MCB 121 - EXAM1

central dogma

flow of genetic information from genotype to phenotype

what is replication carried out by?

DNA polymerase

what is transcription mediated by?

RNA polymerase

what is translation carried out by?

ribosomes and tRNAs

what do telomeres do in replication?

add sequences to the DNA

examples of noncoding RNAs

rRNA and tRNA

gene

chromosome segment that codes for functional protein or RNA

genome

one copy of all genetic information encoded by cell or virus

genotype

genetic constitution; same in every cell

typically DNA but some viruses have RNA genomes

proteins/RNA

carry out cellular functions

transcriptome/proteome

all the mRNA protein products in a given cell type

phenotype

observable characteristic

product of gene

proteins/RNA

product of genome

transcriptome/proteome

product of genotype

phenotype

In Bacteria, where does coupled transcription and translation occur?

in the same compartment

in eukaryotes, where does transcription take place?

nucleus

in eukaryotes, where does translation take place?

cytoplasm

In DNA what is the chemical composition of nucleotides?

5’ phosphate
3’ hydroxyl

In RNA what is the chemical composition of nucleotides?

5’ phosphate
2’ hydroxyl

what makes up a nucleoside?

sugar and base

what makes up a nucleotide?

sugar, base, and phosphate

purines

nine-membered rings

where is the glycosidic bond position in a purine?

N9

pyrimidines

6-membered rings

where is the glycosidic bond position in pyrimidines?

N1

examples of purines

adenine

guanine

examples of pyrimidines

cytosine
thymine
uracil

5-methylcytosine

modified base that imparts and additional layer of information on top of the DNA code

what is 5-methylcytosine modified by?

DNA methyltransferases after DNA replication

what is 5-methylcytosine considered?

epigenetic mark since the modification is not coded in the genome

where is the repressive chromatin mark found in 5-methylcytosine?

“silenced” regions of the genome in CpG dinucleotide repeats

dAMP

monophosphate

dADP

diphosphate

dATP

triphosphate

phosphodiester linkages

join nucleotides

what kind of energy do phosphodiester bonds have?

high energy

what is the polarity of the DNA chain?

5’-3’

what is the overall net charge of the DNA?

negative

gel electrophoresis

separate nucleic acids by size and shape

circular DNA in gel electrophoresis

travel slower

linear DNA in gel electrophoresis

migrate faster

How many hydrogen bonds are present in an A-T (adenine-thymine) base pair?

two H bonds

How many hydrogen bonds are present in a G-C (guanine-cytosine) base pair?

three H bonds

What links the two antiparallel DNA strands together?

Hydrogen bonds between complementary bases.

What is the direction of the Watson strand in DNA?

5’ to 3’

What is the direction of the Crick strand in DNA?

3’ to 5’

What is the most common structural form of DNA?

B-form

What are the two types of grooves found in B-DNA?

major and minor grooves

major groove

contains most of the information for sequence-specific protein binding

How many base pairs are there per turn in B-form DNA?

10.5 bp/turn

How do positively charged amino acids in DNA-binding domains interact with DNA?

They form electrostatic interactions with the negatively charged phosphate backbone of DNA.

what kind of structure is favored?

planar

which interactions favor base stacking?

hydrophobic, van der Waals, and electrostatic interactions

Besides contributing to instability, what is another role of the 2' OH group in RNA?

It allows for extra hydrogen bonding that helps stabilize RNA secondary structures.

What do glycosidic bonds connect in nucleic acids?

The 1' carbon of the pentose sugar to a nitrogenous base (in both RNA and DNA), regardless of purine or pyrimidine.

How do DNA loops contribute to genome organization?

They help compact long genomes into tight volumes.

What is the effect of cytosine methylation at the 5th position?

It is typically associated with transcriptionally silenced DNA.

What ensures DNA replication occurs only once per cell cycle?

Phosphorylation of Cdc6 by cyclin-dependent kinase.

At what stage does the genotype-to-phenotype transition occur?

At translation.

Do histones bind to exons of actively transcribed genes?

Yes, histones can bind to exons, and these regions often show higher nucleosome occupancy than introns.

How do proteins interact with B-form DNA?

Through both non-specific interactions with the backbone and sequence-specific contacts in the major/minor grooves.

Do all life forms use DNA as their molecule of heredity?

No, some viruses use RNA instead of DNA.

What is a replisome?

A multi-protein complex responsible for DNA replication at the replication fork.

What is the role of the clamp in DNA replication?

It increases the processivity of DNA polymerase, boosting the rate of nucleotide incorporation.

Are replication forks in E. coli bi-directional or unidirectional?

Bi-directional.

Can genetic information flow from RNA to DNA?

Yes, via reverse transcription.

Do all RNAs encode proteins?

No, many RNAs are non-coding and serve other cellular functions.

What does the ribosome use to synthesize proteins?

mRNA, not DNA directly.