Whether this is your first time reading a journal article or you need a refresher, here is the general breakdown of the parts of a journal article.
The following examples are provided from Oncogenic mutation or overexpression of oncogenic KRAS or BRAF is not sufficient to confer oncogene addiction by Ito et al.: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0249388
There are seven main parts to a journal article. They are:
Abstract
Introduction
Methods
Results
Discussion
Conclusion
References
Supplemental Figures and Data - if applicable
The abstract is the first body of text that is present in a journal article. The goal of an abstract is to provide a complete summary of the article in less than 250 words (usually). If you are confused while reading an article, a great way to regain your bearings is by re-reading the abstract. The abstract is usually written in a clear and concise manner. Here is an example abstract from Ito et al: 
The next part of the journal article is the introduction. The goal of the introduction is to provide background information on the topic, discuss why the topic is important to society at large, discuss previous research performed on the topic, and state the research question of the article. Introductions contain a lot of important information that can help you to understand why the topic is important and the current research status of the topic in the field. Citations to previously performed research related to/on the topic are present in the introduction. It is very important to read the introduction to understand the logic for certain methodologies and decisions within the article. Background information and citations to previous research are often re-mentioned in the discussion section. Here is an example introduction from Ito et al.:
Introductions do not traditionally contain figures. Ito et al. included a figure in the introduction that provides an overview of the acquisition of oncogene addition in cancer cells (background information). This figure has nothing to do with the results of the experiment.
The next section of the journal article is the methods section. The methods section is a strictly quantitative section, much like a cookbook. The goal of the methods section is to list reagents, scientific machinery, and procedures used in the experiment. It is not a step-by-step guide as one may see in a lab manual or a student lab report. It is an overview of the unique aspects of the experiment with enough information for it to be theoretically performed by another researcher. Standard procedures and basic reagents (such as pipetting, water, base nucleotides) are not listed in the methods section. For example, the following section is listed in the methods section for Ito et al:
This methods section does not include information about standard procedures such as nanodropping/using a spectrophotometer, determining dilution ratios, or centrifuging samples within their Genomic DNA preparation and sequencing phase. Nor does it include information such as: add 1uL of a stock 10mM dNTPs mix, keep PCR tubes on ice, "initial denaturation temperature was set to 75C for 5 minutes", and etc. Only the unique aspects of the experiment should be listed in the methods section. Ito et al. lists information such as: the brand of the DNA extraction kit (QuickExtract solution - Nalgene) as DNA extraction protocols and reagents can differ between brands, the brand of the PCR machine (KOD FX Neo - Toyobo) as there may potentially be different PCR reaction set-ups, PCR cycle protocols, or minor systematic errors within the brand of machinery. The authors also list the sequences of their uniquely designed primers and the company that performed the sequencing reaction. This information is unique to the experiment and is important for theoretical experimental replication, understanding the overall methodology and results, and for understanding possible explanations in the discussion section of the article. Results of the experiment or individual steps are not listed in the methods section.
The results section is also a strictly quantitative section. There is no speculation or discussion about the results of the experiment. It can be one of the hardest sections to read and understand. The results section does not report raw data from the experiment. It only reports Results, not data. For data to become results, it must be manipulated or correlated in some way. It is common to find figures within this section. 
This section has the most variability between different journal articles. For example, Ito et al. makes references to outside experiments. This is not traditionally done within a results section. The authors also use personal pronouns, which are also not traditionally used within a results section or scientific writing in general.
The discussion section is the true information center of the article. The other sections' purpose is to support the arguments, speculations, and thoughts of the authors within the discussion section. The discussion section is when the authors analyze the significance of their results, explain their interpretation of the results, describe how the experiment contributes to the field at large, identify possible errors that may have occurred during the experiment, and improvements that can be made if the experiment is performed again. The discussion commonly makes references back to the results or figures within the results section. The discussion section can also be lengthy depending on how it is written by the authors. 
The discussion section can have a lot of variability between different journal articles. This particular discussion by Ito et al. includes a figure, which is not common. Personal pronouns are also used, which is not encouraged in traditional scientific writing.
The conclusion section is the last section of the article. The goal of the conclusion section is to write an overall summary of the article, similar to the abstract. However, abstracts begin with general information to grab the readers attention and end with specific information about the experiment. Conclusions are the opposite. They start with specific information related to the experiment and end with general information on how the experiment relates to science at large. Conclusions are shorter than the other sections in an article, and they tend to have easier readability. Traditionally, conclusions always end with the authors' ideas for future experiments that build upon the errors and shortcomings of their current experiment.
Ito et al. does not include a conclusion within their article. It is traditional to include a conclusion section at the end of an article to give the readers an overall wrap-up. When a conclusion section is not present, the conclusion is written into the end of the discussion section instead.
The end of Ito et al.'s discussion reads exactly like a traditional conclusion without it being denoted as a separate section. References to other articles can be included in the conclusion, although it is not traditional to make references to figures. Since this "conclusion" is technically a part of the discussion, the authors took more liberties with the conclusion format.
The reference section includes all the references for the citations that were made throughout the article. This section is very important for verifying cited information, for discovering more information, and for reviewing previous research on a given topic. The reference section is not usually analyzed during a journal club, but it is very important for readers or researchers who are researching a given topic. Every journal article MUST have a reference section to comply with anti-plagiarism and good scientific practices. An article's citation/reference style can vary depending on the parent journal's standards and policies. Here is a sample reference section from Ito et al.:
The reference section tends to be very long. The above example is only a small depiction of Ito's et al. full reference list.
Articles may include supplemental and supporting information after the references. Although these figures/information are not the main findings, authors may include additional figures/information that relate to the experiment. Ito et al. includes a supporting information section at the end of the article.
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