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Spring Sophomore Year > Cell Bio Exam 2 > Flashcards

Cell Bio Exam 2 Flashcards

1
Q

Central Dogma of molecular genetics

A

Replication
Transcription
Translation

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2
Q

3 steps in DNA replication, Transcription, and Translation

A

Initiation
Elongation
Termination

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3
Q

Initiation in DNA replication

A
  • Creating an origin for replication
  • Origin of replication tends to occur at the AT rich segments
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4
Q

Why does the origin of replication occur at the AT rich segments?

A

Because it’s easier for initiator proteins break two hydrogen bonds in A-T than three hydrogen bonds in C-G

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5
Q

In DNA Replication Strands are separated at

A

the origin of replication

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6
Q

After strands are separated how the origin of replication, what is left?

A

Two separate strands
On each of the original DNA strands, proteins will come and attach new complementary strands to them

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7
Q

Each of the two strands created through DNA replication contains

A

one old and one new strand
DNA is called semiconservative

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8
Q

DNA is antiparallel because

A

one strand 5’ is attached to the other strand’s 3’ end

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9
Q

The 5’ end terminal of DNA

A

phosphosphate group

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10
Q

The 3’ end has a terminal

A

hydroxyl group

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11
Q

What binds nucleotide bases together in a DNA helix?
(double stranded DNA)

A

Hydrogen bonds

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12
Q

What binds single stranded DNA nucleotides together?

A

Phosphodiester bonds

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13
Q

Elongation in DNA Replication

A

This is where new strands are created
There are several enzymes that aid in this process

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14
Q

Helicase

A

“Unzips: the wound DNA by breaking H-bonds

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15
Q

How do we prevent strands from snapping back together?

A

Single-strand binding proteins: they attach to each strand of uncoiled DNA to keep them separated

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16
Q

When helicase unwinds the DNA, it creates tension at the

A

replication fork (where the strands separate)

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17
Q

The tension from the replication fork is known as —— and is relieved by ——-

A

supercoiling
Topoisomerase

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18
Q

Topoisomerase

A
  • Relieves built-up tension on the replicating strand
  • Creates small nicks within the DNA double helix
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19
Q

DNA polymerase

A
  • adds new nucleotides
  • synthesis & repair
  • Proofreading to double check and correct eros
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20
Q

Primase

A
  • Places RNA primer at the origin of replication
  • Give DNA polymerase a 3 hydroxyl group to attach free nucleoside triphosphates to create phosphodiester bond via condensation reaction
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21
Q

Where does the energy for creating these bonds come from?

A

HYDROLYSIS OF 2 PHOSPHATES FROM EACH NEW BASE

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22
Q

Sliding clamp proteins

A

hold DNA polymerase to the template strand

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23
Q

As the replication fork opens, the ——- is synthesized continuously from a single ——

A

LEADING STRAND
RNA primer

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24
Q

Leading strand

A

Leading strand is extending the same direction as the DNA polymerase
Leading strand is the template strand

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25
Q

Lagging strand

A

is synthesized discontinuously, opposite direction to how DNA polymerase is traveling

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26
Q

Small Okazaki fragments

A

make up the discontinuous strand and one RNA primer is required for each fragment

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27
Q

DNA ligase

A

DNA ligase ligates (gluing together) the separated strands

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28
Q

Termination in DNA Replication

A
  • Occurs when the replication fork can no long progress forward
  • DNA polymerase requires an RNA primer to end the DNA
  • As a result, a small segment of DNA is not replication at the ends of the chromosomes
  • This is why telomeres exist
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29
Q

Telomeres

A
  • Telomeres are sequences of repeated nucleotides at the end of a chromosome that don’t code anything
  • This way, as replication occurs and that small segment of DNA at the end is not replicated, we don’t lose crucial pieces of genetic information
  • Telomerase is the enzyme that extends telomeres to prevent DNA from losing information
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30
Q

Where does transcription happen?

A

Transcription happens in nucleus

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31
Q

Transcription

A
  • DNA contain genes, which are instructions for making things our cells need to function, grow, and divide
  • In order for cells to convert genetic instructions into proteins, they must first be transcribed into RNA and then translated.
  • Transcription is the first step of gene expression, and its main goal is to convert a sequences of DNA into a single strand of messenger RNA (mRNA) (product of transcription)
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32
Q

What is the product of transcription?

A

Main goal is to convert a sequences of DNA into a single strand of messenger RNA (mRNA)
(product of transcription)

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33
Q

Initiation In transcription

A

RNA polymerase binds to a spection section near the gene to be transcribed: promoter sequence

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34
Q

Promoters

A
  • Promoters help attract RNA polymerases to bind to DNA in the correct location to transcribe a gene
  • Promoters can be upstream or downstream from a gene
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35
Q

Elongation in transcription

A

after RNA polymerase has aligned with the promoter correctly and the transcription bubble has been established

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36
Q

RNA polymerase travels along —-(also called what?)
in the 3’ → 5’ directions
Extends in the 5’ → 3’ direction

A

the template strand
(aka noncoding or antisense strand)

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37
Q

Termination in transcritption

A

occurs when RNA polymerase transcribes a sequence that says the gene is finished

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38
Q

Termination in transcription

A

occurs when RNA polymerase transcribes a sequence that says the gene is finished

39
Q

Eukaryotic transcription

A
  • Transcription of eukaryotic DNA into mRNA occurs in the NUCLEUS
  • Due to this, RNA polymerases cannot directly detect and bind to the promoter region
  • They require binding of TRANSCRIPTION FACTORS
40
Q

Transcription factors

A

regulatory proteins that bind to promoter DNA and affect the recruitment of RNA polymerases

41
Q

Eukaryotic promoter sequences tend to contain a region known as the

A

TATA box

42
Q

TATA boxes are recognized by

A

transcription factors

43
Q

Function of transcription factors

A

they can either increase rate of transcription (upregulation) or decrease rates of transcription (downregulation)

44
Q

Eukaryotic promoters also contain ———— that transcription factors can bind to.

A

enhancer sites and silencer sites

45
Q

enhancer sites and silencer sites

A

can be upstream, downstream, or within the gene.

46
Q

Activator proteins bind enhancers

A

increase transcription

47
Q

Repressor proteins binds silencers

A

decrease transcription

48
Q

What is involved in the terminator sequence for protein coding genes?

A

POLY A SIGNAL (Polyadenylation)

49
Q

POLY A SIGNAL (Polyadenylation)

A
  • This signal tells certain enzymes to cut the transcript away from RNA polymerases → transcription is terminated
  • The poly A signal in mRNA stimulated polyadenylation: Adenine nucleotides are added to the 3’ end.
  • Polyadenylation is poly=many, adenylation=adenine nucleotide
50
Q

Exonucleases

A

cleave nucleotides from polynucleotide chain at the ends

Results in STICKY ends

51
Q

Endonucleases

A

Cleave nucleotides from polynucleotide chain from the inside

Results STICKY OR BLUNT ENDS

52
Q

Post-transcriptional Modification

A

is when pre-mRNA is modified intro processed mRNA

Processed mRNA to exit the nucleus through a nuclear pore and enter the cytoplasm where TRANSLATION OCCUR

53
Q

3 main types of post-transcriptional modifications

A

5’ capping
Polyadenylation of the 3’end
Splicing out introns

54
Q

5’ Capping (5’ G-P-P-P)

A

7-methylguanosine cap is added to the 5’end of the mRNA during elongation, protecting the mRNA from degradation

55
Q

Polyadenylation of the 3’end (A-A-A-A-3’)

A

addition of the poly A to the 3’ end to prevent degradation

56
Q

Splicing out introns

A
  • introns are stretches of noncoding DNA that lie between regions of coding DNA (exons)
  • Splicing refers to removing introns from pre-mRNA using spliceosome
  • “Splice signals” present within intron signal to spliceosome where to cut
  • Splicing allows for increased genetic diversity
57
Q

snRNAs (small nuclear RNA) and proteins make up the

A

functional part of a spliceosome and are collectively referred to snRNPs (small nuclear RiboNucleoProteins)

58
Q

Alternative splicing

A
  • describes a single pre-mRNA having multiple possible spliced mRNA products
  • Thus, the same pre-mRNA can produce many different proteins
59
Q

Where does Translation happen

A

Translation occurs in cytoplasm

60
Q

Translation

A

Translation is the process of converting mRNA to proteins

Important players in translation: ribosomes and tRNA

Assembly of polypeptides based on reading new RNA in the cytoplasm

61
Q

Ribosomes are made up of one small subunit and one large subunit

What is it for Eukaryotes and Prokaryotes?

A

Eukaryotes: 40S (small) & 60S (large), which form 80S ribosomes
Composed of rRNA (ribosomal RNA) and proteins

Prokaryotes: 30S (small) & 50S (large), which form 70S
Composed of rRNA (ribosomal RNA) and proteins but are assembled together in the nucleoid

62
Q

Codon

A

is a groups of THREE mRNA bases (A, U, G, or C) that code for amino acid or terminate translation
There are 64 codon combinations but only 20 amino acids

63
Q

Anticodons

A

three tRNA bases (A, U, G, or C) that base pairs with a codon

Each rRNA carries amino acid to be added to the growing proteins

64
Q

Aminoacyl-tRNA refers to a tRNA bound to an amino acid
Which does what?

A

Aminoacyl-tRNA synthetase is the enzyme that attaches an amino acid to a specific tRNA using energy from ATP

65
Q

Initiation in Translation

A

small ribosomal subunit attaches to the 5’ end of mRNA, a tRNA methionine attaches to the start sequence of mRNA (AUG), and the large ribosomal subunit attaches to form a complete complex. Requires 1 GTP

66
Q

Start Codon
Stop Codon

A

Start codon: AUG (methionine)

Stop codons: UAA, UAG, UGA (end translation, do not code for any amino acids)

67
Q

Elongation in Translation

A

tRNA binds to the A site, peptide bond formation occurs, and the tRNA without methionine is released

The tRNA currently in the A site moves to the P site (translocation) and the nest tRNA comes into the A site to repeat the process

68
Q

Termination in Translation

A

when the ribosome encounters the stop codon (either UAG, UAA, or UGA), the polypeptide and the two ribosomal subunits all release due to a release factors breaking down the bond bond between tRNA and the final amino acid of the polypeptide

69
Q

process that requires assistance from chaperone proteins

A

While the polypeptide is being translated, amino acid sequences are determining the folding conformation, which is a process that requires assistance from chaperone proteins

70
Q

Ribosomal binding sites for tRNA:

A

A site: A for amino acyl-tRNA, which first enters at this site

P site: P for peptidyl-rRNA, which carries the growing polypeptide

E site: E for exit site. The tRNA from the P site is sent here and released from the ribosome

71
Q

A site

A

A for amino acyl-tRNA, which first enters at this site

72
Q

P site

A

P for peptidyl-rRNA, which carries the growing polypeptide

73
Q

E site

A

E for exit site. The tRNA from the P site is sent here and released from the ribosome

74
Q

Post-translation

A

Signals peptides at the beginning of the translated polypeptide at the beginning of the translated polypeptide may direct the ribosome to attach to the endoplasmic reticulum, in which case the polypeptide is injected into the ER lumen

In general, post-translational modification (addition of sugars, lipids, phosphate groups to the amino acids)
Amino acids are placed starting from the 5’ end of the mRNA and move all the way down to the 3’ end
Corresponding rRNA codons are 3’ to 5’

75
Q

Overview of initiation/elongation/termination for translation

A
  • The ribosome catalyzes the formation of a peptide bond between the polypeptide in the P site and the newly added amino acid in the A site
  • After that, the polypeptide is transferred to the A site’s tRNA and the ribosome shifts one codon the mRNA
  • The A site will now be empty and ready to accept another aminoacyl-rRNA
  • The tRNA from the P site will be transferred to the E site and will leave the ribosome
76
Q

siRNAs

A

Small interfering RNA: “short”, or silencing RNA
Inhibits the expression of one specific target mRNA

77
Q

miRNA

A

regulates expression of multiple mRNA

78
Q

TFIID

A

Transcription factor II D: a large multi-protein assembly formed by the TATA box

79
Q

TFIIH

A

Transcription factor IIH: promotor opening and phosphorylation

80
Q

Cell membrane

A

Cell membrane holds cellular contents and are mainly composed of phospholipids, cholesterol, and proteins

81
Q

Phospholipids

A
  • glycerol backbone
  • 1 phosphate group (hydrophilic)
  • 2 fatty acid tails (hydrophobic)
  • Amphipathic because the molecules have both polar and nonpolar parts, this allows them to form a LIPID BILAYER in an aqueous environment
82
Q

Cholesterol

A

4 fused hydrocarbon rings
Precursor to steroid hormones
Amphipathic
Regulates membrane fluidity
Less permeable and less fluid

83
Q

Membrane proteins are either

A

integral or peripheral

84
Q

Integral (transmembrane) proteins

A

transfer the entire bilayer
Amphipathic
Cell signaling or transport

85
Q

Peripheral membrane proteins

A

are found on the outside of the bilayer, and they are generally hydrophilic

86
Q

CRISPER-Cas9

A

its a protien that works on DNA

87
Q

Sarah Lucas

A

Rrna

88
Q

RNAseq

A

RNAseq in transcription takes a snap shot of which genes expressed

89
Q

Activators and repressors regulate gene expression

A

Regulatry protiens in RNA Pol 2
Bind DNA through non covalent interactions
with sepficis protiens and major groove

90
Q

Defult location of protiens lacking any signals directing their sorting

A

cytosol

91
Q

What will incrase in unstaturated phosphlipids cause?

A

more fluid

92
Q

What happens at the N-terminal tail of core histones?

A

acetylation
phosphoshorylation
methylation

93
Q

Types of RNAs found in eukaryotes

A

mrna
rrna
trna

Spring Sophomore Year (11 decks)

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