Bio Test 2

Front 1

Nucleic Acids are made of...

Back 1

- Sugar group (ribose vs. deoxyribose)
- Phosphate group (PO4)
- Nitrogren base (pyrimidines vs purines)

Front 2

5 Nucleotides:

Back 2

Purines:
- Adenine
- Guanine
Pyrimidines:
- Cytosine
- Thymine (DNA)
- Uracil (RNA)

Front 3

DNA is created from...

Back 3

5' ------> 3'

Front 4

Difference between Ribose and Deoxyribose

Back 4

Deoxyribose doesn't not have an oxygen molecule at it's 2' location.

Front 5

Chargaff's Rule

Back 5

The amount of double looped purines is always equal to the amount of single looped pyrimidines because they pair with each other (A to C and T to G).

Front 6

What bonds form between adjacent hydrogen bases?

Back 6

Hydrogen Bonds

Front 7

What bonds form between stacked base pairs?

Back 7

Van der Waals

Front 8

Orientation of the strands

Back 8

Complimentary and anti - parallel

Front 9

How can DNA serve as a measure of evolution?

Back 9

- Familial associations
- Molecular genealogy
- Evolutionary kinship/Convergent evolution

Front 10

Why DNA and not RNA?

Back 10

DNA is a more stable structure due to the lack of an oxygen molecule at deoxyribose's 2' location, which prevents slow hydrolysis at neutral pH.

Front 11

DNA replication is semi - ___________. Advantage?

Back 11

Semi - conservative. This replication allows for more changes, abnormalities and mutations to DNA, which makes it an evolutionary advantage due to possible adaptations.

Front 12

Semi - Conservative Replication:

Back 12

In semi - conservative replication, the original copy of DNA is made into two new copies, each containing a strand of the original DNA.

Front 13

Conservative Replication:

Back 13

In conservative replication, the original copy of DNA remains intact and an entirely new copy is created.

Front 14

Replication Bubble

Back 14

Replication begins at multiple origins along the parent strand, where a "bubble" forms, and proceeds bidirectionally.

Front 15

Topoisomerase

Back 15

Breaks kinks in DNA, moves in front of helicase.

Front 16

Helicase

Back 16

Unzips the helix

Front 17

Single Strand Binding Proteins (SSBPs)

Back 17

Prevent the re-zipping of strands after helicase unzips them.

Front 18

DNA Polymerase 1

Back 18

Replicates DNA along the leading strand

Front 19

DNA Polymerase 3

Back 19

Removes RNA primer from lagging strand, replaces it with DNA and proofreads for mistakes in the 5' to 3' direction.

Front 20

RNA Primase

Back 20

Lays sections of RNA primer along the lagging strand of DNA for Polymerase 3 to replace with DNA.

Front 21

DNA Ligase

Back 21

Joins together each Okazaki Fragment along the lagging strand via Phosphoester bonds.

Front 22

Okazaki Fragment

Back 22

Discontinuous segments of RNA primer on the lagging strand due to it's growth in the opposite direction of replication fork.

Front 23

How many hydrogen bonds in A-T pairs?

Back 23

2

Front 24

How many hydrogen bonds in G-C pairs?

Back 24

3

Front 25

Melting point of DNA is dependent upon...

Back 25

The concentration of G-C pairs. The higher the concentration, the higher the melting point because of the extra hydrogen bond present in G-C pairs, making them more stable than A-T pairs.

Front 26

How to renature DNA:

Back 26

1. Increase ion content
2. Increase ion concentration
3. Lower Temp

Front 27

3 stages of PCR

Back 27

1. Denaturation
2. Annealing
3. Extension

Front 28

Denaturation:

Back 28

94º Temperature is raised to break hydrogen bonds between base pairs.

Front 29

Annealing:

Back 29

54º Temperature is lowered so that DNA Primers can bind to strands.

Front 30

Extension:

Back 30

72º Temperature is raised slightly, quickening the process of replication with taq polymerase.

Front 31

Torsional Stress

Back 31

Stress on unwound DNA caused by partial unwinding of DNA because the ends of the strands are not free to rotate.

Front 32

Topoisomerase 1

Back 32

Creates a nick (break in phosphdiester bond on one strand) in order to unwind supercoils.

Front 33

Topoisomerase 2

Back 33

Crease a break in both strands of DNA & religates them. Breaks apart and rejoins DNA.

Front 34

Telomeres

Back 34

Repetitive non-coding sequences at the end of chromosomes that protect it from deterioration or fusion with another chromosome.

Front 35

Telomere sequence in humans and mice:

Back 35

TTAGGG

Front 36

Telomerase

Back 36

Responsible for synthesis of telomeres; typically only active in stem cells, germ cells, hair follicles and 90% of cancer cells.

Front 37

Hayflick limit

Back 37

The number of times a human cell will divide before division stops.

Front 38

Senescene

Back 38

Process of aging

Front 39

Cancer

Back 39

Shortened telomeres result in activation of telomerase, preventing cell death.

Front 40

Progeria

Back 40

Shorten telomeres result in increased aging.

Front 41

DNA Repair Mechanisms

Back 41

1. Proofreading with Polymerase III
2. Mismatch Repair
3. Excistion Repair

Front 42

Proofreading

Back 42

DNA Polymerase III locates an incorrect base, immediately excises it and replaces it with correct base.

Front 43

Mismatch Repair

Back 43

Mismatch repair proteins remove misplaces base and some adjacent bases, Polymerase I adds correct bases and ligase repairs the nicks in the strand.

Front 44

Excision repair

Back 44

A base in DNA is damaged and not functional, so excision repair proteins remove damaged bases and some adjacent bases, Polymerase I adds correct bases and Ligase repairs nicks in the strand.

Front 45

Nucleotide Excision Repair

Back 45

Repairs chemical abducts (bulges) in helix, such as thymine-thymine dimers caused by UV radiation. Bulge is recognised, dimer with damaged bases is removed along with adjacent bases, polymerase fills in with undamaged bases and ligase seals the nicks.

Front 46

Regulating protein function via noncovalent modification

Back 46

Often involves noncovalent binding of a ligand, resulting in allostery (change in proteins tertiary or quaternary structure). Can either increase or decrease protein activity.

Front 47

Cooperation

Back 47

Refers to the positive/negative influence the binding of a ligand at one site has on the binding of another ligand at a different site.

Front 48

Positive cooperation

Back 48

Hemoglobin; the binding of one oxygen molecule increases the proteins affinity for the binding of the next oxygen molecule.

Front 49

Negative cooperation

Back 49

Called feedback inhibition, where the activity of a protein/enzyme is reduced from the binding of substrate.

Front 50

Calcium/Calmodulin-Mediated switching

Back 50

Calmodulin is an EF hand protein that binds to Ca2, which alters conformation and allows it to bind with certain target proteins.

Front 51

SDS PAGE

Back 51

SDS dissociates multimeric proteins and denatures all polypeptide chains. Small complexes move through gel faster than larger ones during electrophoresis, so proteins separate into bands as they migrate. Determines chain length (mass) of proteins.

Front 52

Centrifugation

Back 52

Separates proteins based on mass/density.

Front 53

Western Blotting

Back 53

Separates proteins and identifies proteins of interest. 2 antibodies used; 1 binds to desired protein and 2nd binds to 1st and is linked to an enzyme that permits detection of first antibody. These enzymes generate visible light, which the antibodies increase the signal of.