How can I mark a foreign key constraint using Hibernate annotations?

@Column is not the appropriate annotation. You don’t want to store a whole User or Question in a column. You want to create an association between the entities. Start by renaming Questions to Question, since an instance represents a single question, and not several ones. Then create the association:

@Entity
@Table(name = "UserAnswer")
public class UserAnswer {

    // this entity needs an ID:
    @Id
    @Column(name="useranswer_id")
    @GeneratedValue(strategy = GenerationType.AUTO)
    private Long id;

    @ManyToOne
    @JoinColumn(name = "user_id")
    private User user;

    @ManyToOne
    @JoinColumn(name = "question_id")
    private Question question;

    @Column(name = "response")
    private String response;

    //getter and setter 
}

The Hibernate documentation explains that. Read it. And also read the javadoc of the annotations.