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Micro BIO 220 Part 1 > Lecture 6 > Flashcards

Lecture 6 Flashcards

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Biology 101 flashcards
1
Q

What is the definition of a genome?

A

sum total of genetic material of an organism, : All DNA within a cell (or RNA in the case of RNA viruses). consist of chromosome(s), may also include plasmids and DNA in organelles.

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2
Q

What different components of typical prokaryotic and eukaryotic cells make up the genome?

A

prokaryotic: chromosome plasmids
eukaryotic: chloroplast,mitochondrial DNA, chromosomes, nucleus, plasmids

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3
Q

What are some differences between prokaryotic and eukaryotic chromosomes (mostly this is review)…which are only haploid?

A

Prokaryotes-ONLY haploid usually have single, circular chromosomes
Located in the cytoplasm
DNA is condensed into a packet by means of histone-like proteins

eukaryotes-multiple,linear Located in the nucleus; DNA wound around histones
Diploid (in pairs) or haploid (single); may have other ploidy

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4
Q

What differentiates a chromosome from a plasmid?

A

Chromosomes contain ESSENTIAL genes and are usually large in comparison to…
Plasmids contain NON-ESSENTIAL accessory genes that often confer benefits on the host

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5
Q

In what way can viral genomes differ in content from cellular genomes?

A

Viruses may have DNA or RNA as genomic material. It may be single stranded or double stranded.

Genome of cells composed entirely of double stranded DNA
Genome of viruses can contain either DNA or RNA

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6
Q

What are genes, as defined in classical genetics and as defined in molecular/biochemical terms?

A

In CLASSICAL genetics, a gene is the fundamental unit of heredity responsible for a given trait in an organism

MOLECULAR/BIOCHEMICAL terms: a gene is the site on the chromosome that provides information for a certain cell function

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7
Q

Do all genes code for proteins?

A

NO
STRUCTURAL genes: code for proteins such as enzymes
Genes encoding RNAs used in protein production (e.g. rRNAs, tRNAs)
REGULATORY genes: control gene expression (proteins or RNA)

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8
Q

What is the difference between genotype and phenotype?

A

GENOTYPE: the sum of all gene types; an organism’s distinctive genetic makeup
PHENOTYPE:
the expression of certain traits (structures or functions)
all organisms contain more genes in their genotypes than are manifested in the phenotype at any given time

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9
Q

What are the basic structural units (monomers) of nucleic acids, and what are the three main components of these monomers?

A

Nucleotides are the basic unit of DNA structure, and consist of…
Phosphate
Deoxyribose sugar
Nitrogenous base (A, T, G, or C)

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10
Q

What do the nitrogen base abbreviations A, T, G and C stand for?

A

Adenine (A) Thymine (T) Guanine (G) Cytosine (C)

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11
Q

Which are purines and which are pyrimidines?

A

Purines (A and G) and pyrimidines (T and C)

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12
Q

How do these bases pair with each other? Which pairs have two hydrogen bonds and which have three?

A

Adenine (A) always pairs with Thymine (T): 2 hydrogen bonds per pair
Guanine (G) always pairs with Cytosine (C): 3 hydrogen bonds per pair

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13
Q

What is meant by the polarity (directionality) of a single strand of DNA, and how is it denoted?

A

-Polarity: a critical factor in DNA synthesis, protein production, and other molecular biology processes.

  • Antiparallel arrangement: one side of the helix runs in the opposite direction of the other
  • The order of the bond between carbon on deoxyribose and the phosphate is used to keep track of the direction of the two sides
  • One side runs from 5’ to 3’ and the other side runs 3’ to 5’
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14
Q

What role does polarity play when two single strands of DNA form a double stranded (double helix) molecule (what does antiparallel arrangement refer to)?

A

antiparallel: two strands always pair in the opposite direction

The order of the bond between carbon on deoxyribose and the phosphate is used to keep track of the direction of the two sides
One side runs from 5’ to 3’ and the other side runs 3’ to 5

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15
Q

What is the purpose of DNA replication (making RNA, making protein, copying DNA to pass on to progeny?)?

A

Portions of individual strands of DNA molecule are separated

  • Each single strand is copied, producing two complete daughter molecules
  • Each daughter molecule is identical to the parent in composition
  • Neither is completely new; one strand that serves as a template is an original parent of the DNA strand
  • Begins at a specific site called the origin of replication
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16
Q

Double-stranded molecule can be easily unzipped (denatured) into

A

2 single strands to gain access to the information encoded by the bases

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17
Q

Why is DNA replication referred to as semiconservative?

A

Overall replication process is semiconservative replication
-It states that the two strands of DNA first unwind and each strand acts as a template for the building up of a complimentary strand.
The conservative theory,however,states that the entire double helical DNA molecule produces a replica of itself without unwinding.Recent evidence disapproved this, so we work with the semiconservative theory of DNA replication.

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18
Q

Where does replication begin on the chromosome?

A

Begins at a specific site called the origin of replication

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19
Q

What are three important properties of DNA polymerases that help determine how replication can occur? (see top of slide 19)

A
  • unable to begin synthesizing a chain of nucleotides
  • can only add nucleotides to an already existing chain
  • can only add nucleotides in the 5’ to 3’ direction
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20
Q

What are the roles of the following proteins at the replication fork during DNA replication: helicase?

A

Unzipping the DNA helix

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21
Q

Primase

A

Syntesizing an RNA primer

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22
Q

DNA polymerase III

A

Adding basses to the new DNA chain; proofreading the chain for mistakes

23
Q

DNA polymerase I

A

Removing primer, closing gaps, repairing mismatches

24
Q

Ligase

A

Final binding of nicks in DNA during sythesis and repair

25
Q

Topoisomerases I and II

A

Supercoiling and untangling

26
Q

How many replication forks are involved in replication of a circular bacterial chromosome?

A

Two replication forks proceed in each direction on a circular chromosome

27
Q

What occurs during the five major steps in replication?

A
  1. Initiation: Necessary enzymes assemble a replication fork at the origin of replication
    2) Unwinding: Topoisomerase and helicase unwind and open the double helix into 2 single strains by breaking hydrogen bonds.

Single-strand binding proteins keep the single strands from coming back together

3) RNA primase synthesizes short RNA primers on the leading and lagging strands (primer on leading strand is not shown)
4) Replication: DNA polymerase III binds to the DNA and begins replication from the RNA primer.
5) Primer removal and strand sealing: DNA polymerase I (not shown) removes RNA primers and replaces them with DNA (again, by base pairing)

28
Q

What is the difference between the leading strand and the lagging strand (recognize that this has to do with the polarity of the DNA and the “properties” of DNA polymerases)? pg198

A

One of these is called the leading strand, and it is replicated continuously in the 3’ to 5’ direction. The other strand is the lagging strand, and it is replicated discontinuously in short sections.
DNA polymerase is able to synthesize the two new strands simultaneously

29
Q

What is the major energy source that drives replication?

A

ATP ENERGY SOURCE.

30
Q

What enzymes are involved in the last (sixth) step of replication, after the chromosome has been replicated, and why is this important?

A
  • DNA Polymerase I(removes RNA primers, replaces with DNA)

- DNA ligase(seals gaps)

31
Q

What is the central dogma, in terms of the flow of information in biology?

A

Central Dogma: Transcription and Translation

Central theme of biology: information flows from DNA to RNA to protein

32
Q

What are some exceptions to the classical central dogma?

A

Exceptions to the classical central dogma
RNA viruses convert RNA to RNA
retroviruses convert RNA to DNA

33
Q

central dogma, explain? slide 28

A

Transcription: DNA code is used to synthesize an RNA molecule
RNA polymerase transcribes DNA to RNA

Translation: transcribed RNA used to produce protein
Ribosomes translate messenger RNA (mRNA) to protein
This process also requires tRNAs and rRNAs

34
Q

• What are some important ways in which RNA differs from DNA (single vs. double stranded? Uracil vs. thymine?

A

Differences between DNA and RNA

  • RNA sugar is ribose, not deoxyribose
  • RNA bases contain a uracil (U) in place of thymine (T)
  • U pairs with A (just like T, so the code is preserved)
  • RNA is usually single-stranded, not double-stranded
35
Q

Ribose vs. deoxyribose?)

A

Ribose, found in RNA, is a “normal” sugar, with one oxygen atom attached to each carbon atom.

Deoxyribose, found in DNA, is a modified sugar, lacking one oxygen atom (hence the name “deoxy”). This difference of one oxygen atom is important for the enzymes that recognize DNA and RNA, because it allows these two molecules to be easily distinguished inside organisms.

36
Q

What are mRNA, rRNA and tRNA?

A

RNA transcripts that encode proteins are messenger RNAs (mRNA)
-These will subsequently be translated by ribosomes
-RNA transcripts can also be functional just as RNAs
-Ribosomal RNAs (rRNA) and transfer
-RNAs (tRNA) are involved in translation
Additionally, RNAs can have various and complex regulatory roles

37
Q

What is transcription, and what is a transcript?

A

Transcription: DNA code is used to synthesize an RNA molecule
RNA polymerase transcribes DNA to RNA

RNA transcripts that encode proteins are messenger RNAs (mRNA
RNA transcripts can also be functional just as RNAs

38
Q

RNA polymerase

A

enzyme that synthesizes (transcribes) RNA based on a DNA template

39
Q

What are the important components in transcription?

A

RNA polymerase: enzyme that synthesizes (transcribes) RNA based on a DNA template

Template strand: only one strand of DNA that contains meaningful instructions for synthesis of a functioning polypeptide

Nucleotide triphosphates: ATP, GTP, CTP, UTP
Hydrolysis of two of the phosphates provides energy for transcription
The remaining nucleotide monophosphate is incorporated into the RNA

40
Q

What provides the energy source in transcription?

A

Hydrolysis of two of the phosphates provides energy for transcription

41
Q

• What occurs during each of the three major steps in transcription?

A

*Initiation
Elongation
Termination

42
Q

transcriptionStep 1: Initiation

A

RNA polymerase binds to the DNA “upstream” of the gene (3’ end of template strand) in a region of DNA called the promoter.
The promoter has sequences that provide the signal for RNA polymerase to bind.
The DNA double helix is unwound at the promoter

43
Q

transcriptionStep 2: Elongation

A

After binding at the promoter, RNA polymerase begins transcription.
Unlike DNA polymerases, RNA polymerase does not require a primer to begin synthesis of an new strand.
RNA polymerase reads along the template strand in a 3’ -> 5’ direction.
It synthesizes an RNA strand in the 5’ -> 3’ direction (antiparallel, just like DNA replication).
Individual RNA bases are added as nucleotide triphosphates according to their pairing with bases in the DNA.
A added opposite to T, G opposite to C, C opposite to G, U opposite to A.
Hydrolysis of two of the phosphates provides energy to drive transcription, and the remaining nucleotide monophosphate is incorporated into the growing RNA transcript.

44
Q

Step 3: Termination

transcription

A

Usually, termination occurs when RNA polymerase reaches a DNA sequence at the end of the gene (termination sequence) that acts as a signal for the transcript to end
RNA polymerase dissociates (releases) from the DNA and transcript
The DNA reverts to its double helix form, and the transcript is now complete

45
Q

What is a promoter, and what role does it play? What

A

the DNA sequence where RNA polymerase binds

46
Q

What are some ways in which RNA polymerase is similar to and different from DNA polymerases?

A

RNA polymerase transcribes DNA to RNA, enzyme that synthesizes (transcribes) RNA based on a DNA template

Well, starting with the comparison. Both polymerases require a template (DNA). Both DNA and RNA polymerases catalyze the formation of each polymer in the same direction, that is 5’- to 3’-. Each protein moves along the strand, adding each base to the 3’ end of the preceding base.

There are a lot of differences between the two proteins. RNA polymerase does not require a primer whereas DNA polymerase does. DNA polymerase goes until the job is finished, whereas RNA polymerase goes until it reaches a “stop” sequence. RNA polymerase has a subunit that must unwind the DNA template and DNA polymerase follows a helicase that opens the double helix in front of it.

Unlike DNA polymerases, RNA polymerase does not require a primer to begin synthesis of an new strand.

47
Q

What is translation?

A

is the process by which the nucleotide sequence of mRNA is converveted to the amino acid sequence of a polypeptide. In bacteria, this process takes place in the cytoplasm.

48
Q

What are important components of translation, and what is produced as a result?

A

Ribosomes
Consist of both proteins and rRNAs

Transfer RNAs (tRNAs) that are “charged” with a specific amino acid
mRNA transcript to be translated

Hydrolysis of guanosine triphosphate (GTP) provides the energy for protein synthesis by ribosomes

49
Q

produced as an end result of translation?

A

In translation, messenger RNA (mRNA)—produced by transcription from DNA—is decoded by a ribosome to produce a specific amino acid chain, or polypeptide.

50
Q

What is a major energy source that drives translation?

A

Energy to drive translocation is provided by GTP hydrolysis (energetically similar to ATP hydrolysis).

51
Q

What role to mRNA, tRNA and rRNA play in translation?

A
  • Translation: transcribed RNA used to produce protein
  • Ribosomes translate messenger RNA (mRNA) to protein
  • This process also requires tRNAs and rRNAs

Components:
-Ribosomes
-Consist of both proteins and rRNAs
-Transfer RNAs (tRNAs) that are “charged” with a specific amino acid
mRNA transcript to be translated
-Hydrolysis of guanosine triphosphate (GTP) provides the energy for protein synthesis by ribosomes

52
Q

How does the basic process of translation work, involving codons and anticodons?

A

.-mRNAs contain codons (sets of 3 bases) that code for or indicate a specific amino acid

  • tRNAs have an anticodon that base pairs with a given mRNA codon
  • tRNAs also have a site where a specific amino acid is attached
  • This matching of codon-anticodon-amino acid allows for synthesis of a particular protein (amino acid sequence) from a given gene/mRNA
53
Q

What are some major differences between transcription and translation in prokaryotes vs. eukaryotes?

A

First amino acid is slightly different (N-formyl-methionine, or fMet, in Bacteria)

Eukaryotic mRNAs code for just one protein, unlike bacterial mRNAs, which often contain information from several genes in series

Eukaryotic transcription takes place in the nucleus and is transferred to the cytoplasm for translation; all steps in prokaryotes are in the cytoplasm

Eukaryotic genes usually do not exist as an uninterrupted series of triplets coding for a protein, but contain introns and exons

Micro BIO 220 Part 1 (18 decks)

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