Jt 1 A Uhcl Molecular Biology I Exam 1 Ch1,2,4,5,8,9

Front 1

*** interactions drive protein folding where regions associate w/each other and *** water.

Back 1

Hydrophobic --- exclude

Front 2

Enzymes must precisely match w/their *** in order to perform their functions through strong *** type interactions.

Back 2

substrates
non-covalent

Front 3

1) Nucleotides are comprised of a ***, ***, and ***. Function include
2) storing/transmiting genetic information, *** s***e, and m*** t***t.

Back 3

1) base --- sugar --- phosphate
2) energy storage (ATP) --- molecular transport.

Front 4

Ribose has an *** at the # prime carbon.

Back 4

oxygen --- 2

Front 5

1) Bases of all nucleotides are classified as either *** or ***.
2) They are ***(shape) rings typically having a *** charge.

Back 5

1) purines --- pyrimidines
2) planar --- neutral

Front 6

pKa values denote the *** at which *** the molecules are charged.

Back 6

pH
half

Front 7

RNA nucleotides bases are...

Back 7

AUGC
adenine
uracil
guanine
cytosine

Front 8

--- Nucleotides ---
Base joined to sugar through a *** bond between *** C1′ and *** N1' or *** N9'.

Back 8

glycosidic
sugar --- pyrimidine --- purine

Front 9

Nucleosides are composed of there components...

Back 9

Base + sugar

Front 10

Nucleosides bases are....

Back 10

adenosine
thymidine OR uridine
guanosine
cytidine

Front 11

Nucleoside plus phosphate = ***.

Back 11

nucleotide

Front 12

--- Nucleotides ---
1) Two DNA strands associate via *** *** bonds
2) to form a ***-handed double-stranded DNA.

Back 12

1) non-covalent hydrogen
2) right-handed

Front 13

--- DNA Helix ---
Regions rich in *** base pairing tend to be more bendable influencing DNA ***.

Back 13

A-T --- structure

Front 14

1) *** *** DNA can be supercoiled.
2) Open uncoiled circular DNA is said to be ***.

Back 14

1) Closed circular
2) relaxed

Front 15

To induce supercoiling, a *** molecule is *** and held at one end while the other end is twisted.

Back 15

circular
cut

Front 16

--- Supercoiling ---
1) Can be coiled *** or *** depending on CW or CCW twisting.
2) Can be *** with a support or *** without a support.

Back 16

1) positive or negative
2) toroidal or interwound

Front 17

--- Supercoiling ---
*** is the # of times one strand of DNA wraps round the other.

Back 17

Linkage number (Lk)

Front 18

--- Supercoiling ---
*** is the number of turns in a fragment of DNA

Back 18

Twist (Tw)

Front 19

--- Supercoiling ---
A positive number denotes a *** -handed helix
A negative number denotes a ***-handed helix

Back 19

right
left

Front 20

--- Supercoiling ---
*** describes supercoiling of closed circular DNA or constrained linear DNA.

Back 20

Writhe (Wr)

Front 21

--- Supercoiling ---
In *** supercoiling. unwinding the supercoils opens up the DNA strand.

Back 21

negative

Front 22

--- Supercoiling ---
*** number is fixed for a circular DNA, but *** and *** vary.

Back 22

Linking
twist and writhe

Front 23

--- Supercoiling ---
As twist decreases, *** increases and vice versa

Back 23

writhe

Front 24

The 2′ OH also allows RNA to form hydrogen bonds more/less prolifically than DNA, allowing more/less molecular interactions

Back 24

more --- more

Front 25

--- Sugar *** ---
1) Ribose - C#′ endo favors ***-type helix.
2) DeOxyRibose - C#′ endo favors ***-type helix.

Back 25

Puckering
1) 3 --- A
2) 2 --- B

Front 26

In tRNA, # of the double-helices are formed by hairpins, and # is formed from distant complementary regions

Back 26

three
one

Front 27

--- RNA ---
*** RNA structure is formed when short DS helices interact w/SS regions

Back 27

Tertiary

Front 28

--- RNA ---
A base triple interaction has # Watson-Crick bases interacting with a *** via an additional ***-bond

Back 28

two
third
H

Front 29

--- RNA ---
Phosphates are *** charged and repulse each other. When they bind large numbers of *** like Mg2+ this is counteracted allowing for compaction.

Back 29

negatively
cations

Front 30

RNA sequence differences that occur among species are known as ***.

Back 30

covariations

Front 31

--- Amino Acids ---
All amino acids except *** exist as two steroisomers L and D and ***-AA are used to make proteins

Back 31

glycine
L

Front 32

--- Amino Acids ---
End w/exposed amino group is the ***-terminus and the exposed carboxyl end is the ***-terminus.

Back 32

N
C

Front 33

--- Amino Acids ---
Residues in a polypeptide are numbered from the ***-terminus.

Back 33

N

Front 34

--- Amino Acids ---
Most single bonds can rotate however, electron *** prevents free rotation locking the atoms into a *** structure.

Back 34

delocalization --- planar

Front 35

--- Amino Acids ---
The N-Cα bond, rotation angle ***
The C-Cα bond, rotation angle ***

Back 35

ϕ - Phi
ψ - Psi

Front 36

--- Amino Acids ---
Common secondary structures are *** helices and *** sheets.

Back 36

alpha
beta

Front 37

--- Amino Acids ---
Protein folding is driven by *** interactions of the atoms in the polypeptide

Back 37

non-covalent

Front 38

--- Amino Acids ---
1) Alpha helix forms a ***-handed helix.
2) ***-bonds form between the C=O of one residue & the N-H *** residues away
3) The structure is *** with side chains protruding.

Back 38

1) right
2) H-bonds --- four
3) cylindrical

Front 39

--- Amino Acids ---
1) Beta sheets are slightly ***, largely *** structures.
2) Side chains protrude *** and *** the beta sheet
3) Amphipathic sheets tend to be found at protein ***.

Back 39

1) twisted --- planar
2) above and below
3) surfaces

Front 40

--- Amino Acids ---
*** has a very small side chain (-H) and so is very flexible

Back 40

Glycine

Front 41

--- Amino Acids ---
*** has an unusual structure that introduces kinks in the polypeptide chain.

Back 41

Proline

Front 42

--- Protein Folding ---
Folding is energetically favorable – "*** increases/decreases" as water molecules become more disordered

Back 42

entropy
increases

Front 43

--- Protein Folding ---
Proteins often fold spontaneously in aqueous solution, though some require *** like the protein ***.

Back 43

chaperones
albumin

Front 44

--- Protein Folding ---
*** structure is very complex and cannot yet be reliably predicted from primary sequence, but *** structures can be predicted

Back 44

Tertiary
secondary

Front 45

--- Protein Folding ---
1) Proteins sharing # % AA sequence likely have identical structures.
2) with # % the structures are fairly similar.

Back 45

1) 50%
2) 25%

Front 46

--- Protein Folding ---
The arrangement of secondary structural elements in a proteins is known as *** ***.

Back 46

protein fold

Front 47

--- Protein Folding ---
*** evolution is less common.

Back 47

Convergent

Front 48

--- Protein Folding ---
*** proteins (b) are roughly spherical.

Back 48

Globular

Front 49

--- Protein Folding ---
Many polypeptides have more than one structurally distinct region called a *** which can *** on its own.

Back 49

domain
fold

Front 50

Carbohydrates are built from simple ***.

Back 50

monosaccharides

Front 51

Some sugars form closed circular structures when a *** group reacts with the *** or *** group.

Back 51

hydroxyl
ketone or aldehyde

Front 52

Hexose sugars can cyclize as a #-member pyranose ring or as a #-member furanose ring

Back 52

6
5

Front 53

Hexose sugars can cyclize as a 6-member *** ring or as a 5-member *** ring.

Back 53

pyranose
furanose

Front 54

Monosaccharides can be joined by a condensation reaction between two hydroxyl groups

Back 54

This results in a disaccharide joined by a glycosidic bond

Front 55

*** are more diverse than proteins or nucleic acids.

Back 55

Carbohydrates

Front 56

Furanose and pyranose rings can have isomers – *** – which differ in the orientation of the hydroxyl on the C1 carbon.

Back 56

anomers

Front 57

Carbohydrate + protein = ***

Back 57

glycoprotein

Front 58

Carbohydrate + lipid = ***

Back 58

glycolipid

Front 59

Glycosylation is important for cell-cell interactions. These patterns can be recognized by *** (special proteins) which mediate the interactions.

Back 59

lectins

Front 60

1) Lipids are strongly *** and are comprised of *** ***.
2) However, they still have a *** acid group at one end...

Back 60

1) hydrophobic --- fatty acids
2) carboxylic

Front 61

--- Fatty Acids ---
Double bonds can be in *** or *** formation... affecting chain kink.

Back 61

cis or trans

Front 62

Loosely packed *** fats are more fluid at room temperature.

Back 62

unsaturated

Front 63

Loosely packed *** fats are solid at room temperature.

Back 63

saturated

Front 64

Harmful *** fats are produced by this artificial ***.

Back 64

trans
hydrogenation

Front 65

Different types of lipids are defined by the *** group.

Back 65

head

Front 66

--- Lipid Class ---
Glycolipids have *** attached to their head groups.

Back 66

sugars

Front 67

--- Lipid Class ---
Glycerol derived phospholipids, are distinguished by the type of head group *** and by the *** and **** of the fatty acids.

Back 67

alcohol
length and saturation

Front 68

***is an important precursor of steroid hormones.

Back 68

Cholesterol

Front 69

--- Cell Membrane ---
*** interactions between the tails stabilize the bilayer.

Back 69

van der Waals

Front 70

--- Cell Membrane ---
Fluidity is affected by the *** and *** of the fatty acids and by ***.

Back 70

size and saturation
cholesterol

Front 71

--- Cell Membrane ---
*** membrane proteins are embedded largely w/in the membrane and are composed mainly of alpha helices or beta sheets.

Back 71

Integral

Front 72

--- Cell Membrane ---
Peripheral membrane proteins do not span the membrane and bind *** to the membrane.

Back 72

reversibly

Front 73

Lk?
Tw?
Wr?

Back 73

Linkage
Twist
Writhe

Front 74

*** (psi- Ψ) is an isomer of uridine.

Back 74

Pseudouridine

Front 75

***(D) is uridine except w/two extra H+atoms... a fully saturated *** ring.

Back 75

Dihydrouridine --- pyrimidine

Front 76

--- All Organisms ---
1: *** in some way from environment
2: store *** in a stable way
3: reliably *** and pass ***
4: extract *** from their surroundings

Back 76

1) Separate
2) information
3) replicate --- information
4) energy

Front 77

Living organisms are constructed from four basic classes of molecule....

Back 77

Nucleic acids
Proteins
Lipids
Carbohydrates

Front 78

The genome of the single-celled amoeba is more than # times the size of the human genome.

Back 78

200

Front 79

Genomes often have *** elements – pieces of DNA that copy themselves within a genome and increase genome size.

Back 79

transposable

Front 80

The protein *** *** synthesizes RNA.

Back 80

RNA polymerase

Front 81

*** do not have internal membrane-bound compartments.

Back 81

Prokaryotes

Front 82

Prokaryotes have their chromosomal DNA in a region called the ***.

Back 82

nucleoid

Front 83

Copies of a gene that are similar but different are referred to as ***.

Back 83

alleles

Front 84

In some organisms, a wild-type gene is written in ***letters and the mutant in ***.

Back 84

uppercase
lowercase

Front 85

In some organisms, a gene is represeted with italics and *** for the protein produced.

Back 85

italics
non-italics

Front 86

--- Nucleotide BASES ---
1) A
2) T
3) G
4) C
5) U

Back 86

1) Adenine
2) Thymine
3) Guanine
4) Cytosine
5) Uracil

Front 87

--- NucleoSides ---
1) A
2) T
3) G
4) C
5) U

Back 87

1) Adenosine
2) Thymidine
3) Guanosine
4) Cytidine
5) Uridine

Front 88

DNA polymerase is associated with DNA via the clamp *** and the *** clamp.

Back 88

loader
sliding

Front 89

The *** site is the most highly conserved region of DNA polymerase.
The three domains are called...

Back 89

catalytic
the thumb, the fingers and the palm

Front 90

***, which is needed to synthesize chromosome ends, is a specialized *** transcriptase

Back 90

Telomerase
reverse

Front 91

The E. coli helicase, ***, has # identical subunits. In eukaryotes, the MCM complex is formed of different subunits, ***

Back 91

DnaB --- six
MCM2-7

Front 92

-- Single-stranded binding proteins ---
In eukaryotes, DNA is wrapped round a # subunit protein called....

Back 92

three
replication protein A.

Front 93

*** resolve the overwinding by transiently breaking DNA and allowing supercoils to relax.

Back 93

Topoisomerases

Front 94

Type *** topoisomerases break one of the two strands and do not require ATP. Type *** toposiomerases use ATP and break both strands.

Back 94

IA and IB
II

Front 95

Up to *** rotations have been observed in Type IB Topoisomerases... it doesn't use ATP.

Back 95

five

Front 96

--- Topoisomerases ---
A *** OH group attacks the DNA backbone forming a phosphodiester bond.

Back 96

tyrosine

Front 97

*** does not require an existing 3′ OH for synthesis, unlike DNA polymerase. Bacterial version synthesizes an RNA of *** bases.

Back 97

Primase
10-30

Front 98

After the polymerase α subunit of the primase complex makes a short stretch of DNA, replicative polymerases take over – a phenomenon called *** ***......

Back 98

polymerase switching

Front 99

Because DNA polymerase synthesizes DNA in a 5′ to 3′ direction, DNA is made in short discontinuous fragments on the lagging strand – *** fragments

Back 99

Okazaki

Front 100

Flap endonuclease (Fen1) cleaves the *** DNA

Back 100

flap

Front 101

--- DNA Replication ---
Bacteria / Eukaryote
1) Replication Origiin
2) Initiator Protein
3) Sliding Clamp
4) Clamp Loader

Back 101

1) OriC --- ~~~
2) DnaA --- ORC (Origin Recognition Complex)
3) DnaB --- PCNA (Proliferating Cell Nuclear Antigen)
4) DnaC --- RFC (Replication Factor C)

Front 102

*** proteins are AAA+ ATP binding proteins.

Back 102

Initiator

Front 103

DNA is transcribed into RNA by...

Back 103

RNA polymerase

Front 104

TSS?
denoted as what bp?

Back 104

transcription start site
+1

Front 105

RNA Pol *** is most well-studied, as it transcribes protein-encoding genes

Back 105

II

Front 106

RNA Pol *** are responsible for ~80% of a cell’s transcription

Back 106

I and Pol III

Front 107

Plants have a fourth RNA polymerase that transcribes *** RNAs

Back 107

regulatory

Front 108

Bacteria and archae have *** RNA polymerase

Back 108

a single

Front 109

Eukaryotes usually have *#* RNA pol.

Back 109

three

Front 110

--- Eukaryotic Transcription ---
3 additional enzymes required:
1) Nucleosome *** enzymes reposition histones away from DNA.
2) Histone *** disassemble/reassemble the histone octamer
3) Enzymes that *** modify histone proteins.

Back 110

1) remodeling
2) chaperones
3) reversibly

Front 111

*** RNA polymerase is the smallest (400kD), with 5 subunits – two α, one ***, one ***, and one ω.

Back 111

Bacterial
β --- β’

Front 112

RNA polymerases all have *#* central subunits that are similar in amino acid sequence, especially at the *** site.

Back 112

five

Front 113

The three eukaryotic RNA polymerases share a core of *#* subunits – in total Pol I has *#*, Pol II has *#* and Pol III has *#*.

Back 113

10
14 --- 12 --- 17

Front 114

Pol *** couples transcription to processing of the RNA transcript

Back 114

II

Front 115

--- Bacterial RNA Polymerases ---
1_ The core enzyme requires an extra subunit, the *** factor (***), which directly contacts the promoter.
2) Together are called the bacterial ***.

Back 115

sigma --- σ
holoenzyme

Front 116

--- chromosomes ---
Humans have ***.
kingfisher has ***.
fission yeast has ***.

Back 116

46
132
6

Front 117

Bacterial *** often encode proteins conferring antibiotic resistance.

Back 117

plasmids

Front 118

Polyploidy is particularly common in cultivated plants. However, a small number of human *** cells are also polyploid.

Back 118

liver

Front 119

The first two histone dimers to associate with DNA are... then these dimers associate to form an ***mer nucleosome.

Back 119

H3-H4
H2A-H2B
octomer

Front 120

The special histone *** is needed to form a functional centromere.

Back 120

CENP-A

Front 121

Up to three methyl groups can be added to a ***, and up to two can be added to an ***.

Back 121

lysine
arginine

Front 122

CHROMODOMAINS bind to specific methylated *** AAs and are often associated with transcriptional ***.

Back 122

lysines
silencing

Front 123

The parental strand of DNA is methylated and is called "***". This type of DNA is used for these two reasons...

Back 123

“hemi-methylated”
correcting DNA mispairs
stops Restriction enzymes

Front 124

*** in eukaryotes is used to silence transcription – epigenetic silencing. Usually consisting of CpG or CpXpG sites.

Back 124

Methylation

Front 125

Up to ***% of human CpGs are methylated and can be inherited.

Back 125

60

Front 126

*** *** act as physical barriers to heterochromatin.

Back 126

Boundary elements

Front 127

The total length of the repetitive region ranges from *** to ***bp, depending on the species.

Back 127

50-30,000

Front 128

DNA polymerase cannot copy the ends of a DNA molecule – *** maintain the ends of the chromosomes.

Back 128

telomerases