Cell and molecular biology midterm exam

DNA is the carrier of genetic information in the ______, but it can be present in the ______ in diseased cells

nucleus, cytoplasm

DNA is built from four nucleotides and it forms double helix by _____ of two strands

base pairing

DNA is packaged into ________, which host various numbers of genes and form _______ in the nucleus

chromosomes, territories

____ is a DNA segment that makes RNA or protein

gene

DNA and histones form nucleosomes, which show _________ structure in the chromatin

beads on a string

histone modifications regulate chromatin states, including ______ and ______

heterochromatin, euchromatin

histone modifications regulates gene activity, and _________ is functionally important

epigenetic regulation

DNA replication is ________ and by using one DNA strand as a template to synthesize a new strand

semiconservative

DNA replication begins at the replication origins, and the lagging strands is synthesized in __________

Okazaki fragments

DNA synthesis requires __________, which has both polymerization and proofreading activities

DNA polymerase

The _________ includes primase, ligase, helicase, sliding clamp, clamp loader, and topoisomerase

DNA replication machine

the common reactions that create DNA damage include _________ and _________, which causes mutations

depurination, deamination

The _________ of DNA repair includes three key steps: excision, resynthesis, and ligation

basic mechanisms

_______ causes DNA mutations and mismatch repair avoids DNA mutations

mismatch

Double strand breaks repair includes __________ and ________

nonhomologous end joining, homologous recombination

RNA and DNA are chemically different in compositions of ____ and _____

base, sugar

RNA transcription is mediated by _________ and TFs that reorganize the _______ and _________

RNA polymerase, promoters, terminators

mRNA is processed by ______, ______, and _______

5’capping, 3’polyadenylation, splicing

Processed mature RNAs are ______ from the nucleus to the cytoplasm and used for protein translation

exported

Translation from RNA to protein uses ______ and is mediated by ____ and ___________

genetic code, tRNA, aminoacyl-tRNA synthetase

Proteins are made in ______, comprising a large and a small subunit that contain 4 rRNAs and around 80 proteins

ribosomes

Ribosome contains 3 sites: _ for binding new tRNA, _ for binding polypeptide chain, and _for exiting used tRNA

A, P, E

Functional proteins require folding and post-transcriptional modifications, and proteins are degraded by ________

proteosome

Proteins are folded by forming _______ between amino acids, reversible in different conditions

noncovalent bonds

Protein folding forms various shapes and sizes of proteins, which is important for __________

protein functions

Two common patterns of protein folding are ______ and ______, which can form separate domains in a protein

a-helix, b-sheet

Identical protein subunits can assemble into complex structures, depending on the _________ on the subunit

binding sites

________ allow proteins to interact with other
molecules and execute specific functions

binding sites

Protein modifications (e.g. phosphorylation) can function
as ________ to control the protein’s behavior

molecular switches

Protein interactions can form ________ or
intracellular ________to carry out complex functions

protein machines, condensates

Different cell types of a multicellular organism share the
same ______, and their nuclei are ______

genome, totipotent

Gene activation can occur at a _________ and is controlled
by combinations of different transcriptional regulators

distance

___________ by transcriptional regulators can
generate various cell types during development

Combinatorial control

____________ can directly convert one cell
type into another or induce forming pluripotent stem cells

Transcriptional regulators

DNA methylation and histone modifications are important
for regulating ____________

cell memory

MicroRNAs, siRNAs, and lncRNAs can regulate __________ at the post-transcriptional level

gene expression

The human genome is predominantly made of _________ and _________

repetitive sequences, noncoding DNA

_____, _______, ________, _______, and _______ contribute to genome evolution

Mutation, duplication, exon shuffling, transposition,
and horizontal transfer

cutting vector and targe DNA with
restriction enzymes and pasting them with DNA ligase

DNA cloning

used to amplify DNA in vitro and is a powerful tool for many applications

Polymerase Chain Reaction

_______ can be studied by using reporter genes,
GFP, RNAi, transgenics or editing by CRISPR/Cas9

gene functions

_____________ are powerful tools to
study gene structure and function

recombinant DNA techniques

Chromosomes form _______ in nucleus

territories

Chromatin states regulate __________

gene activity

New DNA strand is synthesized only in a ______ direction

5’->3’

RNA can fold by __________

internal base pairing

a _________ can direct the formation of an entire organ

master transcription regulator

Automated dideoxy sequencing using uniquely colored fluorescent

ddNTPs

DNA packaging

DNA is packaged to form chromosomes-beads on a string nucleosomes (dna wound around histones),then chromatin fiber is packed of beads on a string, then the chromatin fiber is folded into loops

DNA replication

starts at the replication origin, where two replication forks form, and new strands are synthesized in the 5’ to 3’ direction (lagging has okazaki fragments). RNA primer-DNA strand synthesized and extended by DNA polymerase- nicks between dna fragments sealed by dna ligase

DNA damage repair

Three steps:

1. Excision- segment of damaged strand is excised

2. Resynthesis- Repair DNA Polymerase fills in missing nucleotide in top strand using bottom strand as template

3. Ligation- DNA ligase seals nick

RNA transcription

Bacteria: Initiation( RNA polymerase binds to the promoter (a specific DNA sequence), sigma factor helps rna polymerase recognize promoter, and dna unwinds), Elongation(RNA polymerase moves along the DNA, adding RNA nucleotides (A, U, G, C) that are complementary to the DNA template strand.), and Termination (Transcription stops when RNA polymerase reaches a terminator sequence.)

Eukaryotes: Initiation – RNA polymerase II binds to the promoter with the help of transcription factors. Elongation – RNA polymerase adds RNA nucleotides (A, U, G, C) to build the RNA strand. Termination – Transcription stops at a termination signal. Processing – The pre-mRNA gets a 5' cap, poly-A tail, and introns removed (splicing).

mechanisms of genome evolution

Mutation (a change in DNA sequence), Duplication (copying of a dna segment), Exon shuffling(mixing of exons between genes, creating new proteins), Transposition (movement of DNA segments within the genome), Horizontal transfer (gene transfer between different organisms, not by inheritance)

Polymerase Chain Reaction

Amplifies DNA segments

• Denaturation (95°C) – DNA strands separate due to heat.

• Annealing (50–65°C) – Primers bind to target DNA sequences.

• Extension (72°C) – Taq polymerase adds nucleotides to build new DNA strands.

• These steps are repeated around 30 times

DNA cloning

Cut DNA with Restriction
Enzymes and Paste with DNA Ligase

what can pcr be used for

disease diagnosis, genetic testing, forensic science (to identify suspects from dna at a crime scene), cloning and research, identify genetic changes that can cause disease

CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats)

can be used to edit genes and study their function by removing, adding or altering sections of the DNA sequence.

Steps-Guide RNA Binding – A guide RNA (gRNA) directs the Cas9 enzyme to the specific DNA sequence.

• DNA Cutting – Cas9 acts like scissors, cutting both strands of the target DNA.

• DNA Repair – The cell repairs the cut:

  • Non-homologous end joining (NHEJ) – Creates random mutations to disable a gene.

  • Homology-directed repair (HDR) – Uses a DNA template to insert a new gene.

Applications- potentially can cure/treat genetic diseases such as sickle cell EX: Victoria Gray had alleviated symptoms after participating in a sickle cell disease trial with CRISPR.