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Bio 211 > Lecture Final Study > Flashcards

Lecture Final Study Flashcards

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Biology 101 flashcards
1
Q

What are the seven characteristics of living things?

A 
Homeostasis
Energy usage/metabolism
Reproduction
Organization
Growth and development
Adaptation
Stimuli response
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2
Q

Which four elements compose 95% of living material?

A

carbon, hydrogen, oxygen, nitrogen

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3
Q

Who published the cell theory?

A

Matthias Schleiden and Theodor Schwann

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4
Q

List hydrogen bonds, ionic bonds, covalent bonds, and van der Waals interactions in order from strongest to weakest bond type

A

covalent > ionic > hydrogen > van der Waals interactions

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5
Q

hydrophilic functional groups

A

carboxyl, phosphate, hydroxyl, amino, carbonyl

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6
Q

hydrophobic functional groups

A

methyl and thiol (sulfyhydryl)

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7
Q

protein monomer

A

amino acid

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8
Q

protein bond type

A

peptide bond

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9
Q

carbohydrate monomer

A

saccharide

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10
Q

carbohydrate bond type

A

glycosidic linkage

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11
Q

nucleic acid monomer

A

nucleotide

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12
Q

nucleic acid bond type

A

phosphodiester bond

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13
Q

when amino acids are polymerized, covalent bonds form between which two functional groups?

A

amino and carboxyl

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14
Q

what type of bond forms between the glycerol head and fatty acid tails of a triglyceride?

A

ester linkage

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15
Q

primary protein structure

A

bonds between amino acids (peptide bonds), looks like a straight chain

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16
Q

secondary protein structure

A

involves hydrogen bonding between the amino acid backbones, looks like alpha helixes or beta-pleated sheets

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17
Q

tertiary protein structure

A

folding occurs due to side-chain interactions, looks like a clump or knot

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18
Q

quaternary protein structure

A

involves 2+ protein chains bonded to each other

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19
Q

Anton Van Leeuwenhoek was the first to observe what?

A

living organisms under a microscope

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20
Q

Glycolysis

location

A

cytoplasm

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21
Q

Glycolysis

substrates

A

1 glucose

2 ATP

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22
Q

Glycolysis

products

A

2 pyruvate
2 NADH
4 ATP

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23
Q

Glycolysis

ATP production process

A

substrate-level phosphorylation

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24
Q

Pyruvate Oxidation

location

A

intermembrane space of the mitochondria

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25
Q

Pyruvate Oxidation

substrates

A

2 pyruvate

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26
Q

Pyruvate Oxidation

products

A

2 Acetyl CoA
2 NADH
2 CO2

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27
Q

Krebs Cycle

location

A

mitochondrial matrix

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28
Q

Krebs Cycle

substrates

A

2 Acetlyl CoA

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29
Q

Krebs Cycle

products

A

6 NADH
2 FADH2
4 CO2
2 ATP

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30
Q

Krebs Cycle

ATP production process

A

substrate-level phosphorylation

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31
Q

Electron Transport Chain

location

A

inner mitochondrial membrane space

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32
Q

Electron Transport Chain

substrates

A

3 O2
10 NADH
2 FADH2

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33
Q

Electron Transport Chain

products

A

6 H2O

28 ATP

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34
Q

Electron Transport Chain

ATP production process

A

oxidative phosphorylation

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35
Q

What molecule transports electrons and hydrogen ions from glycolysis and the Krebs cycle to the ETC?

A

NAD+

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36
Q

helicase function

A

opens DNA helix by breaking h-bonds between nucleotide pairs to separate the DNA during DNA replication

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37
Q

primase function

A

provides 3’ end for adding new nucleotides during DNA replication

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38
Q

topoisomerase function

A

nicks DNA to relieve tension from unwinding during DNA replication

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39
Q

DNA polymerase III

A

adds nucleotides to an RNA primer or existing DNA strand during DNA replication

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40
Q

DNA polymerase I function

A

removes RNA nucleotides of primer from 5’ end and replaces them with DNA nucleotides at the adjacent fragment during DNA replication

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41
Q

DNA ligase function

A

links Okazaki fragments to form a continuous strand

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42
Q

indicate the hierarchy of DNA organization in eukaryotic cells

A

double helix > nucleosomes > chromatin fibers > looped domains > chromosomes

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43
Q

splice-o-some complex function

A

to process pre-mRNA into mRNA by removing introns and adding the Poly A tail and 5’ cap

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44
Q

what is the start codon’s amino acid?

A

methionine

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45
Q

ribosomes use ____ to produce ____________ based on the ____ copy of DNA code

A

tRNA; polypeptides; mRNA

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46
Q

where do most proteins reside in a cell?

A

cytoplasm

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47
Q

three process involved in synthesizing proteins from genes

A
  1. Transcription
  2. RNA processing
  3. Translation
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48
Q

what is the purpose of transcription?

A

RNA copy of DNA is made

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49
Q

what happens during transcription?

A
  • Template Strand: contains gene to be expressed
  • RNA Polymerase: creates a complimentary RNA strand of the template strand
  • rNTPs: Used as building blocks for the primary transcript
  • pre-mRNA/primary transcript: The exact complimentary RNA strand created by
    RNA polymerase
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50
Q

RNA processing purpose

A

RNA is added or deleted to make mRNA

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51
Q

what happens during RNA Processing?

A
  • splice-o-somes remove introns, adds 5’ cap to the 5’ end to help ribosomes locate the beginning of the mRNA molecule more quickly, adds 3’ Poly Adenine tail to aid in stability
  • mRNA: contains sequences necessary for protein synthesis
  • preMRNA/primary transcript: the exact complimentary RNA strand created by RNA polymerase
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52
Q

translatio purpose

A

turning RNA into proteins

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53
Q

what happens during translation?

A
  • mRNA: contains sequences necessary for protein synthesis, contains codons to be translated at the ribosomes into polypeptides
  • ribosomes: protein complexes that mRNA runs through and acts as a vessel for protein synthesis
  • tRNA: matches codon sequences to their corresponding amino acids to create polypeptides
  • C-terminus and N-terminus: completes and stabilizes the polypeptide chain produces at the ribosomes
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54
Q

what does the regulatory gene code for in prokaryotes?

A

repressor protein

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55
Q

what was the first DNA sequencing method?

A

Sanger sequencing method

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56
Q

what are the structures that resemble beads on a string when DNA is in Euchromatin form?

A

nucleosomes

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57
Q

who discovered the operon model?

A

Francois Jacob and Jacques Monod

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58
Q

for gene regulation in eukaryotes, transcription factors bind to

A

promotor proximal element

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59
Q

promotor-proximal element definition

A

any regulatory sequence in eukaryotic DNA that is located near (within 200 bp) a promoter

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60
Q

what form of control is a bacterial inducible operon?

A

negative control

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61
Q

in prokaryotic operons, what does RNA polymerase bind to?

A

promoter sequence

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62
Q

in prokaryotic operons, which molecule binds to the operator sequence?

A

regulatory molecules (repressor protein)

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63
Q

The condensation of DNA into heterochromatin prevents _____________ because genes cannot be accesed

A

transcription

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64
Q

examining the metabolism of tryptophan led to the discovery of:

A

the repressible operon

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65
Q

what binds to the leader segment of an mRNA molecule to regulate protein synthesis by preventing the mRNA from binding to a ribosome?

A

a regulator protein

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66
Q

nucleosomes are formed by winding a DNA strand around:

A

histones

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67
Q

when an _________ _______ binds to the ________ ________ of a eukaryotic gene, the transcription rate increases

A

activator protein; enhancer sequence

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68
Q

what does PCR stand for?

A

polymerase chain reaction

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69
Q

what is the purpose of PCR

A

to make several copies of one specific sequence of DNA

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70
Q

denaturing step

A
  • 95 degrees celsius

- hydrogen bonds are broken in the DNA molecule

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71
Q

annealing step

A
  • temperature is lowered to 60 degrees celsius

- primers bond to template DNA

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72
Q

extension step

A
  • temperature is raised to 73 degrees celsius

- Taq Polymerase makes new complementary strands

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73
Q

what is a genomic library?

A

A collection of bacteria cells transformed with plasmids composed of recombinant DNA.

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74
Q

what is the function of ddNTPs?

A

dideoxynucleotide triphosphates remove a hydroxyl group from a nitrogenous base, halting DNA synthesis

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75
Q

what process are ddNTPs used for?

A

Sanger method of DNA sequencing

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76
Q

what resources do you need for DNA sequencing?

A
  • gel electrophoresis
  • PCR
  • ddNTP
  • restriction enzymes
  • DNA polymerase
  • genomic library
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77
Q

what is the function of reverse transcriptase?

A

to allow a virus to be in the form of RNA and not DNA; it makes DNA without introns from RNA
-makes cDNA to be amplified by PCR

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78
Q

who was the first person to sequence an entire human genome?

A

John Craig Venter

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79
Q

fruit fly scientific name

A

Drosophila melanogaster

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80
Q

zebra fish scientific name

A

Danio rerio

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81
Q

in order for genes from two different organisms to be combines, they must be cut by..

A

the same restriction enzyme

82
Q

genes are not expressed when a _________ _______ attaches to the control region in the operon

A

repressor protein

83
Q

proteasome

A

a protein complex that breaks down proteins that are tagged by ubiquitin

84
Q

the nucleic acid of a viral particle is enclosed in what?

A

capsid

85
Q

what is the function of telomerase enzymes?

A

catalyzes the lengthening of the telomeres in eukaryotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication

86
Q

in order to create a transgenic bacterium through transformation, new genes are inserted into the _______

A

plasmid

87
Q

pluripotent

A

capable of differentiating into many different cell types (but can only differentiate once)

88
Q

John Dalton

A

wrote the atomic theory

89
Q

Robert Hooke

A

made the first microscope

90
Q

Anton Van Leeuwenhoek

A

viewed first living organism under microscope

91
Q

Gregor Johann Mendel

A

studies patterns of inheritance in garden pea plants

92
Q

Matthias Schleiden and Theodor Schwann

A

published the cell theory

93
Q

Thomas Hunt Morgan

A

confirmed that genes are the hereditary units

94
Q

Frederick Griffith

A

discovered DNA is the carrier of genetic information

95
Q

Erwin Chargaff

A

ratios of adenine to thymine and cytosine to guanine are almost exactly equal

96
Q

dNTPs

A

inserts nucleotides into the existing chain to generate a completely new DNA strand using the DNA polymerase enzyme

97
Q

origins of replication

A

places in the DNA molecule where the strands seperate, forming bubbles that can be replicated on the inside

98
Q

replication forks

A

where the origins of replication meet the regular DNA strand

99
Q

primers

A

lays down RNA nucleotides to prepare for DNA polymerase, they are replaced with DNA nucleotides

100
Q

primase

A

synthesizes primers

101
Q

DNA polymerase

A

accurately and efficiently replicate the genome

102
Q

phosphodiester bonds

A

bonds linking nucleotides together: joins a phosphate group in the pentose sugar of one nucleotide to the hydroxyl group in the pentose sugar of the next nucleotide

103
Q

leading and lagging strands

A

leading strand goes from the 3’ side to the 5’ side

lagging strand is replicated from the 5’ side to the 3’ side in chunks using Okazaki fragments

104
Q

Okazaki Fragments

A

short fragments of DNA that are laid down on the lagging strand of DNA and later joined together by DNA ligase

105
Q

helicase

A

opens helix

106
Q

single strand binding proteins

A

wraps single-stranded DNA with high affinity to protect it from degradation and prevent secondary structure formation

107
Q

DNA ligase

A

joins breaks in the phosphodiester backbone of DNA that occur during replication and recombination

108
Q

DNA proofreading

A
  1. DNA Polymerase (III) corrects as it goes and chops off incorrect piece and replaces with correct piece
  2. “other” DNA repair enzymes (100+ known)
109
Q

Methylation: directed mismatched base repair

A
  1. where a mismatch occurs, the correct base is located on the methlyated strand; the incorrect base occurs on the unmethylated strand
  2. enzymes detect mismatch and nick unmethylated strand
  3. DNA Polymerase I excises nucleotides on unmethylated strand
  4. DNA polymerase I fills in gap in 5’ -> 3’ direction
  5. DNA ligase links new and old nucleotides
110
Q

DNA Methylation

A
  • addition of CH3 group to adenine molecules

- identifies template strand

111
Q

Excision Repair System

A
  1. DNA nuclease: removes damaged nucleotide
  2. DNA Polymerase (I): replaces with undamaged nucleotide
  3. DNA ligase: joins phosphodiester bonds
112
Q

DNA nuclease

A

catalyze cleavage of phosphodiester bonds

113
Q

telomeres

A

a sequence of repetitive base pairs that prevent a DNA molecule from losing its length

114
Q

telomerase enzymes

A

an enzyme made of protein and RNA subunits that elongates chromosomes by adding TTAGGG sequences to the end of existing chromosomes; found in fetal tissues, adult germ cells, and also tumor cells

115
Q

gene

A

specific sequences of DNA on a nucleic acid that codes for characteristics in an organism

116
Q

DNA template strand

A

each original strand of DNA (unreplicated)

117
Q

RNA polymerase

A

used during transcription:synthesizes RNA by following a strand of DNA

118
Q

problem with linear DNA

A

5’ ends are lost with each replication, so DNA molecules grow shorter and shorter with each replication

119
Q

introns

A

DNA sequences that do not code for amino acids

120
Q

exons

A

codons that dictate amino acid production

121
Q

how many introns and exons are in a nucleic acid?

A

95% introns and 5% exons

122
Q

splice-o-some complexes:

A

remove introns

123
Q

5’ cap

A

added to 5’ end to help ribosomes locate the beginning of the mRNA molecule

124
Q

Poly Adenine tail

A

aids in stability of the molecule

125
Q

codon

A

3-nucleotide-long sequence that tells what amino acid to produce

126
Q

anticodon

A

the RNA counterpart of a DNA molecule that is used to create the amino acid in a ribosome

127
Q

ribosome small subunit

A

decodes genetic message

128
Q

ribosome large subunit

A

catalyzes peptide bond formation (think of the video of the chain moving along and forming amino acid chains)

129
Q

ribosomal RNA (rRNA)

A

non-coding RNA that helps to form ribosomes

130
Q

biotechnology

A

the use of bacteria and viruses to create biological tools that can contribute to medicine

131
Q

proteomics

A

the study of the entire complement of proteins that is or can be expressed by a cell, tissue, or organism

132
Q

virus

A
  • phage
  • have proteins sticking out of them that only help them gain access to 1 cell
  • viruses either have RNA inside or DNA
133
Q

genome

A

the complete set of genes or genetic material present in a cell or organism

134
Q

capsid

A

the thing that contains a virus’s genetic material

135
Q

retrovirus

A

any of a group of RNA viruses which insert a DNA copy of their genome into the host cell in order to replicate

136
Q

reverse transcriptase

A

allows virus to be in the form of RNA, not DNA

137
Q

spike proteins

A

allow the virus to enter a specific cell

138
Q

viral envelope

A

outermost layer of many types of viruses

139
Q

lytic cycle

A
  • fast viruses

- as soon as the virus enters the body, it immediately starts taking over cells

140
Q

lysogenic cycle

A
  • slow viruses
  • sits in a cell and injects its DNA into the cell, and inserts itself into your DNA
  • viral infection can last for years
141
Q

provirus

A

the genetic material of a virus as incorporated into, and able to replicate with, the genome of a host cell

142
Q

bacteriophage

A

viruses that infect bacteria and archaea

143
Q

phytophage

A

viruses that infect plants

144
Q

zoophage

A

viruses that infect animals

145
Q

DNA loop

A

bacteria DNA is organized in a loop

146
Q

plasmids

A

a genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium or protozoan; used in the laboratory manipulation of genes

147
Q

bacterial transformation

A

a section of bacterial DNA is removed and replaced with DNA from another organism for storage

148
Q

genomic DNA (gDNA)

A

original DNA with introns

149
Q

complimentary DNA (cDNA)

A

a copy made from gDNA using reverse transcriptase that does not contain introns

150
Q

restriction enzymes

A

cleaves DNA molecules at or near a certain sequence of bases (made by certain bacteria)
-used in Venter DNA sequencing

151
Q

recombinant DNA

A

the method of joining two or more DNA molecules to create a hybrid

152
Q

DNA sequencing

A

use of PCR, electrophoresis, ddNTPs to sequence a DNA molecule

153
Q

Frederick Sanger

A

made it easier to sequence DNA

154
Q

Sanger DNA sequencing improvements

A
  1. use of fluorescently tagged ddNTPs

2. DNA fragments are seperated on mass-prouced capillary gels

155
Q

ddNTPs

A

dideoxynucleoside triphosphates

  • chemically similar to dNTPs
  • remove a hydroxyl group from a nitrogenous base
156
Q

John Craig Venter

A

used computer technology and PCR and electrophoresis to make the process of DNA sequencing go faster

157
Q

Whole-Genome Shotgun Sequencing

A
  • created by John Craig Venter, requires restriction enzymes, genomic library, enhanced Sanger method, and computer technology
    1. cut DNA into overlapping fragments short enough for sequencing
    2. clone the fragments in plasmid or phage vecots
    3. sequence each fragment
    4. order the sequences into 1 overall sequence with computer software
158
Q

human genome project

A

multi-million dollar project to sequence the entire human genome

159
Q

RFLP

A

random fragment length polymorphisms

  • variations among people in their DNA sequences at sites recognized by restriction enzymes
  • used for crime scene stuff
160
Q

short tandem repeats

A
  • short repeated sequences of DNA (2–6 bp)
  • number of repeat units is variable among individuals, which offers a high power of discrimination when analyzed for identification purposes
161
Q

transposable elements

A

jumping genes

162
Q

Francois Jacob and Jacques Monod

A

discovered operon gene control in prokaryotic cells

163
Q

inducible operon

A
  • lactose pathway
  • as long as the repressor protein is filled by lactose, the gene for digesting lactose is on because lactose removes the repressor protein from the gene
  • repressor protein attaches in between the promoter sequence and the structural gene
  • inducible operons are off most of the time, unless the repressor protein is removed
164
Q

repressible operon

A
  • tryptophan pathway
  • gene needs to be on most of the time
  • excess tryptophan binds to repressor protein when it needs to stop being consumed
165
Q

parts of an operon

A
  • regulator gene
  • promoter sequence
  • operator sequence
  • structural gene
166
Q

regulator gene

A

codes for synthesis of a repressor molecule that binds to the operator and blocks RNA polymerase from transcribing the structural genes

167
Q

repressor protein

A

inhibits the expression of one or more genes by binding to the promoter sequence

168
Q

promoter sequence

A

DNA sequences that define where transcription of a gene by RNA polymerase begins

169
Q

terminator sequence

A

DNA sequences that define where transcription of a gene by RNA polymerase ends

170
Q

structural gene

A

the gene that codes for the production of an amino acid chain

171
Q

eukaryotic transcription unit

A

Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica

172
Q

positive control

A

requires transcription factors to turn on a gene

173
Q

promoter proximal element

A

any regulatory sequence in eukaryotic DNA that is located close to (within 200 base pairs) a promoter and binds a specific protein thereby modulating transcription of the associated protein coding gene

174
Q

transcription factors

A

proteins that attach RNA polymerase to the promoter sequence

175
Q

activator proteins

A

consist of two main domains: a DNA-binding domain that binds to a DNA sequence specific to the activator, and an activation domain that functions to increase gene transcription by interacting with other molecules

176
Q

enhancer sequence

A

a DNA sequcne that enhances the transcription of a gene

-activator proteins bind to the enhancer sequence

177
Q

transcription level control

A

-determines whetehr DNA can be reached by transcription factors

178
Q

euchromatin

A

transcription is possible when DNA is in this form

179
Q

heterochromatin

A

transcription is prevented when DNA is in this form

180
Q

histones

A

wind DNA into nucleosomes

181
Q

nucleosomes

A

a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones

182
Q

DNA methylation

A
  • addition of methyl (-CH3) groups to nitrogenous bases of DNA
  • prevents transcription
  • long-term inactivation of genes
  • methylated genes are passed on to daughter cells
183
Q

histone acetylation

A
  • addition of CH3COO gropus to amino acids of histones
  • acetelyated histones hold DNA less tightly
  • gives easier access to genes in an acetylated region
  • prevents DNA from becoming heterochromatin
184
Q

post-transcription level control

A
  1. RNA processing

2. mRNA degradation

185
Q

RNA processing

A
  • alternative splicing of mRNA

- splice-o-some complex takes out multple introns and and a some exons out, which goes on to form alternative proteins

186
Q

mRNA degradation

A
  • trailer segment of mRNA determines stability
  • a poly A tail: a long train of adenines at the end of mRNA that creates a more stable mRNA
  • cells can determine how strong a gene expression is
187
Q

translation level control

A
  1. regulatory proteins
188
Q

regulatory proteins

A
  • bind to mRNA leader segments
  • prevents ribosomes from binding
  • useful if you have 2 cells with similar characteristics, but a gene should only be made in one, so the regulatory proteins should only be found in the other one
189
Q

post-translation level control

A
  1. protein passing and degradation

2. affecting concentration of active enzymes

190
Q

protein processing and degradation

A
  1. cleavage activation
  2. phosphorylation activation
  3. transport to activating environment
  4. change concentration of active enzymes
191
Q

cleavage activation

A
  • more effective than cofactors
  • if the protein/enzyme is not meant to be used yet, a piece can be added to it in order to prevent the substrate from binding to it
192
Q

phosphorylation activation

A

activates a protein or turns it off with kinase

193
Q

transport to activating environment

A

some proteins are denatured the moment they are produced because they were produced in the wrong pH environment, so to save it they are transported to an environment with the right pH

194
Q

ubiquitin

A

tags a protein for destruction by proteasome

-needs 3 molecules of ubiquitin to be tagged

195
Q

proteasome

A

protein shredder

-degrades proteins

196
Q

affecting concentration of active enzymes

A
  1. create/destroy
  2. change reaction environment
  3. activate/deactivate existing enzymes
  4. localization/containment
197
Q

model organisms

A

organisms that represent other organisms for genetic purposes

198
Q

Drosophila melanogaster

A

fruit fly; representative of all flying insects

199
Q

Mus musculus

A

mouse; representative of vertebrates

200
Q

Caenorhabditis elegans

A

nematode worm; representative of invertebrates

-transparent body so good for studying

201
Q

Danio rerio

A

zebrafish; representative of all fish

-transparent during enbryonic stage

202
Q

Arabidopsis thaliana

A

wall cress plant; representative of plants

Bio 211 (15 decks)

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