Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry II > Lecture Exam 4 > Flashcards

Lecture Exam 4 Flashcards

1
Q

Phenotype

A

visible property; a gene was defined as a portion of a chromosome that determines or affects a single phenotype

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Gene

A

all the DNA that encodes the primary sequence of some final gene product (polypeptide or RNA with a structural or catalytic function)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Mutation

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Mutation

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the relationship between DNA, RNA, and protein?

A

-Each amino acid of a polypeptide chain is coded for by three consecutive nucleotides in a single strand of DNA (“codon”)
-a polypeptide chain of 350 amino acid residues (an average-size chain) corresponds to 1,050 base pairs (bp) of coding DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

How large are bacterial cells and viruses in comparison to the length of the DNA/RNA molecule contained within them?

A

-DNA viral genomes vary greatly in size and tend to be circular for at least part of their life
-The contour lengths of their DNA are typically hundreds of times longer than the long dimensions of the viral particles that contain them
-an E.coli cell contains ~100x as much DNA as a bacteriophage particle
-the E. coli chromosome is a single, double-standard circular DNA molecule of 4,641,652 bp; the genome is ~850 times the length of the cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How much DNA is in a diploid human cell?

A

-Total: 3,096,649,726
-46 chromosomes
-20,454 protein-coding genes
-2m of DNA in each human cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are introns and exons in a gene?

A

-Introns: nontranslated, intervening DNA segments that do not code for the amino acid sequences of the polypeptide product
-Exons: coding DNA segments; makes up only ~1.5% of human DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are repeat sequences? Where are these located on a chromosome typically?

A

-Highly repetitive sequences: short sequences, generally less than 10 bp long, that are sometimes repeated millions of times per cell
-make up ~3% of the human genome
-do not encode proteins or RNAs
-associated with centromeres and telomeres

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the telomere? How does it influence cell aging and the ability to replicate and divide?

A

-Telomeres: sequences at the ends of eukaryotic chromosomes that help stabilize the chromosome; shortened after each round of replication; end with multiple repeated sequences of the form

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is DNA supercoiling? What is relaxed DNA?

A

-Supercoiled: neutralizing the negative charges of the phosphoryl groups in the DNA backbone with cations and polyamines
-underwound DNA: state where DNA has fewer right handed turns per given length of DNA than B-form DNA; places structural strain on the DNA causing it to twist upon itself (supercoiling)
-most cellular DNAs are supercoiled; this is an intrinsic property of DNA tertiary structure
-Relaxed DNA: state where there is no net bending of the DNA axis upon itself

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What enzymes remove (relax) supercoils?

A

Topoisomerases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is linking number and how does it quantify supercoiling?

A

-Linking Number: the number of times the twisting strand penetrates a surface; topological property of double-stranded DNA
-always an integer
-positive strands interwound in a right-handed helix
-the linking number is negative for strands interwound in a left-handed helix; not encountered in DNA
-Lk=number of bp/number of bp per turn

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How do topoisomerases change linking number?

A

-Topoisomerases: enzymes that increase or decrease the extent of DNA underwinding
-change the linking number; play an important role in replication and DNA packaging

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is a general mechanism for type I topoisomerases?

A

-act by transiently breaking one of the two DNA strands, passing the unbroken strand through the break, and rejoining the broken ends
-change Lk in increments of 1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is a general mechanism for type II topoisomerases?

A

-break both DNA strands
-change Lk in increments of 2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is a catenane, how are they formed, and what topoisomerases can remove them?

A

-Catenanes: DNA circles that are topologically linked
-Type II Topoisomerases can pass one duplex DNA segment through a double-stranded break in another duplex; allows these enzymes to untangle catenanes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What components make up chromatin?

A

-Chromatin: eukaryotic chromosomal material composed of DNA ,RNA, and proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

How is the DNA packaged in a nucleus? What are the roles of histones?

A

-Histones: proteins that are tightly associated with chromatin and function to package and order the DNA
-Nucleosomes: the fundamental structural unit of chromatin; composed of core histone proteins bound to DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the roles of histone tails?

A

-Play a key role in forming contacts between nucleosomes in chromatin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What are the differences between the active and inactive compartments in the nucleus?

A

-Active Compartments: have reduced chromatin condensation
-Inactive Compartments (heterochromatin): highly condensed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Describe the roles of the SMC proteins cohesins and condensins.

A

-SMC proteins (structural maintenance of chromosomes): responsible for maintaining the structure and integrity of chromosomes following replication; consist of 5 district domains
-Cohesions: link sister chromatids together after replication and keep them together as the chromosomes condense to metaphase
-Condensins: essential to chromosomal condensation as cells enter mitosis; create positive supercoils
-as DNA is compacted to form tighter and tighter loops, condensins stabilize the loops by binding at the base of each one

23
Q

How does gene and protein naming differ between prokaryotes and eukaryotes?

A

-Prokaryotes:
-Genes: typically names using three italicized letters reflecting a function; capital letters added to abbreviation reflect order of discovery, not enzymatic order
-Proteins: often named after their genes using nonitalcized, roman types with the first letter capitalized
-Eukaryotes:
-Genes: no single convention exists for all eukaryotic systems, three gene names are three italicized uppercase letters followed by an italicized number
-Proteins: complex and variable; in yeast, some proteins have long common names; other yeast proteins have the same name as the gene, with one uppercase and two lowercase letters in roman type, followed by a number and the letter “p”

24
Q

What is semiconservative DNA replication?

A

-Semiconservative replication: each DNA strand serves as a template for the synthesis of a new strand; produces two new DNA molecules.\, each with one new strand and one old strand

25
Q

What are the lagging and leading strands during replication?

A

-Lagging Strands: 5’–> 3’ synthesis proceeds in the opposite direction that the replication fork moves; discontinuous synthezise through the synthesis of Okazaki fragments
-Leading Strands: 5’–>3’ synthesis proceeds in the same direction that the replication fork moves; synthesized continuously

26
Q

What is the difference between an endonuclease and an exonuclease?

A

-Exonuclease: degrade nucleic acids from one end of the molecule; many operate in only one direction (either 5’–>3’ or 3’–>5’)
-Endonuclease: degrade nucleic acids at specific internal sites in the molecule

27
Q

What is a DNA polymerase? What is does proofreading enable a polymerase to do?

A

-DNA polymerase: complex enzymes that can synthesize DNA; many have additional activities
-the reaction is a phosphoryl group transfer
-the 3’-OH of the nucleotide at the 3’ end of the strand (the nucleophile) attacks the alpha-phosphorous of the incoming dNTP
-Proofreading: DNA polymerase activity that involves the replacement of the incorrect nucelotide; improves accuracy by 100-1000 times
-permits the enzyme to remove a newly added nucleotide

28
Q

How accurate is DNA replication?

A

-DNA polymerases insert one incorrect nucleotide for every 10,000-100,000 correct nucleotides; this may occur because a base is in a tautomeric form

29
Q

What are the main classes of proteins/enzymes involved in replication?

A

-Helicases: enzymes that move along the DNA and separate the strands
-require chemical energy from ATP
-Topoisomerases: relieve topological stress created by strand separation
-DNA-binding proteins: stabilize short segments of RNA to serve as primers
-Primases: synthesize short segments of RNA to serve as primers
-Ligases: seals nicks in the DNA backbone following removal and replacement of an RNA primer

30
Q

What are the main phases of replication?

A

-Three stages:
-Initiation
-Elongation
-Termination

31
Q

What are Okazaki fragments?

A

-Okazaki Fragments: short DNA fragments that are synthesized in the replication of one of the new DNA strands

32
Q

What are mismatch and base excision repair?

A

-Mismatch: mismatches are corrected to reflect template strand information
-distinguished from the newly synthesized strand by the presence of methyl group tags on the template DNA
-Base Excision Repair: recognize common DNA lesions and remove the affected base by cleaving the N-glycosyl bond in the process of base-excision repair; generally specific for one lesion type

33
Q

WHat is recombination in meiosis?

A
34
Q

What is nonhomologous end-joining?

A

-process by which broken chromosomes ends are processed and ligated back together
-occurs when recombinational DNA repair is not feasible because replication is not occurring and sister chromatids are not present; mutagenic process; does not randomly join ends

35
Q

How is recombination used to make diverse antibodies?

A
36
Q

What is a ribozyme?

A

-Ribozyme: catalytic RNAs that act as enzymes

37
Q

What is transcription? And what is the transcriptome?

A

-Transcription: process by which an enzyme system converts the genetic information in dsDNA into an RNA strand with a complementary base sequence
-the entire chromosome is usually copied during replication; transcription is more selective
-Trascriptome: the sum of all the RNA molecules produced in a cell under a given set of conditions
-~76% of the human genome is transcribed into RNA
-most products are ncRNAs

38
Q

What are the major classes of RNAs and what do they do?

A

-mRNA: encode the amino acid sequences of polypeptides
-tRNA: read the mRNA and transfer the appropriate amino acid to a growing polypeptide chain during protein synthesis
-rRNA: constituents of ribosomes, the cellular machines that synthesize proteins
-ncRNA: have a variety of catalytic, structural, and regulatory functions

39
Q

What are the relationships between the template DNA, nontemplate DNA, and the transcript sequence?

A

-Template strand: DNA strand that serves as a template for RNA synthesis
-Nontemplate strand (coding strand): DNA strand that is identical in base sequence to the transcribed RNA, with U in RNA in place of T in DNA

40
Q

What are the three types of RNA polymerases in eukaryotes and what do they transcribe?

A

-RNA polymerase I: responsible for the synthesis of a transcript called pre-ribosomal RNA; pre-rRNA contains the precursor for the 18S, 5.8S, and 28S rRNAs
-RNA polymerase II: responsible for synthesis of mRNAs and many ncRNAs; can recognize 1000s of promoters
-RNA polymerase III: responsible for the synthesis of tRNAs, the 5S rRNA, and other ncRNAs; are well characterized

41
Q

What is the difference between the terms transcription factors and general transcription factors?

A

-Transcription factors: an array of proteins that work with Poly II form the active transcription complex
-General Transcription Factors: those required at every Poly II promoter

42
Q

What are the main phases of transcription?

A

-Elongation: elongation factors bound to RNA poly II enhance processivity and coordinate posttranslational modifications; some are bound to phosphorylated CTD
-termination: Poly II CTD is dephosphorylated and transcription machinery is recycled
-release

43
Q

What are the main modifications made to eukaryotic mRNAs?

A

-At the 5’ end, a 5’ cap (a modified nucleotide structure) is added
-At the 3’ end, cleavage occurs and 80 to 250 A residues are added to create a poly (A) tail

44
Q

What is the 5’ cap made from?

A

-a residue of 7-meethylguanosine linked to the 5’-terminal residue of the mRNA through an unusual 5’-5’-triphosphate linkage

45
Q

What is a self-splicing intron?

A

-Group II intron: catalytic RNA; maturase and reverse transcription proteins; self splicing using a nucleophile within the intron to form a lariat; primarily found in the mitochondria and chloroplast genes of fungi, algae, and plants. Can be found in bacteria

46
Q

What is the spliceosome and what are snRNAs and snRNPs?

A

-Spliceosome: a large complex made up of multiple specialized RNP complexes called small nuclear ribonucleoproteins (snRNPs) and dozons of other proteins
-Small nuclear RNAs (SnRNAs): 100-200 nucleotide RNAs that make up snRNPs
-snRNP: small nuclear ribonucleoproteins

47
Q

What is alternative splicing?

A

-Alternative splicing: process in which a particular exon may or may not be incorporated into the mature mRNA transcript; occurs in >95% of human genes

48
Q

What are some roles of nucleoside modifications?

A

-Conversion of uridine to pseudouridine
-adoMet-dependent nucleoside methylation
-Slide 59, 62,63

49
Q

What are miRNAs?

A

-Micro RNAs (miRNAs): a special class of non-coding RNAs that promote mRNA degradation and suppress translation to fine-tune gene expression
-22 nucleotides long
-complemetary in sequence to particular regions of mRNA
-found in plants and animals

50
Q

What are reverse transcriptases and what types of reactions do they catalyze?

A

-Reverse transcriptase: an RNA-dependent DNA polymerase
-contained within certain RNA viruses called retroviruses
-discovery showed genetic information can flow “backward” from RNA to DNA
-catalyzes conversion of viral RNA to dsDNA, which is often integrated into teh host genome
-Reactions: RNA-dependent DNA synthesis, RNA degradation, DNA-dependent DNA synthesis

51
Q

How are transposons, retroviruses and introns similar?

A

-Slide 70 and beyond
-Retroviruses have a genome that is desiggned to integrate into a host
-In our cells, we already have tag elements (transpospons) like retroviruses do

52
Q

What is telomerase and how does it extend telomeres?

A

-Telomerase: a ribonucleotideprotein that synthesizes the telomere endsd of linear chromosomes; act as a specialized reverse transcriptase; contains an internal RNA repeat sequence that serves as a template for synthesis of the TG strand of the telomere

53
Q

What are ribozymes? Why do some people believe that these are critical to the origin of life?

A

-Ribozymes: RNA enzymes
-RNA world hypothesis: proposal that the evolution of life on Earth may have included an “RNA world”, RNAs not proteins act as catalysts; the discovery of ribozymes gave life to the RNA world hypothesis; the parent of all life on this planet might have been a self-replicationg RNA, or a polymer with equivalent chemical characteristics

Biochemistry II (5 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions