Mmbio 240 Midterm #1

Front 1

Cloning

Back 1

A simple way to create large amounts of DNA

Front 2

Cloned DNA

Back 2

A fragment of recombined DNA that can be replicated in host cells

Front 3

Recombinant DNA

Back 3

Joining of 2 or more DNA fragments together that came from separate sources

Front 4

Restriction endonuclease
(Restriction Enzyme)

Back 4

Enzyme that cuts nucleic acids
Used by bacteria as defense mechanism

Front 5

DNA ligase

Back 5

Seals together separate fragments to create a single fragment

Front 6

Restriction map

Back 6

A diagram that shows relative positions of various restriction enzyme cut sites on the DNA molecule

Front 7

Restriction digest

Back 7

Procedure to prepare DNA for analysis
(circle with base pairs and then the lines in the gel)

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Palindrome

Back 8

Nearly all restriction enzyme sites

Front 9

Cloning Vector

Back 9

Something that carries something else??

Front 10

Plasmid

Back 10

Small accessory DNA molecules in bacteria
Circular and double stranded
Used to house non-essential genes that may be necessary in the future

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3 components that make up nucleic acids:

Back 11

1. Base
2. Sugar
3. Phosphate

Front 12

Difference between the chemical structure and sequence of DNA and RNA:

Back 12

DNA uses thymine
RNA uses uracil

DNA lacks hydroxyl group on ribose (2')
DNA double stranded

Front 13

Which bases are purines?

Back 13

Bases with double rings:
Adenine
Guanine (double bonded oxygen)

Front 14

Which bases are pyramidines?

Back 14

Bases with single rings:

Cytosine (NH2 and only ONE double-bonded oxygen)
Thymine (CH3 and TWO double-bonded oxygens)
Uracil (just TWO double-bonded oxygens)

Front 15

nucleic acids

Back 15

Chains of many nucleotides (ex = DNA or RNA)

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nucleotide vs. nucleoside

Back 16

Nucleotide has phosphate. Nucleoside does not.

Front 17

polymerization

Back 17

Adding polymers onto an existing strand

Front 18

5’ and 3’ ends

Back 18

Addition ONLY occurs at 3' end!

Front 19

base-pairing

Back 19

Guanine - cytosine (3 hydrogen bonds)
Adenine - thymine/uracil (2 hydrogen bonds)

Front 20

anti-parallel base-pairing

Back 20

5' end of one strand ALWAYS lines up with 3' of other strand

Front 21

genetic material

Back 21

DNA (amino acids and nucleotides)

Front 22

transformation

Back 22

Uptake of DNA into bacterial cells

Front 23

bacteriophage

Back 23

Virus that attack bacteria and use them as host to replicate itself

Front 24

radioisotopes

Back 24

Used to label things

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semi-conservative replication

Back 25

One new copy of genetic material stays paired with an original copy

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Aspects that are no longer true about the central dogma of molecular biology:

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1. No longer turned up side down
2. RNA self-replicates in viruses using RNA dependent RNA-polymerase

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Classical experiments that lead to the discovery of DNA.

Back 27

1. Griffith's Transformation Experiment: Genetic material could be transferred between living organisms. Did not know what exactly genetic material was.

2. Avery, MacLeod, & McCarty repeat Griffith experiment in a test tube. Provided good evidence for existence of DNA

3. Chargaff disproves the tetranucleotide structure of DNA

4. Hershey and Chase show that you can strip away proteins of phage but genetic material remains in cells

Front 28

Amino acid

Back 28

Basic building block of protein

Front 29

Peptide

Back 29

Short polymers of amino acids held together by peptide bonds

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Protein

Back 30

Chain of amino acids held together by peptide bonds

Front 31

Side chain/R group

Back 31

Part of amino acid that is different for each different acid.

Front 32

Hydrophobic

Back 32

Does not mix with water and generally is on structure in a way that prevents it from coming into contact with water.

Front 33

Hydrophilic

Back 33

Mix with water and are usually surrounded by water

Front 34

Chromatography

Back 34

A method used to purify molecules from a mixture of many types of molecules

Front 35

The 4 parts that surround the central carbon in an amino acid

Back 35

- Carboxy
- Hydrogen
- Amino
- R-group (this is what is different)

Front 36

Which amino acids belong to the basic class?

Back 36

R-groups have (+) charge because they accepted a hydrogen
- Lysine
- Arginine
- Histadine

Front 37

Which amino acids belong to the acidic class?

Back 37

R-groups have a carboxylic acid (COO-)
- Aspartic acid
- Glutamic acid

Front 38

Which amino acids belong to the polar class?

Back 38

Serine
Threonine
Tyrosine
Asparagine
Glutamine
Cysteine

Front 39

Which amino acids belong to nonpolar class? (Hydrophobic)

Back 39

Made mostly of C's, H's, and rings Cannot H-bond
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Phenylalanine
- Tryptophan
- Proline
- Methionine

Front 40

Why is protein structure critical to protein function?

Back 40

- They have a particular structure so they can interact with different things
- Cannot carry out intended function without proper structure

Front 41

Protein folding

Back 41

Often spontaneous as protein exits ribosome
Chaperone proteins assist by detecting improper folding

Front 42

Alpha-helix

Back 42

interactions with other proximal amino acids form a helix and stabilize the overall structure

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Beta-sheet

Back 43

interactions with distant amino acids stabilize the structure

Front 44

Loop

Back 44

a region with poorly defined structure, commonly found between regions of alpha-helices and beta-sheets

Front 45

Disulfide bond

Back 45

Covalent bond
Can be changed by heating or adding chemicals
(ex: perms)

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Primary structure

Back 46

Primary sequence of a chain of amino acids
Held together by peptide bonds
Ex: ala-glu-val-thr-asp

Front 47

Secondary structure

Back 47

Interactions b/n components on main chain. Determines basic structure
Ex: alpha helix or beta sheet

Front 48

Tertiary structure

Back 48

interactions b/n R-groups. Differentiates between different proteins.

Ex: hydrogen, disulfide and ionic bonds

Front 49

Quaternary structure

Back 49

How separate peptide chains interact with each other

Front 50

Protein functional domain

Back 50

A region of protein that has a specific function, location, or shape

Front 51

Protein modifications

Back 51

- Phosphate to hydroxyl group
- Glycosylation
- Hydroxylation (+ O and H2O)
- Acetylation
- Methylation

Front 52

Enzyme

Back 52

Protein that catalyzes a chemical reaction, usually speeding it up dramatically
Work on substrates

Front 53

Why are protein modifications important?

Back 53

So you can change protein properties, (de)activate them,

Front 54

How/where do restriction endonuclease enzymes cut DNA?

Back 54

- Exonucleases cut it at the end at RANDOM sequences
- Endonucleases cut it at SPECIFIC sequences

Front 55

Rationale for blue/white screening

Back 55

Shows whether or not DNA was successfully inserted because BLUE colonies indicated the B-gal gene was NOT disrupted and therefore DNA insertion was unsuccessful.
White indicates the opposite. Sucessful insertion.

Front 56

Blotting

Back 56

Transferring nucleic acids or proteins from a gel onto a paper

Front 57

Hybridization/annealing

Back 57

Annealing: coming together/sticking together
Hybridization: the annealing of 2 single-stranded nucleic acids to make 1 double-stranded molecule

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Probe

Back 58

Nonradioactive fluorescent molecule

Front 59

Loading control

Back 59

- Allows comparison of independent samples
- Verify that samples are intact and loaded in equal amounts

Front 60

In situ hybridization

Back 60

- Detection of nucleic acids in living cells or in intact tissues
- Can learn about molecules in specific types of cells

Front 61

Polymerase chain reaction (PCR)

Back 61

Detect and amplify specific DNA sequences, modifiy or sequence ends of DNA

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Primers

Back 62

Single stranded DNA oligonucleotides that are complementary and anti-parallel to the target sequence

Front 63

TAQ DNA polymerase

Back 63

From bacteria that lives in very high temperature locations, so enzymes do not denature at high temps

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Mutagenesis

Back 64

Using PCR to make specific changes (mutations) to particular DNA sequences

Front 65

DNA sequencing

Back 65

Identify genotype of a person

Front 66

PCR:
Temperatures used
Ingredients for the reaction
What happens during each step

Back 66

Temperatures:
94-95° C - denaturation
55-60° C - primer annealing
68-72° C - primer extension

Ingredients: Thermostable DNA, polymerase, Primers, Nucleotides, Appropriate pH, Divalent cations (e.g., Mg+2)