Name: base excision repair pathway
Uploaded: 2023-04-30T18:28:49.000Z
Duration: 1 min 54 s
Channel: JoVE

K12 Standards

north-carolina-k-12-science-standard-course-of-study

NC K-12 Science Standard Course of Study

9-12

Biology

heredity-inheritance-and-variation-of-traits

Heredity- Inheritance and Variation of Traits

LS.Bio.6.2

Base Excision Repair

The most common way to repair damaged DNA is to cut out the damaged part, recopy the undamaged complementary strand and ligate, or &#8220;re-seal&#8221;, the nick. This general scheme of cut, copy, and paste follows in all types of excision mechanism.
Base excision repair, or BER, corrects small base damages caused by deamination, oxidation, or alkylation that occur spontaneously or are caused by environmental toxins.
In BER, a group of around 11 different enzymes called DNA glycosylases recognize different altered bases and catalyze their removal. The modified bases make weak base pairs that are detected by the glycolases.&#160;
Upon encountering such a weak base pair, DNA glycosylase wedges apart the neighboring base pairs and flips out the modified base. This flip allows the enzyme to interact with all facets of the base to accurately identify it.
Upon recognition, DNA glycosylase cleaves the bond between the modified DNA base and the deoxyribose, releasing the free base and leaving a gap in the DNA helix. This gap is recognized by an enzyme called AP endonuclease, or APE, which, along with another enzyme called phosphodiesterase, cuts the phosphodiester backbone within the polynucleotide chain.
The missing base in the DNA helix is filled by DNA polymerase &#946;, which copies the correct base from the complementary strand at that position. Next, an enzyme called DNA ligase seals the remaining nick to give an intact, repaired DNA molecule.

base excision repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of BER is the recognition of DNA damage, which is done by DNA glycosylases. Depending on the type of base, a specific glycosylase cuts the N-glycosidic bond between the nucleotide base and ribose, leaving the phosphate backbone of the DNA intact but creating an apurinic or apyrimidinic (AP) site. Bifunctional glycosylases make an incision in the phosphodiester chain, resulting in the formation of a 5&#8217; or 3&#8217; phosphate. Monofunctional glycosylases do not exhibit this property and have to depend on an AP Endonuclease to cleave the sugar-phosphate link, 5&#8217; to the abasic site, producing a 3&#8217;OH and a 5&#8217; deoxyribophosphate. Based on the corresponding W-C pairing, DNA polymerase inserts the correct base and uses its associated AP-lyase activity to remove the deoxyribose phosphate. The nick in the backbone is sealed by DNA ligase. Both DNA ligase III and DNA polymerase use the protein XRCC1 as a scaffold to bind the site of repair.
Mutations in the proteins of the BER pathways can lead to various types of cancer. For example, a mutation in the human glycosylase OGG1 is associated with an increased risk for lung and pancreatic cancers.

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and ...

Education

JoVE Core

Cell Biology

Unit 1

DNA Replication and Repair

KEY TERMS AND CONCEPTS

base excision repair pathway

Base excision repair is a DNA repair pathway that fixes small base damage. It helps cells correct changes that can appear in DNA before they cause larger problems.

In this pathway, a damaged base is removed first. The cell then processes the site and replaces the missing part with the correct DNA building block. This repair step helps keep genetic information accurate.

Base excision repair is one of the main ways cells handle everyday DNA damage. It is an important part of maintaining DNA stability in high school biology and genetics topics.

Base Excision Repair Pathway

base-pairing and dna repair

DNA Pairing Rules in Repair

DNA pairing rules help guide DNA repair. In DNA, bases pair in a specific way, and those matching pairs support accurate copying and fixing of the molecule. When DNA is damaged or copied incorrectly, repair systems can use the normal base-pairing pattern as a reference. This helps cells find mismatched bases and restore the correct sequence. The process depends on the idea that each base has a preferred partner. Understanding base-pairing is important because it explains how cells protect...

the dna replication fork

DNA Replication Fork in Action

The DNA replication fork is the active region where DNA copies itself. It forms when the two strands of the double helix separate so each strand can serve as a template for a new partner strand. At the fork, the copying process moves in a set direction. The two strands are built in different ways as replication continues, so the fork helps organize how the new DNA is made. The replication fork is a key part of accurate DNA duplication. It shows how the cell opens the double helix, copies the...

lagging strand synthesis

Okazaki Fragments on the Lagging Strand

Lagging strand synthesis builds new DNA in short pieces called Okazaki fragments. This happens during DNA replication because the lagging strand runs in the opposite direction from the direction the replication machinery moves. As the DNA double helix opens, DNA polymerase adds nucleotides only in the 5' to 3' direction. On the lagging strand, this forces the cell to copy the template in segments instead of one continuous stretch. Each segment begins near the replication fork and extends away...

the replisome

Replisome Components in DNA Copying

The replisome is the protein machine that copies DNA during cell division. It works at the replication fork, where the double helix opens so new strands can be made. DNA polymerase is the core enzyme in the replisome. It adds nucleotides to the growing DNA strand. In bacteria, two DNA polymerases work together at the fork. These enzymes are linked to the helicase by a clamp-like protein so they stay attached to the DNA. Helicase unwinds the DNA ahead of the fork. Single-stranded binding...

proofreading

DNA Polymerase Error Correction

DNA polymerase uses proofreading to help correct errors during DNA replication. As it builds the daughter strand, the enzyme adds nucleotides that match the template DNA strand. This matching helps keep DNA copying accurate and supports replication fidelity. DNA is made in the 5' to 3' direction, and several DNA polymerases help with this process. In nuclear DNA replication, DNA polymerase delta and DNA polymerase epsilon have proofreading ability. After a new base is added, these polymerases...

replication in prokaryotes

How Prokaryotic DNA Copies Itself

Prokaryotic DNA copies itself through a set of coordinated steps called initiation, elongation, and termination. In bacteria, replication starts when initiator proteins bind to a single origin of replication, or ori, on the circular chromosome. The DNA is then copied in both directions until two DNA molecules are made. Several proteins help open and stabilize the DNA during replication. Topoisomerase cuts one side of the double-stranded phosphate-sugar backbone so the helix can unwind faster.

replication in eukaryotes

Eukaryotic DNA Replication Steps

Eukaryotic DNA replication copies the genome before cell division. It happens in a tightly regulated way so each daughter cell gets a complete set of chromosomes in the nucleus. The process has three stages: initiation, elongation, and termination. Eukaryotic cells use many proteins to manage replication because their chromosomes are linear and their genomes are larger than those of prokaryotes. Replication begins at multiple origins of replication along each chromosome. Initiator proteins...

telomeres and telomerase

Telomeres and Telomerase in DNA Replication

Telomeres and telomerase help protect chromosomes during DNA replication. Telomeres are repeated DNA sequences at chromosome ends, and telomerase is the enzyme that can extend them. Together, they help keep important genetic information from being lost when cells divide. Each time a chromosome is copied, the very end of the DNA strand can be difficult to replicate fully. Telomeres act like a buffer zone at the tips of chromosomes. Telomerase adds new repeats to these ends, which helps maintain...

overview of dna repair

DNA Repair and Genetic Recombination

DNA repair and genetic recombination help cells respond to damage in DNA. DNA can be harmed by normal cell activity or by outside factors. When damage is not fixed, it can affect how genetic information is copied and used. Cells use repair pathways to detect and correct many kinds of DNA damage. Some repair steps remove damaged bases or replace missing pieces of DNA. Other pathways help keep the DNA sequence stable after damage has occurred. Genetic recombination is also part of this process.

Base excision repair is a DNA repair pathway that fixes small base damage. It helps cells correct changes that can appear in DNA before they cause larger problems. In this pathway, a damaged base is removed first. The cell then processes the site and replaces the missing part with the correct DNA building block. This repair step helps keep genetic information accurate. Base excision repair is one of the main ways cells handle everyday DNA damage. It is an important part of maintaining DNA...

nucleotide excision repair

UV Damage and DNA Repair by NER

UV damage can bend DNA and block replication or transcription. Cells often face mutagens, which are outside factors that damage DNA and can create mutations. If these changes are not repaired, they can lead to disease or cancer, depending on which DNA sequences are affected. Nucleotide excision repair, or NER, is the pathway that helps cells find and remove damaged DNA. In prokaryotes, three proteins carry out this work: UvrA, UvrB, and UvrC. UvrA and UvrB move along the DNA together and look...

mismatch repair

DNA Mismatch Repair and Cancer Risk

DNA mismatch repair fixes copying errors that happen during DNA replication. It helps cells find the wrong nucleotide, remove it, and replace it with the correct one before the cell divides. Human cells carry more than 3 billion base pairs of DNA, so replication must be very accurate. Even with DNA polymerase proofreading, a copying error can still occur about once every 1 million base pairs. One common error is a mismatch, such as A paired with G or T paired with C. The Mutator protein family...

dna damage can stall the cell cycle

DNA Repair Checkpoints in the Cell Cycle

DNA repair checkpoints help cells pause the cell cycle after DNA damage. This pause gives the cell time to check for breaks and repair them before division continues. Cells must do this at critical stages of the cycle. The amount of DNA in the cell depends on when the pause happens. If the cycle stops before DNA replication, the cells will contain twice the normal amount of DNA. If cells stop after DNA replication but before mitosis, they will contain four times the normal amount. Cells use...

fixing double-strand breaks

Repairing DNA Double-Strand Breaks

Repairing DNA double-strand breaks is an important part of DNA maintenance. A double-strand break happens when both strands of the DNA molecule are cut. Cells must fix this damage to keep genetic information stable. The repair process can happen by more than one pathway. Some breaks are repaired by direct joining of the broken ends. Other breaks are repaired by using a matching DNA sequence as a template. These pathways help cells respond to damage in different ways. This topic is closely...

homologous recombination

Homologous Recombination in DNA Repair

Homologous recombination is a DNA repair process that uses a matching DNA sequence as a template. It helps cells fix breaks in DNA and keep genetic information accurate. The process begins when a broken DNA strand finds a similar, or homologous, piece of DNA. That matching sequence guides repair and allows the damaged DNA to be restored. Because the repair uses a copied sequence, the final DNA can closely match the original information. Homologous recombination is also important in genetic...

gene conversion

Gene Conversion During DNA Repair

Gene conversion is a DNA repair event linked to genetic recombination. It can change the sequence of one DNA region by using a related DNA strand as a template. This process is important for understanding how cells repair damage and reshuffle genetic information. During recombination, gene conversion can copy information from one DNA molecule to another. The result is not a simple swap of DNA segments. Instead, one sequence is corrected or replaced while the related partner sequence remains...

restarting stalled replication forks

Restarting DNA Replication After Stalls

DNA replication can stop before it is finished when the fork stalls. A stalled replication fork is a point where the DNA-copying machinery slows down or pauses during chromosome duplication. Cells can restart these forks to keep copying DNA. This process helps the replication machinery move forward again after the pause. It is an important part of maintaining normal DNA replication when problems arise during copying. The term stalled replication fork describes the stopped or delayed state of...

key terms and concepts

Learn how base excision repair fixes small DNA base damage and helps cells maintain genetic stability in a key DNA repair pathway.

Base Excision Repair Pathway | JoVE K12

cell biology

JoVE Core Cell Biology illustrates complex cellular processes in easy-to-understand yet comprehensive animated video lessons. This collection focuses on the essential components and functions of cells, including organelles and membranes, cellular transport, and cell energetics. It is complemented by scientist-in-action videos that demonstrate the application of cell biology in real-world research experiments.

Next Generation Science Standards

High School

Life Science

Heredity: Inheritance and Variation of Traits

HS-LS3-2

Texas Essential Knowledge and Skills

BIO.7

BIO.7.C

new-york-state-science-learning-standards

New York State Science Learning Standards

Inheritance and Variation of Traits

HS-LS3-1.

What is Meiosis?

Meiosis is the process by which diploid cells divide to produce haploid daughter cells. In humans, each diploid cell contains 46 chromosomes, half from ...

Meiosis I

Meiosis II

Meiosis vs. Mitosis

Crossing Over

Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to ...

Nondisjunction

Nondisjunction is the failure of homologous chromosomes or sister chromatids to separate correctly and move to the opposite poles of the cells. This ...

Spermatogenesis

Spermatogenesis is the process by which haploid sperm cells are produced in the male testes. It starts with stem cells located close to the outer rim of ...

Oogenesis

In human women, oogenesis produces one mature egg cell or ovum for every precursor cell that enters meiosis. This process differs in two unique ways from ...

Fertilization

During fertilization, an egg and sperm cell fuse to create a new diploid structure. In humans, the process occurs once the egg has been released from the ...

Cleavage and Blastulation

After a large-single-celled zygote is produced via fertilization, the process of cleavage occurs while zygotes travel through the uterine tube. Cleavage ...

Gastrulation

Gastrulation establishes the three primary tissues of an embryo: the ectoderm, mesoderm, and endoderm. This developmental process relies on a series of ...

Neurulation

Neurulation is the embryological process which forms the precursors of the central nervous system and occurs after gastrulation has established the three ...

Cell Migration

Cell migration, the process by which cells move from one location to another, is essential for the proper development and viability of organisms ...

Determination

During embryogenesis, cells become progressively committed to different fates through a two-step process: specification followed by determination. ...

Use models to explain how DNA is passed from parents to offspring through the processes of meiosis and fertilization in sexual reproduction.

LS.Bio.6.1

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations ...

genome-size-and-the-evolution-of-new-genes

Genome Size and the Evolution of New Genes

types-of-genetic-transfer-between-organisms

Types of Genetic Transfer Between Organisms

Base-pairing and DNA Repair

The DNA Replication Fork

Lagging Strand Synthesis

The Replisome

Proofreading

Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template ...

Replication in Prokaryotes

DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the ...

Replication in Eukaryotes

In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before ...

Overview of DNA Repair

Nucleotide Excision Repair

DNA Distortion and Damage
Cells are regularly exposed to mutagens&#8212;factors in the environment that can damage DNA and generate mutations. UV ...

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the ...

Fixing Double-strand Breaks

Homologous Recombination

Gene Conversion

Restarting Stalled Replication Forks

Construct an explanation to summarize how inheritable genetic variations may result from: new genetic combinations in meiosis, mutations during replication, or mutations caused by environmental factors.

An Overview of Genetic Analysis

An organism&#8217;s physical traits, or phenotype, are a product of its genotype, which is the combination of alleles (gene variants) inherited from its ...

Genetic Crosses

To dissect genetic processes or create organisms with novel suites of traits, scientists can perform genetic crosses, or the purposeful mating of two ...

Punnett Squares

Monohybrid Crosses

Dihybrid Crosses

Trihybrid Crosses

Trihybrid Crosses
Some of Mendel&#8217;s crosses examined three pairs of contrasting characteristics. Such a cross is called a trihybrid cross. A ...

Law of Independent Assortment

Chi-square Analysis

The chi-square test is a statistical hypothesis test. It is used to check whether there is a significant difference between an expected value and an ...

Pedigree Analysis

Multiple Allele Traits

Incomplete Dominance

Gregor Mendel&#39;s work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid ...

Lethal Alleles

Agouti: A Lethal Allele
Lucien Cu&#233;not discovered lethal alleles in 1905 while studying the inheritance of coat color in mice. The agouti gene is ...

Polygenic Traits

background-and-environment-affect-phenotype

Background and Environment Affect Phenotype

Although the genetic makeup of an organism plays a major role in determining the phenotype, there are also several environmental factors, such as ...

Use mathematics and computational thinking to predict the variation and distribution of expressed traits based on: Mendelian inheritance, co-dominance, incomplete dominance, multiple alleles, and sex-linked inheritance.

LS.Bio.7.1

Overview

A pedigree is a diagram displaying a family&#x2019;s history of a trait. Analyzing pedigrees can reveal (1) whether a trait is dominant or ...

Probability Laws

Overview

The probability of inheriting a trait can be calculated using the sum and product rules. The sum rule is used to calculate the probability of ...

The Concept of Multiple Allelism

Multiple allelism describes genes that exist in three or more allelic forms. Although diploid organisms, like humans, ...

Analyze and interpret data to explain how polygenic traits result in a wide range of phenotypes.

LS.Bio.7.2

Pleiotropy

Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause ...

Nature and Nurture

Many human characteristics, like height, are shaped by both nature&#x2014;in other words, by our genes&#x2014;and by nurture, or our environment. For ...

Construct an explanation to summarize how traits result from interactions of genetic factors (multiple genes and/or alleles) and environmental factors.

LS.Bio.7.3

PCR: The Polymerase Chain Reaction

The polymerase chain reaction, or PCR, is a technique used to amplify DNA through thermocycling &#8211; cyles of temperature changes at fixed time ...

DNA Gel Electrophoresis

DNA gel electrophoresis is a technique used for the detection and separation of DNA molecules. An electric field is applied to a gel matrix comprised of ...

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further ...

Restriction Enzymes

Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called ...

DNA Agarose Gel Electrophoresis

Agarose gel electrophoresis is a laboratory technique commonly used to separate DNA fragments by size. However, it can also be used to isolate and purify ...

dna-isolation-and-restriction-enzyme-analysis

DNA Isolation and Restriction Enzyme Analysis

The revelation of DNA as the hereditary molecule in all organisms has led to enormous scientific and medical breakthroughs and significantly enhanced our ...

Preparation of Solutions and Materials
ExpandNOTE: For this lab to run smoothly, it is recommended to not exceed 12 samples per laboratory class.
First ...

DNA Isolation
ExpandNOTE: In this experiment you will perform DNA isolation under two experimental conditions: one using a buffer containing the detergent ...

Analyze and interpret data to compare DNA samples.

LS.Bio.8.1

Transgenic Organisms

Reproductive Cloning

CRISPR

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, ...

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences ...

Obtain and communicate information that summarizes the impact of biotechnology applications on the individual, society, and the environment, including agriculture and medicine.

LS.Bio.8.2

Understand genetic mechanisms for variation.

Base Excision Repair Pathway

Description

Transcript

Tags

More videos by Standards