protein and genes

Question 1

why study proteins

Answer 1

Roles:

1. Form enzymes: control synthesis and breakdown
2. Form transport proteins and pores in the plasma membrane and in organelles membranes: regulate movement
3. Form the structural skeleton of cells and tissues * *Have tremendous variability and specificity * * structure is encoded within our DNA

Question 2

mRNA and tRNA roles - steps trough translation

Answer 2

• In the cytoplasm, mRNA associates with a ribosome
  
  • tRNA molecules transfer specific AA (anticodon) to the mRNA which is read in triplicate at the ribosome
  • As AA are brought into place, peptide bonds join them - eventually producing an entire tRNA polypeptide chain

Question 3

what is molecular structure, who discover DNA structure

Answer 3

• Who we are, how we react to the environment whether we get a disease, and what we look like largely dependent on our DNA sequence
  
  • The identification of DNA structure= greatest discoevery by WATSON AND CRICK, WILKINS, ROSALIND FRANKLIN
  • Since= rapid evolution of a new scientific discipline known as MOLECULAR GENETICS
  • MOLECULAR GENETICS: study of how genes are turned on and off + how they affect phenotype

Question 4

rosalind franklin

Answer 4

• 1953 at 33 years olds of age wrote in her lab books that DNA= two chains based on X-rays picture
  
  • 2 weeks later: watson + crick built their DNA double helix model (based on X-ray produced by Franklin because Wilkins showed them without her knowledge

Question 5

histones in nucleosomes

Answer 5

Nucleosome: octamer consisting of 2 each of histones:

H2A/H2B/H3/H4

Question 6

steps of transcription

Answer 6

• TRANSCRIPTION DNA sequence is enzymatically copied by an RNA polymerase to produce mRNA
  
  • In the case of protein-coding DNA, transcription is the beginning of the process that ultimately leads to the translation of the genetic code (via the mRNA intermediate) into a functional peptide or protein
  • DNA is unwound by DNA HELICASE
  • RNA polymerase binds and recognizes start site
  • RNA nucleotides (uracil rather than thymine!!) base pair with the DNA
  • Form a chain of mRNA

Question 7

promoter regions

Answer 7

• DNA sequences that define where trasncription of a gene begins
  
  • Located directly upstream or at the 5prime end of the transcription start site (where the DNA will start to unwind)
  • RNA polymerase and the necessary transcription factors bind to the promoter sequence + initiate transcription
  • Define the direction of transcription + indicate which DNA strand will be transcribed (sense strand)

Question 8

transcription factors

Answer 8

• Def TRANSCRIPTION FACTORS: proteins which assist the RNA polymerase in recognizing promoters
  
  • Ex: OCT4, SOX2, c-MYC
    2 types:
    1. GENE SPECIFIC TRANSCRIPTION FACTORS: can activate specific genes ex: estrogen receptor= estrogen target gene specific
    2. GENERAL TRANSCRIPTION FACTORS: TF that are required to activate all genes
  • General transcription factors bind to DNA regions within promoters and deliver the RNA polymerase to their respective promoter sites

Question 9

CREM and spermiogenesis

Answer 9

In a mice, without a CREM, they notice that they could not process spermiogenesis after a certain point. So the mice will have spermatids but not spermatozoa so the spermiogenesis is not done
After post-meiotic division = apoptis
For spermiogenesis:
1. Mitosis (spermatogonia)
2. Meiosis I (1er spermatocytes)
3. meiosis II (2eme spermatocytes)
4. Spermiogenesis (when you take the product of meiosis which is the spermatids and make it converts to spermatozoa)

JUST TO KNOW THAT CRE IS IN THE PROMOTER REGION, CREM IS A TRANSCRIPTION FACTOR AND WITHOUT IT, THE SPERMIOGENESIS WILL NOT PROCEDE

Question 10

synthesis: DNA to protein (5 steps)

Answer 10

1. GENE ACTIVATION: a section of DNA containing a gene must be activated so that its can be read
   
   2. TRANSCRIPTION: the DNA base sequence of the gene is used to create a piece of RNA in the porcess known as transcription
   3. mRNA PROCESSING: may either undergo alternative splicing before leaving the nucleus or be silenced and destroy by enzymes
   4. TRANSLATION: mRNA in the cytoplasm, tRNA and rRNA help to start translation and bring AA
   5. POSTTRANSLATIONAL MODIFICATION: proteins fold into complex shapes, may be split by enzymes into smaller peptides, have chemicals added…

Question 11

alternative splicing

Answer 11

• Method of processing mRNA
  
  • Occurs when enzymes clip out segments of the middle or off the ends of the mRNA strand
  • Genes contain segments that encode protein (exons=expressed)
  • They also contain regions that noncoding segments called introns
  • The result of alternative splicing is a smaller piece of mRNA tha now contains only the coding sequence for a specific protein
  • One advantage: it allows a single base sequence of DNA to code for more than one protein!

Question 12

epigenetics

Answer 12

Epigeneticsis the study of heritablephenotypechanges that do not involve alterations in theDNA sequence

- Factors and processes that affect epigenetic mechanisms:
1. Development (utero, childhood)
2. Environmental chemicals
3. Drugs/pharmaceuticals
4. Aging
5. Diet

- DNA methylation: methyl group (an epigenetic factor found in some dietary sources) can tag DNA and actovate or repress genes * * histone modification: the binding of epigenetic factors to histone tails alters the extend to which DNA is wrapped around histones and the availability of genes in DNA to be activated

- HEALTH ENDPOINTS: 
1. Cancer
2. Autoimmune disease
3. Mental disorders
4. diabetes

Question 13

2 types of genes

Answer 13

HOUSEKEEPING GENE: are always expressed, so importamt for basic functions
- Other genes have different levels of expression depending on the cell type

Question 14

membrane proteins

Answer 14

1. Channel proteins:
   
   • Gated channels
   • Open channels
   2. Carrier protein (specific substrates)
      - Uniport carriers
      - Symport carriers
      - Antiport carriers

Question 15

active transport

Answer 15

Active transport processes require the expenditure of metabolic energy by the cell
- Transport by pumps
** pumps are membrane transporters that move a substance against its concentration gradient (opposite of diffusion)
Ex: calcium pumps and sodium-potassium pump
- Transport by vesicles: allows substances to enter or leave the interior of a cell without actually moving through its plasma membrane

Question 16

mechanism of SGLT (sodium glucose link transporter)

Answer 16

• • both Na and Glucose are coming from the extracellular
    
    1. Sodium binds first to the transporter and causes a conformational change in the protein that creates a high-affinity binding site to glucose
    2. Glucose binds to SGLT
    3. The protein changes conformation and opens the channel to the intracellular fluid
    4. Na is relaease (down its concentration gradient) and this lost will change the the binding site of the glucose on the protein, so it will create a low affinity binding site. Glucose will then be released

Question 17

epithelium transport

Answer 17

• -epithelium is either leaky or tight
  
  • Capillaries all dissolved molecules can pass through
  • Kidney: held by tight junctions that creates a barrier. Substance must enter cell and pass through it
  • Selectively regulates exchange of ions and nutrients
  • ABSORPTION: from external to internal
  • SECRETION: from internal to external

** tight junctions in a transporting epithelium orevent movement between adjacent cells.substances must instead pass through the epithelial cell, crossing 2 phospholipids cell membranes as they do so

The tight junctions of epithelia seprate the cell membrane into 2 regions:

1. APICAL (or mucosal): the surface of the epithelial cell that face the lumen of an organ ** often folded into microvilli that increases the surface area
2. BASOLATERAL MEEMBRANE: 3 surfaces of the cell that face the extracellular fluid

- Transporting epithelial cells are POLARIZED because their apical and basolateral membranes have different properties:
1. Na+-K+-atpASE are found in the basolateral
2. SGLT: apical membrane * * this polarized distribution of transporters allows the one way movement of certain molecules accross the epithelium

Question 18

secretory epithelium

Answer 18

EXOCRINE GLANDS: release into external environment, skin, airways, digestive. Release into ducts
Ex: GOBLET CELLS secrete mucus into the lumen of hollow organs such as the intestine

ENDOCRINE: release hormones into bloodstream

Question 19

transcytosis to cross epithelium

Answer 19

• Some molecules (like proteins) are too large to cross epithelia on membrane transporters. Instead they are mobe by TRANSCYTOSIS= combination of endocytosis, vesicular transport accross the cell and exocytosis
  Steps:
  
  1. Plasma proteins that are concentrated in caveolae, which then undergo endocytosis and form vesicles
  2. Vesicles cross the cell with help from the cytoskeleton
  3. Vesicle contents are released into interstitial fluid by exocytosis

Question 20

phagocytosis

Answer 20

Cell engulfs bacterium or other paticle into PHAGOSOME

1. The phagocytic white blood cell encounters a bacterium that binds to the cell membrane
   
   2. The phagocyte uses its cytoskeleton to push its cell membrane around the bacterium, creating a large vesicle, the phagosome
   3. The phagosome containing the bacterium separates from the cell membrane and moves into the cytoplasm
   4. The phagosome fuses with lysosomes containing digestive enzymes
   5. The bacterium is killed and digested within the vesicle

Question 21

endocytosis

Answer 21

• Membrane surface indents and forms vesicles
  
  • Active process (needs ATP) nonselectrive= pinocytosis which uses caveolae
    Or receptor-mediated uses clathrin-coated pits
  • The plasma membrane traps some extracellular material and brings it into the cell in a vesicle
    2 basic types of endocytosis:
    1. Phagocytosis
    2. Pinocytosis: condition of cell-drinking; fluid and the substances dissolved in it enter the cell

Question 22

receptor-mediated endocytosis

Answer 22

1. Ligand binds to membrane receptor
   
   2. Receptor-ligand migrates to clathrin-coated pit
   3. Endocytosis
   4. Vesicle lose clathrin coat
   5. Receptors and ligands separate
   6. Ligands go to lysosomes or golgi for processing
   7. Transport vesicle with receptorsmoves to the cell membrane
   8. Transport vesicle and cell membrane fuse (membrane recycling)
   9. exocytosis