Cell Bio Exam 2 Flashcards
1
Q
Central Dogma of molecular genetics
A
Replication
Transcription
Translation
2
Q
3 steps in DNA replication, Transcription, and Translation
A
Initiation
Elongation
Termination
3
Q
Initiation in DNA replication
A
- Creating an origin for replication
- Origin of replication tends to occur at the AT rich segments
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
5
Q
In DNA Replication Strands are separated at
A
the origin of replication
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
7
Q
Each of the two strands created through DNA replication contains
A
one old and one new strand
DNA is called semiconservative
8
Q
DNA is antiparallel because
A
one strand 5’ is attached to the other strand’s 3’ end
9
Q
The 5’ end terminal of DNA
A
phosphosphate group
10
Q
The 3’ end has a terminal
A
hydroxyl group
11
Q
What binds nucleotide bases together in a DNA helix?
(double stranded DNA)
A
Hydrogen bonds
12
Q
What binds single stranded DNA nucleotides together?
A
Phosphodiester bonds
13
Q
Elongation in DNA Replication
A
This is where new strands are created
There are several enzymes that aid in this process
14
Q
Helicase
A
“Unzips: the wound DNA by breaking H-bonds
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
16
Q
When helicase unwinds the DNA, it creates tension at the
A
replication fork (where the strands separate)
17
Q
The tension from the replication fork is known as —— and is relieved by ——-
A
supercoiling
Topoisomerase
18
Q
Topoisomerase
A
- Relieves built-up tension on the replicating strand
- Creates small nicks within the DNA double helix
19
Q
DNA polymerase
A
- adds new nucleotides
- synthesis & repair
- Proofreading to double check and correct eros
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
21
Q
Where does the energy for creating these bonds come from?
A
HYDROLYSIS OF 2 PHOSPHATES FROM EACH NEW BASE
22
Q
Sliding clamp proteins
A
hold DNA polymerase to the template strand
23
Q
As the replication fork opens, the ——- is synthesized continuously from a single ——
A
LEADING STRAND
RNA primer
24
Q
Leading strand
A
Leading strand is extending the same direction as the DNA polymerase
Leading strand is the template strand
25
Lagging strand
is synthesized discontinuously, opposite direction to how DNA polymerase is traveling
26
Small Okazaki fragments
make up the discontinuous strand and one RNA primer is required for each fragment
27
DNA ligase
DNA ligase ligates (gluing together) the separated strands
28
Termination in DNA Replication
- 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
29
Telomeres
- 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
30
Where does transcription happen?
Transcription happens in nucleus
31
Transcription
- 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)
32
What is the product of transcription?
Main goal is to convert a sequences of DNA into a single strand of messenger RNA (mRNA)
(product of transcription)
33
Initiation In transcription
RNA polymerase binds to a spection section near the gene to be transcribed: promoter sequence
34
Promoters
- 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
35
Elongation in transcription
after RNA polymerase has aligned with the promoter correctly and the transcription bubble has been established
36
RNA polymerase travels along ----(also called what?)
in the 3’ → 5’ directions
Extends in the 5’ → 3’ direction
the template strand
(aka noncoding or antisense strand)
37
Termination in transcritption
occurs when RNA polymerase transcribes a sequence that says the gene is finished
38
Termination in transcription
occurs when RNA polymerase transcribes a sequence that says the gene is finished
39
Eukaryotic transcription
- 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
Transcription factors
regulatory proteins that bind to promoter DNA and affect the recruitment of RNA polymerases
41
Eukaryotic promoter sequences tend to contain a region known as the
TATA box
42
TATA boxes are recognized by
transcription factors
43
Function of transcription factors
they can either increase rate of transcription (upregulation) or decrease rates of transcription (downregulation)
44
Eukaryotic promoters also contain ------------ that transcription factors can bind to.
enhancer sites and silencer sites
45
enhancer sites and silencer sites
can be upstream, downstream, or within the gene.
46
Activator proteins bind enhancers
increase transcription
47
Repressor proteins binds silencers
decrease transcription
48
What is involved in the terminator sequence for protein coding genes?
POLY A SIGNAL (Polyadenylation)
49
POLY A SIGNAL (Polyadenylation)
- 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
Exonucleases
cleave nucleotides from polynucleotide chain at the ends
Results in STICKY ends
51
Endonucleases
Cleave nucleotides from polynucleotide chain from the inside
Results STICKY OR BLUNT ENDS
52
Post-transcriptional Modification
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
3 main types of post-transcriptional modifications
5’ capping
Polyadenylation of the 3’end
Splicing out introns
54
5’ Capping (5’ G-P-P-P)
7-methylguanosine cap is added to the 5’end of the mRNA during elongation, protecting the mRNA from degradation
55
Polyadenylation of the 3’end (A-A-A-A-3’)
addition of the poly A to the 3’ end to prevent degradation
56
Splicing out introns
- 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
snRNAs (small nuclear RNA) and proteins make up the
functional part of a spliceosome and are collectively referred to snRNPs (small nuclear RiboNucleoProteins)
58
Alternative splicing
- describes a single pre-mRNA having multiple possible spliced mRNA products
- Thus, the same pre-mRNA can produce many different proteins
59
Where does Translation happen
Translation occurs in cytoplasm
60
Translation
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
Ribosomes are made up of one small subunit and one large subunit
What is it for Eukaryotes and Prokaryotes?
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
Codon
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
Anticodons
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
Aminoacyl-tRNA refers to a tRNA bound to an amino acid
Which does what?
Aminoacyl-tRNA synthetase is the enzyme that attaches an amino acid to a specific tRNA using energy from ATP
65
Initiation in Translation
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
Start Codon
Stop Codon
Start codon: AUG (methionine)
Stop codons: UAA, UAG, UGA (end translation, do not code for any amino acids)
67
Elongation in Translation
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
Termination in Translation
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
process that requires assistance from chaperone proteins
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
Ribosomal binding sites for tRNA:
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
A site
A for amino acyl-tRNA, which first enters at this site
72
P site
P for peptidyl-rRNA, which carries the growing polypeptide
73
E site
E for exit site. The tRNA from the P site is sent here and released from the ribosome
74
Post-translation
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
Overview of initiation/elongation/termination for translation
- 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
siRNAs
Small interfering RNA: “short”, or silencing RNA
Inhibits the expression of one specific target mRNA
77
miRNA
regulates expression of multiple mRNA
78
TFIID
Transcription factor II D: a large multi-protein assembly formed by the TATA box
79
TFIIH
Transcription factor IIH: promotor opening and phosphorylation
80
Cell membrane
Cell membrane holds cellular contents and are mainly composed of phospholipids, cholesterol, and proteins
81
Phospholipids
- 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
Cholesterol
4 fused hydrocarbon rings
Precursor to steroid hormones
Amphipathic
Regulates membrane fluidity
Less permeable and less fluid
83
Membrane proteins are either
integral or peripheral
84
Integral (transmembrane) proteins
transfer the entire bilayer
Amphipathic
Cell signaling or transport
85
Peripheral membrane proteins
are found on the outside of the bilayer, and they are generally hydrophilic
86
CRISPER-Cas9
its a protien that works on DNA
87
Sarah Lucas
Rrna
88
RNAseq
RNAseq in transcription takes a snap shot of which genes expressed
89
Activators and repressors regulate gene expression
Regulatry protiens in RNA Pol 2
Bind DNA through non covalent interactions
with sepficis protiens and major groove
90
Defult location of protiens lacking any signals directing their sorting
cytosol
91
What will incrase in unstaturated phosphlipids cause?
more fluid
92
What happens at the N-terminal tail of core histones?
acetylation
phosphoshorylation
methylation
93
Types of RNAs found in eukaryotes
mrna
rrna
trna
