Biochem- Merp Mini 1 Quiz 1

Front 1

What is the general structure of a nucleotide?

Back 1

N- containing base (U/T/G/C/A) + pentose sugar (ribose/Deoxyribose) + phosphate group

Front 2

What are the pyrimidines?

Back 2

the smaller, 1 ring bases of a nucleotide (cytosine, uracil, and thymine)

Front 3

What are the purines?

Back 3

The larger, 2 ring bases of a nucleotide (Adenine and guanine)

Front 4

What is a nucleoside?

Back 4

one base covalently linked to 1 sugar (ribose/deoxyribose). Adding the phosphate group makes it a nucleotide

Front 5

What chemical bonds exist within a nucleotide?

Back 5

a glycosidic bond (covalent between base + sugar at 1' C) and an ester bond (covalent between the 5' C and the O from the P-group)

Front 6

What forms a nucleic acid?

Back 6

individual nucleotides bonded via phosphodiester bond- gets energy needed to form the bond by cleaving the terminal P-groups from each nucleotide

Front 7

What is a phosphodiester bond?

Back 7

covalent bond- shared phosphate residue connects the nucleotides at the 3' and 5' position- requires energy

Front 8

What is a hydrogen bond?

Back 8

non-covalent interactions between an H atom and an electronegative atom (ex: N or O)

Front 9

How many hydrogen bonds are involved in base pairing?

Back 9

2 in A/T or A/U and 3 on GC

Front 10

What is base stacking?

Back 10

The hydrophobic interactions between adjacent bases in a single nucleic acid strand- helps maintain the "chain" of bases on each side of the DNA strand

Front 11

What are the 3 major structural arrangements of DNA

Back 11

A-Form (short, tightly wound- found in low water), B form (primary form), Z form (longer- present at high ionic concentrations- left handed)

Front 12

What are the major/minor groves?

Back 12

the groves in DNA resulting from the slightly offset sugar/phosphate backbones of 2 different length strands of DNA- major is larger and partially exposes the base pairs

Front 13

Where on a DNA strand do most protein- DNA interactions occur?

Back 13

on the major groove- the base pairs are exposed to the external environment here

Front 14

How many base pairs are present in the human genome?

Back 14

over 3 billion

Front 15

How is the DNA condensed into a chromatid?

Back 15

DNA wraps "beads on a string" around histones --> condenses into 30nm chromatin fiber --> loops (ea loop has 75kbp) --> 6 loops forms a rosette around the nuclear scaffold --> 30 rosettes form a coil --> 10 coils create the chromatid

Front 16

What happens in G1 of the cell cycle?

Back 16

the cell synthesizes millions of proteins needed for the S-phase, mainly those used for DNA replication

Front 17

What happens in the S phase of the cell cycle

Back 17

DNA synthesis- begins when DNA synthesis begins and ends when the cell's genetic material has effectively doubled

Front 18

What happens in the G2 phase of the cell cycle?

Back 18

millions of proteins required for mitosis are synthesized

Front 19

What occurs in the mitotic phase of the cell cycle?

Back 19

the chromosomes are split into 2 identical nuclei, followed by cytokinesis (division of organelles, cytoplasm, cell membrane, etc)

Front 20

What are the major cell cycle promoting factors?

Back 20

interactions between the cyclins and the cyclin-dependent kinases

Front 21

What happens to a cell's S- phase cyclin levels as the cell cycle progresses?

Back 21

The S phase cyclins increase until a certain point in the S phase, at which point their concentration lowers. (wave like function).

Front 22

What is the first significant event of DNA replication?

Back 22

The origin of replication complex (ORC) binds to the origin of replication

Front 23

What is the replication bubble?

Back 23

the site where the MCM (multi-chromosome maintenance) complex has hydrolyzed the H-bonds of DNA to create regions of single strand DNA (ssDNA)

Front 24

What is the function of topoisomerase?

Back 24

it "relaxes" the DNA strand so it can be "unzipped" by helicase and binding proteins can coat the ssDNA

Front 25

What is the function of primase?

Back 25

it arrives with DNA polymerase-α to form RNA primers- begins DNA synthesis as DNA polymerase must build on an existing chain

Front 26

What is the function of DNA polymerase?

Back 26

DNA polymerase α begins synthesizing a new DNA strand after the primase has made the RNA primers- the job is finished by DNA polymerases δ, ε (w/ help from proliferating cell nuclear antigen)

Front 27

What is the function of Geminin?

Back 27

it binds to newly synthesized DNA to prevent re-synthesis

Front 28

What direction does DNA synthesis occur?

Back 28

the polymerase "reads" the template strand in a 3'-->5' direction, adding new nucleotides to the daughter strand in a 5'-->3' direction .

Front 29

What removes the RNA primers?

Back 29

flap endonuclease 1 and RNAse H- the gaps are then filled in by DNA polymerase δ/ε removes incorrect nucleotides from daughter strand

Front 30

What are Okazaki fragments?

Back 30

the short (100-500 bp) fragments of DNA formed on the lagging strand of DNA- eventually sealed by ligase

Front 31

What makes DNA replication a high fidelity process?

Back 31

high fidelity= dna polymerases accurately copy DNA
This is achieved via 3'-->5' exonuclease proofreading- polymerase δ

Front 32

describe the process of 3'--> 5' exonuclease proofreading

Back 32

an unpaired 3' OH end of the primer blocks further elongation of the strand --> the exonuclease activity of polymerase chews back to create a base paired 3' OH end on the primer strand- DNA polymerase continues adding nucleotides to the primer strand

Front 33

In what phase of the cell cycle does the cell attempt to fix any mutations?

Back 33

G-1, it doesn't want the mutation to be copied

Front 34

What elements form DNA?

Back 34

P, O, N, C H

Front 35

How does a strand of DNA behave in an aqueous environment?

Back 35

The hydrophobic bases tend to aggregate together and are "shielded" by the hydrophilic P groups

Front 36

Onto which ribose/deoxyribose carbon does the Base connect?

Back 36

It connects to the 1' C via a N-Beta glycosidic (covalent) bond

Front 37

Onto which ribose/deoxyribose C does the Phosphate group attach?

Back 37

5' via an ester (covalent) bond

Front 38

What are the general rules of nomenclature for a nucleoside?

Back 38

Base + -osine (for purines) and -idine (for pyrimidines)
+ Add deoxy for deoxyribose sugars

ex: Dexoyribose + Adenine = Deoxyadenosine
Ribose + cytosine = Cytidine

Front 39

What are the general rules of nomenclature for nucleotides?

Back 39

Neucleoside name + Mono-, di-, or tri- phosphate
ex: Deoxyguanosine diphosphate
uridine triphosphate

Front 40

How is the energy needed to create phosphodiester bonds?

Back 40

a pyrophosphate (PPi) is cleaved off of the phosphate group via DNA polymerase, breaking the phosphoanhydride bond

Front 41

What happens to the pyrophosphate when it is cleaved off of a nucleotide?

Back 41

It is cleaved into 2 inorganic phosphates by pyrophsophatase, releasing energy

Front 42

What landmarks are present on either end of a nucleic acid chain?

Back 42

there is a terminal phosphate group on the 5' end and a terminal OH on the 3' end

Front 43

What is complementarity?

Back 43

The ability of purines to form hydrogen bonds with their associated pyrimidine

Front 44

Describe the DNA melting temperature

Back 44

Tm- the temperature at which 50% of DNA goes from dsDNA--> ssDNA

Front 45

What are mitosis promoting factors?

Back 45

M-phase cyclins- they increase until a certain point in mitosis, at which point they plummet

Front 46

What happens to a cell's concentration of Cyclin-dependent kinases throughout the cell cycle?

Back 46

There is no change in their concentration, only their activity as cyclins become available

Front 47

What is a likely effect of a mutation in a CDK?

Back 47

cancer

Front 48

Why are there multiple ORCs?

Back 48

It speeds up the DNA replication process, thereby protecting the template strand from damage via the external environment

Front 49

What are the functions of ssDNA binding proteins

Back 49

1. Prevents the DNA from re-annealing
2. Protects the ssDNA from degradation
3. Acts as a licensing factor for replication machinery (helps recruit the next set of proteins to come to the site of replication)

Front 50

What is the purpose of the RNA primers?

Back 50

DNA polymerase cannot start from scratch- must build from an existing strand. DNA polymerase-alpha arrives in conjugation with RNA polymerase

Front 51

Why do DNA polymerases δ, ε take over for DNA polymerase- alpha?

Back 51

alpha has low processivity- falls off after a few bases. δ assists the lagging strand, ε the leading with the help of PCNA

Front 52

What is PCNA?

Back 52

Proliferating Cell Nuclear Antigen- it encircles the DNA polymerases δ and ε to keep them on the template strand

Front 53

What is transcription?

Back 53

The synthesis of a single stranded RNA molecule using a double stranded DNA molecule as a template

Front 54

What are the major differences between DNA and RNA?

Back 54

DNA resides in nucleus while RNA is in cytosol, different sugars (deoxyribose vs ribose), RNA uses uracil where DNA uses Thymine, and DNA is double stranded wheras RNA is single

Front 55

What are the 5 general classes of RNA?

Back 55

mRNA, rRNA, tRNA, Small nuclear RNA (snRNA),and MicroRNA

Front 56

What are the subunit lengths of eukaryotic RNA?

Back 56

one long chain is synthesized and composed of 28S, 18S, 5.8S, and 5S. all but the 18 join the large ribosomal subunit (60S), the 18 joins with ribosomal proteins to form the 40S)

Front 57

What is the size of the full functional ribosome?

Back 57

80S- large subunit is 60S, the smaller is 40S

Front 58

What is the function of mRNA?

Back 58

They carry the genetic info from the nucleus to the ribosome for protein synthesis- the "working copy of the genome"

Front 59

What is the function of tRNA?

Back 59

carries amino acids and identifies the mRNA nucleotide sequence. They translate this code into the amino acid sequence of proteins

Front 60

What is the D Loop of t RNA?

Back 60

it is the recognition site for aminoacyl-tRNA synthases- contains several modified bases

Front 61

What is the anticodon loop of tRNA?

Back 61

recognizes the complementary mRNA codon- base pairing occurs here

Front 62

What is the variable loop of tRNA

Back 62

the loop of tRNA that provides the structural support- variable in length and nucleotide sequence

Front 63

What is the TΨC loop?

Back 63

facilitates association with amino-acyl synthetases- contains the modified base pseudo-uridine

Front 64

What is the function of the tRNA acceptor stem?

Back 64

it links with amino acids via an ester bond- always has an extreme 3' end which reads 5' CCA- 3'

Front 65

What is snRNA?

Back 65

Small nuclear RNA- combines with proteins to form the spliceosome

Front 66

What is the spliceosome

Back 66

the snRNA/protein complex in the nucleus- splices introns and ligates exons from pre-mRNA molecules

Front 67

What is microRNA?

Back 67

a regulator of gene expression via interaction with the RISC (RNA-inducing silencing complex)- binds to and chews up complementary mRNA

Front 68

What is the RISC?

Back 68

The RNA-induced silencing complex- it binds with microRNA and searches for complementary mRNA. It binds to the mRNA and chews it up

Front 69

What are the functions of the 3 types of RNA polymerase

Back 69

RNA polymerase I- transcribes rRNA
RNA polymerase II- transcribes mRNA, snRNA, MicroRNA
RNA polymerase III- transcribes tRNA

Front 70

What are the most common promoter sequences for transcription?

Back 70

The TATA (transcription initiation-30 bp upstream) and the CAAT box (transcription efficiency, 75bp upstream )

Front 71

What is a sequence motif?

Back 71

conserved sequences in promoters- may or may not be correlative with structural motifs

Front 72

What "triggers" transcription?

Back 72

transcription factor proteins recognize/bind to certain sequence motifs (Response elements) at a functional region (domain). If response elements bind as well, RNA polymerase is bound and transcription begins

Front 73

what is an enhancer region?

Back 73

a sequence-specific region of DNA that binds transcription factors to "enhance" the transcription- usually close to the gene

Front 74

What is a silencer region?

Back 74

a sequence-specific region of DNA that binds repressor proteins that decrease/repress the level of transcription for a particular gene- usually farther away from the gene

Front 75

What happens immediately after the binding of RNA polymerase?

Back 75

the RNA polymerase itself will unwind the DNA and form the transcription bubble. It will re-zip the DNA back up behind itself

Front 76

What are the names of the the 2 strands of "parent" DNA used in transcription?

Back 76

The template strand is the non-coding strand and the non-template strand is the coding strand (will have the same base sequence as the new RNA transcript, except U/T)

Front 77

What is translocation?

Back 77

The process of a polymerase enzyme moving along a nucleic acid

Front 78

What is the terminator sequence?

Back 78

the region of DNA that signals the enzyme to stop adding RNA neucleotides to the chain and detach.

Front 79

What is post-transcriptional "capping"?

Back 79

the 5' end of all mRNA molecules are capped with a unique parallel 5'-5' linkage to 7- methylguanosine residue to protect it from cellular nucleases and serve as a "dock".

Front 80

What is the function of the Poly (A) "tail" post-transcription?

Back 80

adenosine residue is added to the 3' end of the new mRNA via PolyA polymerase and an ATP substrate to prevent degradation and assist in the transfer to the cytoplasm (nucleases can chew up the "junk" A bases rather than the coding RNA)

Front 81

what are introns?

Back 81

intravening sequences of RNA that do not code for protein- spliced out by spliceosomes

Front 82

What are exons?

Back 82

the expressed sequences that remain after introns are removed- they are ligated by splisosomes

Front 83

What is alternative splicing?

Back 83

a recombination/reconnection of exons after intron splicing

Front 84

What is the terminal codon for all tRNA?

Back 84

5'-CCA-3'- allows an AA to bind to the A 3'

Front 85

What "holds" the secondary structure in tRNA?

Back 85

intra-strand hydrogen bonding