
• generate energy
• protect from environment
• molecular catabolism
• movement
• removal of senescent molecules

Question 15

how are the various housekeeping fxns of the cells ORGANIZED?

Answer 15

COMPARTMENTALIZED w/in specific specialized ORGANELLES

Question 16

PLASMA MEMBRANE:

structure and fxn

Answer 16

• struc: double lipid layers
  
  • outer: glycolipids & sphingomyelins
  • inner: phosphatidylSERINE & phosphatidylinositol
  • most proteins are transmembrane; can form large complexes
• fxn:
  
  • protect from environment
  • acquire nutrients

Question 17

which lipids are found in the OUTER layer of the plasma membrane?

Answer 17

outer: glycolipids & sphingomyelins

inner: phosphatidylSERINE & phosphatidylinositol

Question 18

glycocalyx:

define, location/ & fxn

Answer 18

• def: carbohydrate-enriched coating w/ polysaccharide chains
• loc: covers the extracellular surface of many cells, along w/ glycoproteins
• fxn:
  
  • cell-cell interactions
  • cell-matrix interactions
  • chem barrier (protection)
  • mech barrier (protection)

Question 19

types of transport through plasma membrane?

Answer 19

• passive diffusion: for small, nonpolar molecules
• aquaporins: water moves by osmosis
• passive/active transport mechanisms: for ions; bc lipid bilayers are impervious to ions
• channel (carrier) proteins: low molecular weight molecules; specific transporters;

Question 20

channel (carrier) proteins:

fxn, mechanism

Answer 20

• fxn: transport low molecular weight (<1000 d) molecules; specific transporter per molecule type; found in plasma membrane
• mech:
  
  1. carrier protein binds solute
  2. conformational changes of carrier protein to make hydrophilic pore
  3. ligand can transport through

Question 21

active vs. passive transport

Answer 21

• active: powered by ATPase
• passive: uses potential electrical difference across plasma membrane

Question 22

endocytosis:

define, and types

Answer 22

• def: receptor-mediated uptake of fluids/macromolecules
• types:
  
  • small molecules: enter membrane invaginations (calveolae); invol. in folate transport and cell signaling; cAMP involved
  • large mol: enter via membrane invaginations (clathrin “basket” molecules)
  • receptor-mediated endocytosis (e.g. trans-ferritin, or low density lipoproteins)

Question 23

which size molecules use the following in endocytosis:

• clathrin “basket” molecules?
• calveolae

Answer 23

• clathrin “basket” molecules = LARGE molecules
• calveolae = small molecues

Question 24

exocytosis:

define, and types

Answer 24

• def: EXPORT of molecules; packaged by RER and golgi –> form secretory vesicles
• types
  
  • transcytosis: mvmt of vesicles b/w diff’t parts of the cell; transference of proteins across epithelia
  • pinocytosis:“pinching off” of membrane to form vesicle; clathrin involvement

Question 25

**cytoskeleton:** composition

Answer 25

* **ACTIN MICROFILAMENTS** * *G-actin ("globular"; free monomer)* * *F-actin ("filamentous"; linear polymer microfilament)* * **INTERMEDIATE FILAMENTS** * *great variety amongst diff't cells* * *incl: laminins, vimentin, desmin, neurofilaments, glial fibrillary acidic proteins, cytokeratins* * **MICROFILAMENTS**: * *thick fibrils* * *ATP is involv. in movement* * *kinesins and dyneins*

Question 26

**cell-cell interactions:** | (3 categories)

Answer 26

* **tight (occluding) junctions:** high resistance barrier; proteins include zonulin, catenin, and occludin * **desmosomes (anchoring) junctions:** attach cells to other cells; proteins incl. cadherins, and integrins * **communicating (gap) junctions:** facilitate electrical or chemical signals b/w cells; connexin proteins

Question 27

**connexon:**

Answer 27

electrical or chemical connections b/w cells

Question 28

**endoplasmic reticulum:** *function, RER vs. SER*

Answer 28

* fxn: **site of synthesis for all transmembrane proteins and lipids** for organelles and all molecules exported from cells * **RER**: membrane-bound ribosomes translate mRNA into proteins * (protein synthesis in FREE ribosomes) * **SER**: involved in hormone synthesis

Question 29

**golgi apparatus:** *function; processes*

Answer 29

* fxn: * modification of proteins * glycosylation transport * processes: * proteins and lipids enter Golgi apparatus **AFTER** synthesis in RER

Question 30

**lysosomes:** *structure, function*

Answer 30

* structure: * membrane-bound; contain 40 acid hydrolases * recognizes mannose-linked proteins * function: * **autophagy:** isolates senescent proteins for transport to lysosomes, where hydrolysis ensues * **phagocytosis:** by neutrophils or macrophages results in a "phagosome", after fusion w/ a lysosome

Question 31

**proteasomes:** *functions, mechanism*

Answer 31

* fxns: (waste disposal) * **degrade denatured or misfolded proteins** * mech: * **tagged by a protein: "ubiquitin"** * **digest proteins into small peptides, which are subsequently degraded to individual amino acids**

Question 32

**mitochondria:** *function; pathology*

Answer 32

* fxn: * contains DNA; maternally inherited * energy generation; drives mitochondrial protein pumps * **thermogenin:** generates heat * pathology: * **mitochondrial genetic diseases** may also be X-linked or autosomally inherited, due to sources of mitochondrial proteins

Question 33

**mitochondria:** *mechanism*

Answer 33

* **intermediate metabolism; Krebs cycle** * **anaerobic glycolysis:** *by rapidly-growing cells (Warburg effect), w/ increased glucose and glutamine uptake* * **role in cell death:** necrosis, failure of ATP generation; apoptosis, programmed cell suicide

Question 34

what is the structure of the **MITOCHONDRIA**

Answer 34