Biochemistry

Question 1

What are Amino Acids and the prevalence of their function?

Answer 1

Amino Acids: Molecules that contain a amino group or a NH2 and a acid like a carboxylic acid COOH
Amino Acids Will attach to an R group (functional Group to the Alpha carbon this R group as unique chemical properties that will enable it to have a specific function in a biological enviorment.

Question 2

Is it necessary to have the amino and carboxylic bonded to the same carbon?

Answer 2

No, In case like the Neurotransmitter GABA the amino group is on the gamma carbon that is three carbons from the carboxyl. Their are some AA in the body that do not look exclusively like the AA some are in the form of intermediates and lysine can be converted to pyrrolysine.

Question 3

Can AA be optically active or have a Chiral Center?

Answer 3

chiral center means that the alpha carbon has four different attachements. In terms of most AA yes it is chiral however their is one exception this is Glycine, because it have a Hydrogen as it s R group so the alpha carbon will have two Hydrogens thus it is anitchiral and it not optically active.

Question 4

Are all AA an L configurations?

Answer 4

all AA are L configurations with the exception of Cystein where the sulfate group will take priority and create and R configuration.

Question 5

What is the break down of the AA side chains?

Answer 5

AA side chains break down into Non-polar, Aromatic, Polar Negativitly charged, Positively charged, hydrophilic, hydrophobic

Question 6

What is the difference between a nucleotide and a nucleoside?

Answer 6

In DNA Nucleosides are just a five carbon sugar that is bonded to a nitrogen base however a five carbon sugar that have a nitrogen base but also have a phosphate group attached which is usually ADP or ATP

Question 7

What is the difference between ribose and dexoyribose?

Answer 7

the key is in the name at the 2’ ribose has an oxygen (OH) attacher where as dexoyribose is missing that (OH) and is replaced by an oxygen.

Question 8

Describe the back bone of DNA or also called the sugar phosphate backbone?

Answer 8

the spine of DNA is made from nucleotides made from the corresponding bases the 3’ carbon and the 5’ carbon are joined by a phosphodietester bond
Phosphodiester bond: phosphate group bind the 3’ carbon and the 5’ carbon forming two ester bond binding the molecules together.
> Phosphates carry a negative charge thus DNA and RNA strands have an overall neg charge

Question 9

What direction do you always read DNA in?

Answer 9

you always read DNA in the 5’-3’ direction

Question 10

Purine:

Answer 10

Bases that contain two rings which is found in Adenine and Guanine (PUR As Gold)

Question 11

Pyrimidines:

Answer 11

bases that contain only one ring which is found in Cytosine, Thymine, and Uracil (CUT)

Question 12

What are the Key Features in DNA that Watson and Crick Discovered?

Answer 12

1. the two strands of DNA are anti parallel so this means that one strand orientates 5’-3’ with DOWN ward polarity and the other orientates 3’-5’ with UPWARD polarity.
   
   2. the sugar phosphate backbone
   3. Complementary base paring
      > A-T, G-C via hydrogen bonds
      > These hydrogen bond and hydrophobic interactions give DNA the stability it needs
   4. Chargaffs rules
      > because of the base pairing rules the amount of A is equal to the amount of T and the amount of C is equal to the amount of G and Purines and Prymadines will be in equal ratios

Question 13

Based on the key features of DNA if a strand of DNA has 10% guanine how many of the other bases are present?

Answer 13

G=10% that means that C=10% 100-20= 80% and you have to divide 80 by two because their are two bases so that would be 40% for A and 40% fro t

Question 14

B-DNA:

Answer 14

RIGHT handed double helix making a turn at 3.4 nm about every 10 bases these contain major and minor grooves where proteins can bind and this is the biological from of DNA

Question 15

Z-DNA:

Answer 15

LEFT handed helix turing at 4.6nm which is about every 12 bases and is not Biological and is usually found in high GC rich environments or high salt.

Question 16

What is the role of Histones in DNA?

Answer 16

Histones play a vital role in DNA they are a protein that makes up a chromosome and creates the chromatin the DNA is wrapped around the histone proteins creating a protein complex called a nuclesome
> Histones are Nucleoproteins which are proteins that are only associated with DNA

Question 17

Helicase:

Answer 17

enzyme that unwinds the DNA creating two single strands of DNA templates

Question 18

single stranded binding proteins:

Answer 18

they help keep the two unstable strands apart

Question 19

Nuclease:

Answer 19

prevents the reassocaition of the DNA strands and the degradation of DNA

Question 20

Topoisomerase:

Answer 20

to alleviate some torisnal strain from supercoiling it induces negative supercoils working ahead of the Helicase.

Question 21

Polymerase:

Answer 21

reads the template strand and creates the new daughter strand
> POLY reads in the 3’-5’ direction and creates daughter strand in the 5’-3’ direction

Question 22

Leading Strand:

Answer 22

strand that is copies in a cont fashion and the parent strand is 3’-5 and the compliment is 5’-3’

Question 23

Lagging strand:

Answer 23

the strand in the opposite direction because the parent strand is 5-3 and POLY can only synth in the 5-3 direction this strand is done in fragments called Okazaki fragments and their will gap from the fragments that will be filled.

Question 24

What is the importance of structural proteins?

Answer 24

structural proteins give the body structure they have highly repetitive secondary structure and structural elements called Mofits

Question 25

What is the importance of collagen?

Answer 25

Collagen is a trihelical maxtric of connective tissue that makes up most of the connective tissue seen throughout the body

Question 26

What is the importance of Elastin?

Answer 26

Elastin is part of the extracellular matrix of connective tissue and stretches and recoils like a spring

Question 27

What is the importance of keratins?

Answer 27

intermediate filament found in proteins around the epithelia cells and help with the integrity of cell and function as regulatory proteins and makes up hair and nails

Question 28

What is the cause of osteogenesis imperfecta?

Answer 28

brittle bone disease where collagen the major component in bone forms a unique and specific secondary helical structure based on the abundance of tha amino acids glycine and can cause improper folding of the collagen protein and cell death leading to fragile bones.

Question 29

What is the function of actin?

Answer 29

Actin is the protein that makes up myofibrils they have a positive side and negative side this polarity allows motor proteins to move in a unidirectional way along the actin filament.

Question 30

What is the function of tubilin?

Answer 30

this is the protein that makes up microtubules and is important for providing the structure for chromosome seperation, and intracellular transport

Question 31

What are some examples of motor proteins?

Answer 31

Cilia and Flagella and the contraction of the muscles sarcomere is also an example of a motor protein

Question 32

Can motor proteins have enzymatic activity?

Answer 32

YES, they can act as ATPases that power conformational changes necessary for motor function and have transient interactions.

Question 33

What is the primary motor protein that interacts with actin?

Answer 33

Myosin which is a thick myofibril that can be involved in cellular transportation

Question 34

Kinesin:

Answer 34

play a key role in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis

Question 35

Dyneins:

Answer 35

sliding movement of cilia and flagella

Question 36

What is the function of Kinesin and Dyneins?

Answer 36

both are involved in vesicle transport but have opposite polarity
K= towards positive ends of the microtubule (bring in NT)
D= towards the negative end of the microtubules (bring cellular waste and recycled NT)

Question 37

What is the function of binding proteins?

Answer 37

binding proteins function the stabilize functions in the cell and body seen in cases of hemoglobin, DNA binding and transcription factors.
> they have an affinity curve because of the specific binding
> transport proteins must be able to bind or unbind its target and maintain a steady concentration and have varying affinity depending on the environment

Question 38

What are CAMs or Cell adhesion molecules?

Answer 38

proteins that are found on the surface of most cells and aid in the binding of cell to the extracellular matrix or other cells

Question 39

What are the three types of CAMS?

Answer 39

1. Integrins
2. Selectins
3. Calherins:

Question 40

Integrins:

Answer 40

Alpha and beta chains that function in binding and communicating within the extracellular matrix and play an integral role in cell signaling.

Question 41

Selectins:

Answer 41

bind to carbohydrates molecules that project from cell surfaces, found on white blood cells and endothelial cells that line the blood vessel and play an important role in host defense, inflammation and white blood cell migration.

Question 42

del

Answer 42

del

Question 43

How can CAMS be important in cancer research?

Answer 43

medications target selections and ingrains and cancer metastasis is association with unique CAMS by targeting these CAMS and the metasitist can be avoided to stop clotting process during heart attach, other medications using platelets.