Information Flow Within Cells Quiz 1

Component parts of nucleic acids

Nucleotides made up of 5-carbon sugar, phospahte group, and nitrogenous base

Compare and contrast the structure of DNA and RNA

DNA-Double stranded

RNA- single stranded

DNA and RNA both essential in living organisms

Compare and contrast the general function of DNA and RNA

DNA stores long-term genetic information, while RNA acts as a temporary working molecule to turn that information into proteins

Both are nucleic acids made of building blocks called nucleotides.

Both contain three parts: a phosphate group, a sugar backbone, and nitrogenous bases.

Both share three bases: adenine (A), cytosine (C), and guanine (G).

Both work together in the central dogma of biology to help the cell build necessary

Compare and contrast the structure and location of DNA in eukaryotic and prokaryotic cells

DNA

deoxyribonucleic acid, a self-replicating material present in nearly all living organisms as the main constituent of chromosomes. It is the carrier of genetic information.

RNA

A single-stranded nucleic acid that passes along genetic messages

5'

The 5' end of a DNA or RNA strand is the terminal end that features a phosphate group attached to the fifth carbon of the sugar ring

3'

The 3′ end of a DNA or RNA strand is the end that terminates at the hydroxyl (-OH) chemical group attached to the third carbon atom in the sugar ring of the terminal nucleotide.

Nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

Pyrimidine

a nitrogenous base that has a single-ring structure; one of the two general categories of nitrogenous bases found in DNA and RNA; thymine, cytosine, or uracil

Purine

a nitrogenous base that has a double-ring structure; one of the two general categories of nitrogenous bases found in DNA and RNA; either adenine or guanine

Antiparallel

The opposite arrangement of the sugar-phosphate backbones in a DNA double helix.

Nucleus

A part of the cell containing DNA and RNA and responsible for growth and reproduction

Process of gene expression

DNA -> RNA -> Protein

Parts of a eukaryotic gene

segments of coding sequences (exons) interrupted by noncoding sequences (introns)

3 stages of transcription

1. Initiation

2. Elongation

3. Termination

mRNA sequence from DNA

If the nucleotide or base sequence of the DNA strand used as a template for messenger RNA synthesis is ACGTT, then the sequence of bases in the corresponding mRNA would be UGCAA.

How and why is eukaryotic mRNA processed

Eukaryotic pre-mRNA is processed in the nucleus through 5' capping, 3' polyadenylation, and RNA splicing to create stable mature mRNA that can safely travel to the cytoplasm for protein translation

How and why is gene expression regulated

Gene expression is regulated to control when, where, and how much protein or RNA is made by a cell, serving as an essential on/off switch and volume control for cellular function

mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome

gene

A segment of DNA on a chromosome that codes for a specific trait

promoter

specific region of a gene where RNA polymerase can bind and begin transcription

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex.

template strand

The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript.

non-template strand

the strand of DNA that is not transcribed into RNA during transcription

transcription factors

A regulatory protein that binds to DNA and affects transcription of specific genes.

RNA polymerase

Enzyme similar to DNA polymerase that binds to DNA and separates the DNA strands during transcription

mRNA processing

- 5' guanine cap

- 3' poly-A tail

- RNA splicing of exons = remove introns + "splice" together exons

5' cap

The 5' end of a pre-mRNA molecule modified by the addition of a cap of guanine nucleotide.

3' Poly A tail

In eukaryotes, a series of 1-200 adenine residues added to the 3' end of an mRNA; the tail appears to enhance the stability of the mRNA by protecting it from degradation.

Intron

a segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes.

Exon

expressed sequence of DNA; codes for a protein

Alternative splicing

regulated process during gene expression that results in a single gene coding for multiple proteins

Gene expression

process by which a gene produces its product and the product carries out its function

Structure of tRNA

Roles of the amino acid site and anticodon

The amino acid attachment site (acceptor stem) carries and links the specific amino acid, while the anticodon recognizes and binds to the matching genetic code on messenger RNA (mRNA)

Structure of a ribosome, role of each tRNA binding site

3 stages of translation

1. Initiation

2. Elongation

3. Termination

Initiation in translation

In this stage, the ribosome gets together with the mRNA and the first tRNA so translation can begin (requires energy)

Elongation

Termination

Peptide sequence from DNA sequence

translate the nucleotide triplets (codons) into their corresponding amino acids using the standard genetic code

Compare and contrast eukaryotic and prokaryotic translation

Both use messenger RNA (mRNA) templates to assemble amino acids into polypeptide chains using codons.

Both rely on ribosomes, transfer RNA (tRNA), and similar steps of initiation, elongation, and termination.

Prokaryotes: Translation happens in the cytoplasm at the same time as transcription.

Eukaryotes: Translation happens in the cytoplasm, but only after transcription and mRNA processing finish in the nucleus

tRNA

transfer RNA; type of RNA that carries amino acids to the ribosome

anticodon

group of three bases on a tRNA molecule that are complementary to an mRNA codon

codon

A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid

genetic code

collection of codons of mRNA, each of which directs the incorporation of a particular amino acid into a protein during protein synthesis

rRNA

ribosomal RNA; type of RNA that makes up part of the ribosome

P site

holds the tRNA carrying the growing polypeptide chain

A site

the entry point where new, charged transfer RNA (tRNA) molecules first bind during protein synthesis

E site

the exit site, where discharged tRNAs leave the ribosome

Ribosomal subunits

The two structural parts of a ribosome, which function together to translate mRNA to build a chain of amino acids that will make up a protein.

Start codon

AUG

Stop codon

UAA, UAG, UGA

Polyribosomes

Strings of ribosomes that work together to translate a RNA message.

Release factor

Proteins that can trigger termination of RNA translation when a ribosome reaches a stop codon.

Differentiate between different types of mutations

o Point mutation: 1 base changes another

EX: sickle cell

o Frameshift mutation: 1 (or few) bases is inserted or deleted (removed) from a gene

All codons 'downstream' from the mutation are affected; protein is likely to be dysfunctional

o Chromosomal mutation: large-scaled change in number or structure of chromosomes

How mutations affect encoded proteins

Silent mutations: Change a DNA letter to encode the exact same amino acid, leaving the protein function largely unaffected.

Missense mutations: Swap one DNA base to code for a different amino acid, which can create a partially or non-functional protein (such as the change causing sickle cell anemia).

Nonsense mutations: Turn a regular amino acid codon into a premature stop codon, producing a shortened, incomplete protein that is usually broken down by the cell.

Mutation

A change in a gene or chromosome.

Point mutations

chemical changes in just one base pair of a gene

Nucelotide pair substitution

the replacement of one nucleotide and its partner with another pair of nucleotides

Silent mutation

A mutation that changes a single nucleotide, but does not change the amino acid created.

Missense mutation

A base-pair substitution that results in a codon that codes for a different amino acid.

Nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

deletion

A change to a chromosome in which a fragment of the chromosome is removed.

insertion

A mutation involving the addition of one or more nucleotide pairs to a gene.

Structure and diversity of genomes

A genome is all the DNA in an organism, and its structure and diversity determine how living things function and evolve

how genomic data is generated

Genomic data is generated by extracting DNA or RNA from a biological sample and using specialized machines to read its chemical building blocks

what we can learn from genomes

Genomes reveal the fundamental biological instructions for life, helping us understand health, evolution, and our connection to other living things

genome

the complete instructions for making an organism, consisting of all the genetic material in that organism's chromosomes

transposable element

Segment of DNA that can move spontaneously within or between chromosomes.

general cell cycle

G1 phase

The first gap, or growth phase, of the cell cycle, consisting of the portion of interphase before DNA synthesis begins.

g2 phase

The second growth phase of the cell cycle, consisting of the portion of interphase after DNA synthesis occurs.

s phase

The synthesis phase of the cell cycle; the portion of interphase during which DNA is replicated.

what it means that DNA replication is semiconservative

each new double-stranded DNA molecule contains one original (parental) strand and one newly synthesized strand

Describe the process of DNA replication

Replication happens in three main steps: initiation, elongation, and termination

Initiation of DNA replication

Replication starts at a specific spot on the DNA molecule called the origin of replication.

Helicase attaches and unwinds the DNA, forming a Y-shaped structure called a replication fork.

SSB proteins coat the split strands, and topoisomerase cuts and relaxes the coiled DNA ahead of the fork

Elongation of DNA replication

Primase adds a short RNA primer to each template strand.

DNA Polymerase binds to the primer and builds a new strand by matching bases

Because DNA strands run in opposite directions (antiparallel) and DNA polymerase only works in one direction, the two new strands grow differently:

Leading Strand: Built continuously in the same direction that the replication fork opens.

Lagging Strand: Built discontinuously in short pieces called Okazaki fragments, moving away from the opening fork

Completion of DNA replication

Special enzymes remove all the temporary RNA primers.

DNA polymerase fills the leftover gaps with real DNA nucleotides.

DNA ligase glues the final sugar-phosphate backbone together, creating two complete and identical double-helix DNA molecules.

Explain generally how mistakes are corrected during DNA replication.

Mistakes during DNA replication are primarily corrected through proofreading by DNA polymerase and the mismatch repair system

cell cycle

series of events that cells go through as they grow and divide

semiconservative

method of replication that implies that each new strand of DNA is half original and half new

origin of replication

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.

replication fork

A Y-shaped region on a replicating DNA molecule where new strands are growing.

helicase

An enzyme that untwists the double helix of DNA at the replication forks.

single stranded DNA binding proteins

- bind to the unraveled strand preventing the re-association of the DNA strands & degradation of DNA by nucleases

-Unpaired strands of DNA are very "sticky" so proteins are required to hold the 2 strands apart

primer

A short segment of DNA that acts as the starting point for a new strand

primase

An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.

DNA polymerase III

synthesizes new DNA only in the 5' to 3' direction

DNA polymerase I

removes the RNA primer and replaces it with DNA

sliding clamp

Holds DNA polymerase in place during strand extension

leading strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.

lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

DNA ligase

A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain.

topoisomerase

corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands

telomeres

Repeated DNA sequences at the ends of eukaryotic chromosomes.

Phases of mitosis

prophase, metaphase, anaphase, telophase