Molecular Biology Exam 1

Front 1

What is an explanation of the structure and function of cells and organisms in terms of the properties of individual molecules?

Back 1

Molecular biology

Front 2

1. DNA (replication is happening)
2. Transcription
3. RNA
4. Translation

A PROTEIN IS PRODUCED

What is this sequence called?

Back 2

The central dogma of molecular biology

Front 3

_______ are free living organisms that lack a cell nucleus and any membrane bound organelles.

Back 3

Prokaryotes

Front 4

The following are characteristics of what?

-Single circular chromosome
-DNA is located in nucleoid
-Simple organization in the cytoplasm

Back 4

Prokaryotes

Front 5

In prokaryotes, translation and transcription occur simultaneously in the cell ______.

Back 5

cytosol

Front 6

In gram negative bacterial cell walls ______% of the wall is peptidoglycan.

Back 6

10-20%

Front 7

In gram positive bacterial cell walls _____% of the wall is peptidoglycan.

Back 7

90%

Front 8

_____ mRNA carries information of several genes, which are translated into several proteins.

Back 8

Polycistronic (in prokaryotes)

Front 9

________ are organisms whose cells contain complex structures enclosed within membranes.

Back 9

Eukaryotes

Front 10

Do eukaryotes contain a nucleus?

Back 10

yes, it is the membrane bound structure that sets theses cells apart from the prokaryotes. It is where genetic material is carried.

Front 11

The following are characteristics of what?

-Single or multicellular organisms- complex structures
-Has a membrane bound cytoplasm
-Multiple linear chromosomes
-Multiple origins per chromosomes
-Monocistronic genes

Back 11

eukaryotes

Front 12

_____ is a small spherical body found within the nucleus.

Back 12

nucleolus

Front 13

______ contain ribosomal RNA (rRNA). Transcription of rRNA takes place here as well as assembly of ribosomal subunits.

Back 13

nucleoli

Front 14

The following are characteristics of what?

-Bound by a double membrane
-contain enzymes that drive citric acid cycle
-powerhouse of cell
-evolved from symbiotic relationship with bacteria and wall
-contain their own DNA

Back 14

Mitochondrion

Front 15

The following are characteristics of what?

-Site of protein synthesis
-not surrounded by a membrane

Back 15

Ribosomes

Front 16

______ is a network of membranes where proteins and glycoproteins are synthesized.

Back 16

Rough ER

Front 17

_______ lacks ribosomes and is where lipids are synthesized.

Back 17

Smooth ER

Front 18

____ are membrane bound sacks that perform a variety of transport functions.

Back 18

vesicles

Front 19

______ are bound by a single membrane which contains hydrolytic enzymes. Internal pH is acidic at 4-5.

Back 19

lysosomes

Front 20

______ is the packaging/processing station for molecular trafficking among parts of the cell. Sorts proteins and lipids.

Back 20

Golgi apparatus

Front 21

______ are storage components. Stores water, ions, waste products, sucrose and nitrogen containing compounds.

Back 21

vacuoles

Front 22

______ is the fluid component of the cell cytoplasm. Has cytoskeletal elements such as microfilaments and microtubules.

Back 22

cytosol

Front 23

Prokaryote or eukaryote??


 Single circular chromosome (exceptions)
 One origin of replication
 Gene sequences same as mRNA sequences
 Polycistronic genes
 Coupled transcription/translation

Back 23

Prokaryotes

Front 24

Prokaryote or eukaryote??


- Multiple linear chromosomes
-Multiple origins per chromosome
-Interrupted coding sequences (introns/exons)
-Monocistronic genes
- Spatially separated transcription/translation

Back 24

Eukaryotes

Front 25

The following are characteristics of what?

-Simple intracellular parasite. Cannot replicate on own
-DNA or RNA genome
-Surrounded by capsid
-Replication depends on host cell metabolism

Back 25

virus

Front 26

_____ is a virus that infects bacteria cells.

Back 26

bacteriophage

Front 27

DNA viruses can integrate their ____ directly into the host genome

Back 27

DNA

Front 28

RNA viruses must first make a _____ copy of the _____ strand which creates _____.

Back 28

DNA
RNA
cDNA (complementary DNA)

Front 29

An enzyme called _________ has the ability to make a DNA copy of RNA.

Back 29

reverse transcriptase

Front 30

If 35% of the bases in a genome are thymine, what percentage of bases will be cytosine?

Back 30

15%

Front 31

In RNA, adenine paris with ______.

Back 31

Uracil

Front 32

The macromolecule that carries the genetic information for all cellular processes is ______.

Back 32

DNA

Front 33

The individual subunits making up each strand of DNA are called ______.

Back 33

Nucleotides

Front 34

DNA _____ joins Okazaki fragments to the high molecular weight DNA chain on the lagging strand.

Back 34

ligase

Front 35

DNA is replicated ______.

Back 35

semi-conservatively

Front 36

Methylation of nucleotides is an _______ change.

Back 36

epigenetic

Front 37

The nucleosome is composed of dsDNA and what else?

Back 37

one molecule of H1
two molecules (copies) each of histones H2A, H2B, H3, and H4.

Front 38

_________ is a macromolecule composed of chains of monomeric nucleotides.

Back 38

nucleic acid

Front 39

______ is the template of the DNA, it carries information from DNA to ribosomes.

Back 39

Messenger RNA
mRNA

Front 40

______ and _______ are involved in protein synthesis.

Back 40

rRNA and tRNA

Front 41

Are phosphate groups basic or acidic in nature?

Back 41

acidic, always has a negative charge

Front 42

The following are examples of what:

-Fused 5 and 6 member ring
-Adenine and guanine (A and G)

Back 42

Purine (nitrogenous bases)

Front 43

The following are examples of what:

-6 member ring
-Cytosine, Thymine and Uracil (C,T,U)
-Methyl group at C5 on thymine (not present on uracil)

Back 43

Pyrimidines

Front 44

________ = nitrogenous base + sugar

Back 44

Nucleoside, the nitrogenous base is linked to 1' carbon on sugar.

Front 45

_________ = nitrogenous base + sugar + Phosphate

Back 45

Nucleotide, phosphate group is attached to the 5' carbon.

Front 46

What are two examples of Purines in DNA?

Back 46

adenine and guanine
A, G
(A:T AND C:G)

Front 47

What are examples of pyrimidines in DNA?

Back 47

cytosine and thymine
C, T
(A:T AND C:G)

Front 48

DNA and the nucleotide are connected together by the _____ bond.

Back 48

phosphodiester

Front 49

DNA is always ______ stranded and they connect to each other by a ____ bond.

Back 49

double
hydrogen

Front 50

DNA is usually _____ handed helix.

Back 50

right

Front 51

What is the only left-handed form of DNA called?

Back 51

Z form DNA

Front 52

The ____ form DNA is the most common double helical structure and is observed at high humidity. (vast majority of DNA)

Back 52

B

Front 53

The B form DNA is _____ handed with about _____ nucleotides per turn.

Back 53

right
10

Front 54

The ___ form DNA is observed under condition of low humidity and the major groove is much narrower than that of the B form.

Back 54

A

Front 55

The A form DNA is ____ handed with about ____ nucleotides per turn.

Back 55

right
11

Front 56

What occurs only in closed structures, when ends are not free to release torsion on the molecule?

Back 56

DNA supercoiling

Front 57

What enzymes can introduce or remove supercoils?

Back 57

topisomerases or gyrases

Front 58

DNA supercoiling structure can be separated by __________.

Back 58

gel-electrophoresis

Front 59

RNA is usually ____ stranded.

Back 59

single

Front 60

In the _______ structure of RNA the noncomplementary sequences become "looped out" to form different structures.

Back 60

Stem-loop

Front 61

______ is formed by base pairing that takes place between noncontiguous complementary sequences in RNA.

Back 61

Pseudoknot

Front 62

RNA and DNA are ____ of nucleotides.

Back 62

polymers

Front 63

DNA molecules and its associated proteins are packaged into threadlike structure in the nucleus called ______.

Back 63

chromosomes

Front 64

Most of _______ cells have only one circular chromosome in their nucleoid

Back 64

prokaryotic

Front 65

All ______ cells have multiple linear chromosomes in their nucleus and the number of chromosomes depends on cell type

Back 65

eukaryotic

Front 66

A ______ cell is a cell that contains two copies of each chromosome. The two copies of a given chromosome are called homologs; One set of chromosome is donated from each parent.

Back 66

diploid

Front 67

A _____ cell is a cell that contains a single copy of each chromosome and involved in sexual reproduction.

Back 67

haploid

Front 68

A _____ cell have more than two copies of each chromosome

Back 68

polyploid

Front 69

in eukaryotic cells, a given region of DNA with its associated protein is also called ______.

Back 69

chromatin

Front 70

The majority of associated proteins in eukaryotic cells are small, basic proteins called _______. Other proteins are also associated with eukaryotic chromosome called ______.

Back 70

histones
nonhistone proteins

Front 71

The fundamental unit of chromatin is _____.

Back 71

nucleosome

Front 72

Each nucleosome is composed of a ____ core and the ____ wrapped around them.

Back 72

histone
DNA

Front 73

A histone core has _____ histone proteins located in the center of the nucleosome.

Back 73

8

Front 74

Histones are ___ charged.

Back 74

positively

Front 75

Histones contain a high proportion of _____ and _____.

Back 75

lysine and arginine

Front 76

Which nucleosome stage of DNA packaging is this:

-Packaging yields chromatin fiber 10nm in diameter
-200 base pair repeating units
-80 base pair spacers between chromosomes
-Appears as "beads on a string" under electron scope

Back 76

1st stage of DNA packaging

Front 77

What is it called when the 30 nm fiber of a chromosome forms loops of 40-90 kb?

Back 77

nuclear scaffold

Front 78

What phase of the cell cycle is this?

-Most of the chromatin is decondensed
-About 10% of euchromatin is undergoing transcription
-10% of total chromatin is highly condensed (heterochromatin)

Back 78

Interphase (non-dividing)

Front 79

What phase of the cell cycle is this?

-Chromosomes become highly condensed to facilitate movement into daughter cells
-30 nm chromosomes fold upon themselves and condense 10,000 fold
-Organized into large loops attached to protein scaffold
-Transcription ceases

Back 79

mitosis

Front 80

What phase of the cell cycle is this?

-occurs immediately after mitosis
-The cell is synthesizing proteins and growing to achieve the size of a normal cell before splitting in two during mitosis

Back 80

GI phase or gap phase

Front 81

What phase of the cell cycle is this?

-DNA synthesis (DNA replication) takes place in preparation for cell division

Back 81

S phase

Front 82

What phase of the cell cycle is this?

-DNA repair of errors that happened during replication

Back 82

G2 phase

Front 83

What phase of the cell cycle is this?

-Mitosis phase, when the cell physically divides

Back 83

M phase

Front 84

What are the levels of DNA packaging and morphology?

Back 84

1. DNA
2. Nucleosome
3. Chromatin fiber
4. Chromatin fiber with protein scaffolding
5. Metaphase chromosome

Front 85

What does the following:
-Make DNA to readily fit inside the cell
-Protect the DNA from damage
-Efficiently transmit DNA to both daughter cells

Back 85

DNA packaging

Front 86

_____ is the entirety of an organism's hereditary information or is an organism's complete set of DNA.

Back 86

Genome

Front 87

A______ genome, found in sperm and egg cells (gametes), contains half of the total genetic material and approximately 3 × 109 base pairs (bp). each chromosome contains 1,000–1,500 genes.

Back 87

haploid

Front 88

_____ is an international scientific research project with a primary goal of determining the sequence of chemical base pairs witch make up DNA and to ID and map the genes of the human genome from both a physical and functional standpoint.

Back 88

human genome project

Front 89

The following are characteristics of what:

-is a unit of heredity in a living organism.
-It normally resides on a stretch of DNA and codes for a type of protein or for an RNA chain or controls various traits
-All living things depend on this as they specify all proteins and functional RNA chains.
-They hold the information to build and maintain an organism's cells and pass genetic traits to offspring.

Back 89

Genes

Front 90

An ___ is an alternative form of a gene for a diploid organism.

Back 90

alleles

Front 91

What is it called when 2 alleles of a gene are the same for a single trait?

Back 91

homozygous

Front 92

What is it called when 2 alleles of a gene are different but code for a single trait?

Back 92

heterozygous

Front 93

The ___ of an organism is the inherited instructions it carries within its genetic code.

Back 93

genotype

Front 94

A ___ is the composite of an organism's observable characteristics or traits. (morphology, development, biochemical or physiological properties)

Back 94

phenotype

Front 95

A sequence of DNA situated between exons that will be removed before translation of messenger RNA and does not function in coding for protein synthesis.

Back 95

introns

Front 96

A sequence of DNA that will be transcribed to messenger RNA, and then directed protein synthesis

Back 96

Exons

Front 97

What are the two important functions of a gene?

Back 97

1. Stable storage of genetic info
2. Transmission of genetic info

Front 98

_____ is the fundamental process that occurs in all living organisms that copies their DNA.

Back 98

DNA replication

Front 99

Bi-directional is ___ to ___.

Back 99

5' to 3'

Front 100

Semi-conservative is _______ and ______.

Back 100

1 new strand and 1 old strand

Front 101

Semi-discountinous is ____________ and ____________.

Back 101

leading strand is continuous and lagging strand is discontinuous

Front 102

_____ separates the 2 strands of DNA at a replication fork and makes a small portion of the dsDNA into ssDNA.

Back 102

helicase

Front 103

_____ allows binding of primase to make primers and stabilizes by single stranding binding proteins (SSB)

Back 103

Helicase

Front 104

_____ is a RNA polymerase that makes short RNA primers on DNA template.

Back 104

Primase

Front 105

_______ is the junction between separated template strand and unreplicated DNA duplex.

Back 105

replication fork

Front 106

The following are characteristics of what:

-DNA is synthesized 5' PO4-3' OH
-Nucleophilic attach of alpha-phosphate of dNTP extends DNA

Back 106

replication elongation

Front 107

The ____ strand is continuously replicated new strand 5' to 3'

Back 107

leading

Front 108

The ____ strand has new DNA synthesized from other ssDNA

Back 108

lagging

Front 109

______ are transient intermediates, short fragments of new DNA.

Back 109

okazaki fragments

Front 110

The following are characteristics of what:

-found in 1957
-Uses a single site to catalyze addition of dNTPs
-Does not detect exact nucleotide
-Monitors base pairing by geometry
-Kinetic selectivity

Back 110

DNA polymerase

Front 111

_____ also has proofreading ability.

-Degrade DNA from 3' end
-Removal of mismatched nucleotides
-"delete key"

Back 111

DNA polymerase

Front 112

______ removes RNA primer and degrades hybrid RNA:DNA, leaving a gap in the dsDNA.

Back 112

Rnase H

Front 113

_______ fills in Rnase H gap with DNA except the break in the backbone between the 3' OH and the 5' PO4.

Back 113

DNA polymerase

Front 114

The following are characteristics of what:

-Ends of eukaryotic chromosomes
-TG-rich head-to-tail repeats
-3' overhanging chromosomal DNA loops back on itself to protect the ends of chromosomes

Back 114

Telomeres

Front 115

The following are characteristics of what:

-Multiple protein subunits and an RNA component
-Extends the 3' OH end of the substrate
-Does NOT require and exogenous DNA template to add dNTPs
-The RNA component acts as a template

Back 115

telomerase

Front 116

The inhibition of _____ may offer potential cancer treatment.

Back 116

telomerase

Front 117

Telomeres are replicated by what?

Back 117

telomerase

Front 118

The following are characteristics of what: -Double Helix
-Deoxyribose sugar
-Adenine pairs with Thymine
-Stays in nucleus

Back 118

DNA

Front 119

The following are characteristics of what:
-Single strand
-Ribose sugar
-Uracil replaces Thymine
-Leaves nucleus to do the work

Back 119

RNA

Front 120

____ is a process that involves the transcribing of genetic information from DNA to RNA (RNA synthesis).

Back 120

Transcription

Front 121

Translation occurs in the ______.
Transcription occurs in the ______.

Back 121

cytoplasm
nucleus

Front 122

What are the 3 stages of DNA transcription?

Back 122

1. Initiation
2. Elongation
3. Termination

Front 123

What is the start site of DNA transcription?

Back 123

DNA base pair

Front 124

What is the promoter of DNA transcription?

Back 124

Binding site on DNA for RNA polymerase

Front 125

_____ is an enzyme that catalyzes DNA transcription.

Back 125

RNA polymerase

Front 126

What are the two transcription factors?

Back 126

1. Repressors
2. Activators

Front 127

RNA polymerase combines with _____ factor to create RNA polymerase holoenzyme.

Back 127

sigma

Front 128

The following are characteristics of what:

-Recognizes promoters and initiates transcription
-Sigma factor is required for efficient binding and transcription
-Different sigma factors recognize different promoter sequences
-Untwists DNA

Back 128

RNA polymerase

Front 129

RNApoly I makes _____. (in eukaryotes)

Back 129

pre-rRNA

Front 130

RNApoly II makes _____. (in eukaryotes)

Back 130

pre-mRNA

Front 131

RNA poly III makes ______. (in eukaryotes)

Back 131

pre tRNA

Front 132

The following are characteristics of what:

-80% RNA polymerase
-Synthesizes ribosomal RNA (rRNA)

Back 132

RNApoly I

Front 133

The following are characteristics of what:

-1-5% RNA polymerase
-Synthesizes messenger RNA (mRNA)

Back 133

RNApoly II

Front 134

The following are characteristics of what:

-15% RNA polymerase
-Synthesizes transfer RNA (tRNA)

Back 134

RNApoly III

Front 135

_______________ are required for efficient and promoter-specific initiation of DNA transcription in eukaryotes.

Back 135

General transcription factors (GTFs)

Front 136

The following are characteristics of what:

-Are proteins and are assembled on the core promoter
-Are required by RNA polymerases
-Works with only one kind of RNA polymerase
-Numbered to match their RNA polymerase

Back 136

General transcription factors
GTF

Front 137

Which step of DNA transcription in Eukaryotes is this:
-TBP recognize DNA promoter
-Binding of GTFs and RNA polymerase occurs in a set order at the promoter
-Complete complex is called a pre-initiation complex (PIC)
-After releases of short RNA transcripts of 23 nucleotides, RNA polymerase escape the promoter and enter the elongation phase.

Back 137

Step 1- Initiation

Front 138

Promoter escape in DNA transcription requires the phosphorylation of the __________.

Back 138

polymerase "tail" (CTD tail)

It controls the elongation and shedding of TFs used for initiation

Front 139

Which step of DNA transcription in Eukaryotes is this:
-Pol II enzyme shed most of its initiation factors and mediators and recruit another set of factors including elongation factors.
-Pol II enzyme is involved in RNA processing via CTD tail
-Phosphorylation of the CTD leads to an exchange of initiation factors required for elongation and RNA processing

Back 139

Step 2- Elongation

Front 140

Which step of DNA transcription in Eukaryotes is this:
-Pol II polymerase leaves DNA
-DNA rewinds itself into the double helix
-RNA strand is processed.

Back 140

Step 3- Termination

Front 141

Which step of DNA transcription in Eukaryotes is this:
-The 5' end of mRNA is capped with a methylated guanine base
-RNA splicing (introns are removed and exons are spliced)
-Poly (A) tail (3' end of mRNA)

Back 141

Step 4- RNA processing

Front 142

True or False:
DNA polymerase translates nucleic acid into proteins

Back 142

False

Front 143

Transcription can produce what type of RNA?

Back 143

tRNA, rRNA and mRNA

Front 144

The coding region of a human gene is called what?

Back 144

Exon